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PDB_EXTRACT


Extracting Information from Output of X-ray Crystallographic Applications




RCSB Protein Data Bank

(June, 18, 2004; last modified Jan. 13, 2005)



Contents


  1. What does PDB_EXTRACT do?

  2. Program access

  3. Installation

    1. Installation of binary distribution

    2. Installation of source code distribution

  4. Run the program

    1. Quick run the program

    2. Explanations of arguments and input/output files

  5. Tutorials

    1. The CCP4i interface

    2. The Web interface

    3. The Unix command line interface

    4. The CNS-like script interface

  6. Some helpful hints for getting the LOG (or output) files from various crystallographic programs

    1. Data collection/reduction

    2. Molecular replacement

    3. Heavy atom phasing

    4. Density modification

    5. Final structure refinement

  7. Program argument description and options

    1. Unix command options for pdb_extract

    2. Examples of pdb_extract using Unix command options

    3. Unix command options for pdb_extract_sf

    4. Examples of pdb_extract_sf using Unix command options

    5. Unix command options for extract

    6. Examples of extract using Unix command options

  8. Tables

    1. Unix command options

    2. Crystallographic software list

  9. References

  10. Frequently asked questions

  11. Appendix (data_template.text)

  12. Appendix (log_script.inp)

  1. What does PDB_EXTRACT do?


PDB_EXTRACT is used to extract information about data processing, heavy atom phasing, molecular replacement, density modification, and final structure refinement from the output files produced by many X-ray crystallographic applications. PDB_EXTRACT merges the information into two mmCIF (macromolecular Crystallographic Information File) files, one with structure factors and one with coordinate and statistic. These two files are ready for PDB deposition.


PDB_EXTRACT can work with/without ADIT (http://deposit.pdb.org/adit) to deposit complete data. When working with ADIT (recommended), users just upload the extracted mmCIF files to ADIT. Enter any additional information into ADIT and submit your file directly from there. When working without ADIT, users just fill any additional information to a plain text file (called data_template.text) and run the program. Users can email the extracted two files to the Protein Data Bank (PDB) ‘[email protected]’.


The advantage of using pdb_extract:


a. Faster to prepare your deposit mmCIF file. User just provide the LOG files from the software used and filled some information to the data_template.text file from your local computer. Some items are pre-calculated for you. For example, Matthews coefficient and solvent constant, molecular entities.


b. Complete and accurate to deposit your file. pdb_extract automatically extract information from your LOG file. This reduces many typing errors.


c. Great for multiple structural deposition. Users just keep one data_templete.text file and copy and paste the unchanged information to the newly generated one for individual structural deposition.

Collectively, these software tools reduce the human effort required to assemble very complete and validated protein structure entries ready for PDB deposition.


IMPORTANT NOTES:


  1. If you have several structures ready to be deposited to the PDB site, you need to apply the pdb_extract program to each individual structure, since each structure requires a single PDB ID for deposition.


  1. You may have a lot of trials for each step (data processing, heavy atom phasing, or density modification, or final structure refinement), but information extracted from each step should be only from the best trial that leads to next step toward solving your structure.


  1. You may use different programs for heavy atom phasing solution. For example, you used program A to locate heavy atom positions and you used program B to refine heavy atom parameters (like x, y, z, occupancy and B factors etc.). Phasing statistics information will be extracted from the output of program B; therefore, pdb_extract should be applied to the output of program B. However, if you want to give credit to program B, you can type '-p program-name' without giving LOG files. For example, ARP/Warp is a intermediate step, you may just type '-p Warp'.


  1. You may also use different programs for final structure refinement, but pdb_extract should be only applied to the program which leads to your final structure deposition.



  1. Program access

The source and binary versions of PDB_EXTRACT can be downloaded from the address http://deposit.pdb.org/software. The source is available under an Open Source license. The binary distributions are available for Intel-Linux, SGI-IRIX, DEC-Alpha, and Sun-Solaris.

The web interface can be accessed at http://pdb-extract.rutgers.edu for PDB_EXTRACT and http://deposit.pdb.org/adit/ for ADIT.

PDB_EXTRACT has been integrated into CCP4 (http://www.ccp4.ac.uk/main.html) and the CCP4i interface(Version 5.0 and above). Users can run PDB_EXTRACT under the CCP4 environment.



  1. Installations


NOTE: if you have installed CCP4 (version 5.0 and above), you do not have to install pdb_extract. You just use the CCP4 environment to run the pdb_extract program.

Requirements:

  1. plantforms Intel-Linux, SGI-IRIX, DEC-Alpha, and Sun-Solaris:

  2. disk space great than 140 Mbytes for source distribution and 30 Mbytes for binary distribution

  3. C/C++ compilers


3.1 Installation of binary distribution

It is recommended to install the binary distribution, since it is very fast to install and it takes very small space. The binary distributions are available for Intel-Linux, SGI-IRIX, DEC-Alpha, and Sun-Solaris.


Step 1 Uncompress and unbundle the distribution using the following command:

zcat pdb-extract-vX.XXX-XXX.tar.gz | tar -xf -


The result of this command is a subdirectory pdb-extract-vX.XXX-XXX in the

current directory, which contains the following:


bin - subdirectory that contains application executables

pdb-extract-vX.X - subdirectory that contains an example in its "examples" subdirectory.

data - subdirectory that contains some data files needed by the application.

etc - subdirectory that contains utility scripts and application software license agreement.

Step 2 Set up the environment variables.


A. Define RCSBROOT environment variable to point to the installation directory.


Assuming that the installation directory is

/home/username/pdb-extract-vX.XXX-XXX, execute in the shell:


For C shell users:

setenv RCSBROOT /home/username/pdb-extract-vX.XXX-XXX

For Bourne shell users:

RCSBROOT=/home/username/pdb-extract-vX.XXX-XXX; export RCSBROOT


B. Add "bin" subdirectory to the PATH environment variable.


Assuming the installation directory is /home/username/pdb-extract-vX.XXX-XXX,

For C shell users:

setenv PATH "/home/username/pdb-extract-vX.XXX-XXX/bin:"$PATH

For Bourne shell users:

PATH="/home/username/pdb-extract-vX.XXX-XXX/bin:"$PATH; export PATH


Step 3 Make binary data from ASCII data


Position in the pdb-extract-vX.XXX-XXX/etc directory and run the script

binary.sh:

cd pdb-extract-vX.XXX-XXX/etc

./binary.sh


This command will create certain binary data files, using the ASCII data files in data/ascii directory. The resulting files are stored in data/binary directory. Note that it may take several minutes for this step to complete. This step must be executed before the tool can be utilized.


    1. Installation of source code distribution


Step 1. Uncompress and unbundle the distribution using the following command:


zcat pdb-extract-vX.XXX-XXX.tar.gz | tar -xf -


The result of this command is a subdirectory pdb-extract-vX.XXX-XXX in the current directory. It contains subdirectories of various source modules and the following items important for the user:


bin - subdirectory in which the application executables will be placed after the build process.

pdb-extract-vX.X - subdirectory that contains several examples in its "examples" subdirectory.

data - subdirectory that contains some data files needed by the application.


Step 2. Set up the environment variables.


A. Define RCSBROOT environment variable to point to the installation directory.


Assuming that the installation directory is

/home/username/pdb-extract-vX.XXX-XXX, execute in the shell:


For C shell users:

setenv RCSBROOT /home/username/pdb-extract-vX.XXX-XXX

For Bourne shell users:

RCSBROOT=/home/username/pdb-extract-vX.XXX-XXX; export RCSBROOT


B. Add "bin" subdirectory to the PATH environment variable.

Assuming that the installation directory is /home/username/pdb-extract-vX.XXX-XXX,


For C shell users:

setenv PATH "/home/username/pdb-extract-vX.XXX-XXX/bin:"$PATH

For Bourne shell users:

PATH="/home/username/pdb-extract-vX.XXX-XXX/bin:"$PATH; export PATH


Step 3. Building the Application (compile the program)

Position in the pdb-extract-vX.XXX-XXX directory and run "make" command:


cd pdb-extract-vX.XXX-XXX

make


The application executables will be placed in the "bin" subdirectory.




NOTE: The users who are working on Sun platform are advised to check the compiler flags in etc/make.platform.sunos5 file. Depending on the compiler version, users may be required to make modifications to those compiler flags.

Step 4. Make binary data from ASCII data

Position in the pdb-extract-vX.XXX-XXX directory and run "make" command as

follows:


make binary


NOTE: This command will create certain binary data files, using the ASCII data files in data/ascii directory. The resulting files are stored in data/binary directory. Note that it may take several minutes for this step to complete. This step must be executed before the tool can be utilized.



  1. Run the program


There is an example included in this distribution. User can find more examples from the location http://pdb.rutgers.edu/mmcif/PDB_EXTRACT/index.html.



    1. quick run the program

This example is located in the subdirectory of "pdb-extract-vX.X/examples/Example_1".


The directory contains the following:

input_data - contains the input data for the example

deposit - contains the resulting files (after running the program):

validation_result - contains all validation results (after running the program)


To execute the example, position in the appropriate directory and invoke test.sh and test_script.sh scripts. For example:


cd pdb-extract-vX.XXX-XXX/pdb-extract-vX.X/examples/Example_1

./test.sh

./test_script.sh


    1. Explanations of arguments and input/output files


The output files:

After you run the above commands (for example ./test.sh), you will get the following files in the directory pdb-extract-vX.X/examples/Example_1/deposit/

Example_1.cif - this is the merged mmCIF file created by "pdb_extract"

Example_1_deposit.cif - this is the new mmCIF file by "maxit".

Example_1.sf.cif - this is the structure factor created by "pdb_extract_sf"

You can deposit the two files Example_1.sf.cif and either Example_1.cif or Example_1_deposit.cif


The files generated by the validation program are in the directory.

pdb-extract-vX.X/examples/Example_1/validation_result

Example_1.ps – this is the postscript file for a picture of molecules in asymmetric

unit and crystal packing in a unit cell.

Example_1.-asym.wrl – this is a VRML file for a picture of molecules in asymmetric unit (viewed dynamically by internet browsers).

Example_1.-packing.wrl – this is a VRML file for a picture of molecular crystal

packing (viewed dynamically by internet browsers).

Example_1.html – this is a HTML file for essential information by the structure.

Example_1.letter – An important file. It contains all the diagnostic errors of the structure.

User should read this file (Example_1.letter) with care and correct any geometrical errors before submission of the structure.



The input files:

MAD experiment


Data files:








The script to run the programs (test.sh)

The script for “test.sh” is a combination of various Unix command line programs.


The script is in the directory “pdb-extract-vX.X /examples/Example_1/” and the content of the script is the following:


#!/bin/sh


# use pdb_extract to extract the required statistics and get a mmcif file.

pdb_extract -e MAD -r CNS -iCIF input_data/deposit_cns.mmcif \

-iENT input_data/data_template.text \

-p CNS -iLOG input_data/mad_sdb.dat input_data/mad_summary.dat input_data/mad_fp.dat \

-d CNS -iLOG input_data/density_modify.dat -o Example_1.cif


# use pdb_extract_sf to convert the structure factor to mmCIF format.

pdb_extract_sf -dt I -dp HKL -c 1 -w 1 -idat input_data/w1.sca \

-c 1 -w 2 -idat input_data/w2.sca

-c 1 -w 3 -idat input_data/w3.sca -o Example_1.sf.cif


# use validation-v8 to validate the mmcif file.

validation-v8 -f Example_1.cif -o 2 -public -exchange -adit


# use maxit-v8.01-O to reorder the mmcif format

maxit-v8.01-O -i Example_1.cif -o 8 -exchange_in -exchange_out


# move the files to some directory and delete some log files.

mv Example_1.cif.cif Example_1_deposit.cif

mv Example_1.cif deposit

mv Example_1_deposit.cif deposit

mv Example_1.sf.cif deposit

mv Example_1* validation_result

rm -f *log *err procheck* SEQUENCE.DAT *ERR validation.alignment


The script to run the programs (test_script.sh)

The script for “test_script.sh” is an alternative way to obtain the same result as above. It is also a combination of various programs. The difference is that it used “extract” instead of the “pdb_extract” and “pdb_extract_sf”. All the information is included in the file “log_script.inp”.


The script is in the directory “pdb-extract-vX.X /examples/Example_1/” and the content of the script is the following:


#!/bin/sh


# use extract to run everything in example_1.inp and get a mmcif file.

extract -ext input_data/log_script.inp


# use validation-v8 to validate the mmcif file.

validation-v8 -f script_example_1.cif -o 2 -public -exchange


# use maxit-v8.01-O to reorder the mmcif format

maxit-v8.01-O -i script_example_1.cif -o 8 -exchange_in -exchange_out


# move the files to some directory and delete some log files.

mv script_example_1.cif.cif script_example_1_deposit.cif

mv script_example_1.cif deposit/

mv script_example_1_deposit.cif deposit/

mv script_example_1_sf.cif deposit/

mv *.html *.ps *.letter *.wrl validation_result/

rm -f *log *err procheck* SEQUENCE.DAT *ERR validation.alignment


  1. Tutorials


There are four ways to extract crystallographic information and deposit complete data to the Protein Data Bank.


1. Use CCP4i (http://www.ccp4.ac.uk/main.html/)

2. Use the Web interface (http://pdb-extract.rutgers.edu/).

3. Use Unix Command Line Interface.

4. Use Script Interface.


Three interfaces have different features. For example, The CCP4i or Web interface provide a simple graphic interface. Users just select the program name and output file names to do the job. The full Unix command line method provides the greatest flexibility. User need to read the command options to run the program. The script input method provides a simple local interface.


Here, we give a concrete example to show how to use pdb_extract for complete data extraction.


In this example, the experimental method for solving the protein structure was multiple anomalous diffraction (MAD). The information for the experiment is as the following:


The LOG files generated from above programs are the following:



    1. Using CCP4i interface


Step 1. From the main window of CCP4i, select the ‘Data Harvesting Management Tool’ option.


Step 2. From the option of ‘Run program to’, select the ‘Extract additional information for deposition’


Step 3. Select the ‘Generate a data template file’ from various steps


Step 4. Select the ‘Generate a complete mmCIF file for PDB deposition’ from various steps


NOTE: The characters of file name should always start from beginning of each yellow box. There should be no white space in each box, even no file name is typed in.


    1. Using the Web interface (http://pdb-extract.rutgers.edu/)

Follow on line tutorial!


    1. Using Unix Command Line Interface



STEP 1. Obtain the template data file 'data_template.text' using the command


extract -pdb coordinate_PDB_file_name

or

extract -cif coordinate_CIF_file_name

After running the program, you will get a file called 'data_template.text'. There are 19 CATEGORIES for data entries in the file 'data_template.text'. CATEGORY 1-2 contains the extracted unit cell parameters and the unique molecular chemical sequence group. Please modify the two CATEGORIES as necessary. Additional structure information can be filled into CATEGORIES (3-19).


The content of the data template file 'data_template.text' is given in Appendix




STEP 2. Obtain coordinates and all the statistics


Run the pdb_extract program:


pdb_extract -e MAD \

-p SOLVE -iLOG solve.prt \

-d RESOLVE -iLOG resolve.log \

-r refmac5 -icif peak.refmac -ipdb refmac.pdb\

-s HKL –iLOG scale-refine.log \

-sp HKL scale1.log scale2.log scale3.log \

-iENT date_template.text \

-o output.cif



STEP 3. Obtain structure factors


Run pdb_extract_sf to convert HKL format to mmCIF format and merge all the files to one file.


pdb_extract_sf -rt F -rp refmac5 -idat refmac_sf.mmcif \ (for refinement)

-dt I -dp HKL \ (for phasing)

-c 1 -w 1 -idat scale1.sca \

-c 1 -w 2 -idat scale2.sca \

-c 1 -w 3 -idat scale3.sca \

-o output_sf.cif


Since REFMAC5 use MTZ file for refinement, the reflection data file must be converted to CIF format using ccp4i or mtz2various. The file name is refmac_sf.mmcif.


The output file (output_sf.cif) contains one reflection data block for refinement and one data block for protein phasing.



STEP 4 Validation and deposition


Note: the PDB-Validation program is not provided in CCP4 package.


Either upload the two files (output.cif, output_sf.cif) to ADIT, or use the following commands:


validation-v8 -f output.cif -o 2 –public -exchange

maxit-v8.01-O -i output.cif -o 8 -exchange_in -exchange_out -keep_contact_author


Then upload the validated file and the structure factor file to ADIT for on-line submission. The alternative is to email the file to '[email protected]'



    1. Using the script interface


This script is similar to the CNS script input. Users just enter all the LOG file name and the program names to the plain text file ‘log_script.inp’ and run the program.


STEP 1 obtain the plain text file ‘log_script.inp’


extract -pdb refmac.pdb


You will get one script file called 'log_script.inp' and one data template file ‘data_template.text’. Edit the data template file according to the instruction in the file. Fill all the Log file names and the program names as well as the data_template file to the script file 'log_script.inp'.


The content of the file ‘log_script.inp’ is shown in the Appendix.



STEP 2 run the program:


extract -ext log_script.inp


You will get the same results as using the Unix command line option.


STEP 3 Validation and deposition: (as in the Unix command line option).



  1. Some helpful hints to get LOG (or output) files from various crystallographic applications


Listed below are the programs used from data collection to structure determination.


    1. Data collection/reduction/scaling


This is the early stage of solving a crystal structure. The statistics for integrating, scaling the data tells the quality of the structure factors. Information can be extracted from this step is the following:



      1. Using HKL/HKL2000/scalepack (http://www.lnls.br/infra/linhasluz/denzo-hkl.htm)


HKL is a package by Otwinowski for data collection/reduction/scaling. You can use graphic interface or the scalepack script to scale your data. The LOG file (e.g. scale1.log) containing statistics is from the step of scaling data.


To extract statistics:

pdb_extract –s HKL –ilog scale1.log (one data for refinement)

pdb_extract –sp HKL –ilog scale1.log scale2.log … (multiple data for phasing)


      1. Using D*trek (http://www.msc.com/protein/dtrek.html)


D*trek is a package by Rigaku/MSC for data collection/reduction/scaling. You can use graphic interface to scale (or merge/average) your data. The LOG file (e.g. scale1.log) containing statistics is from the step of scaling data.


To extract statistics:

pdb_extract –s Dtrek –ilog scale1.log (one data for refinement)

pdb_extract –sp Dtrek –ilog scale1.log scale2.log … (multiple data for phasing)


      1. Using SAINT (http://xray.chm.bris.ac.uk/facilities/smart.html)


SAINT is a package by Bruker (Siemens Molecular Analytical Research Tool) for data collection/reduction/scaling. The LOG file (e.g. scale1.ls) containing statistics is from the step of scaling data.


To extract statistics:

pdb_extract –s SAINT –ilog scale1.ls (one data for refinement)

pdb_extract –sp SAINT –ilog scale1.ls scale2.ls … (multiple data for phasing)


      1. Using 3DSCALE (?)


3DSCALE is a program by Fu et al. for data scaling. The LOG file (e.g. scale1.log) contains statistics.


To extract statistics:

pdb_extract –s 3DSCALE –ilog scale1.log (one data for refinement)

pdb_extract –sp 3DSCALE –ilog scale1.log scale2.log … (multiple data for phasing)


      1. Using SCALA (http://www.ccp4.ac.uk/dist/html/scala.html)


SCALA is the CCP4 supported program. It scales together multiple observations of reflections. SCALA can generate mmCIF file containing useful statistics. When you run the programs, you must ask the program to export the data harvest file. For example the file will be name.scala. If you do not use the mmCIF file, you can use the LOG file generated by SCALA.


To extract statistics:

pdb_extract –s scala –icif name.scala (one data for refinement)

or

pdb_extract –s scala –ilog scala.log (one data for refinement)


    1. Programs for molecular replacement


If your structure was solved by molecular replacement, you can use the pdb_extract program to extract information from the LOG files. The information may be the followings:


      1. Using CNS/XPLOR (http://cns.csb.yale.edu/v1.1/)


CNS can be used to do molecular replacement. After you finish the translation search, you can get a log file called translation.list which contains all the information of molecular replacement.


The command to extract information is:

pdb_extract -o test.mmcif –e MR –m CNS –ilog translation.list


      1. Using Amore (CCP4 version 4.1- above): (http://www.ccp4.ac.uk/dist/html/INDEX.html)


Amore is a popular program for molecular replacement. It is distributed in the CCP4 package. After rotation and translation search, you will generate two log files rotation.log and translation.log. You may extract information from both log files


The command to extract information is:

pdb_extract –e MR –m amore –ilog rotation.log translation.list -o test.mmcif


      1. Using Morep (CCP4 version 4.1-above): (http://www.ccp4.ac.uk/dist/html/INDEX.html)


Morep is a program for molecular replacement. It is distributed in the CCP4 package. When you run the script, you can give a log file name like morep.log. All the statistic information will be recorded in the log file.


The command to extract information is:

pdb_extract –e MR –m morep –ilog morep.log -o test.mmcif


      1. Using EPMR: (http://www.msg.ucsf.edu/local/programs/epmr/epmr.html)


EPMR is a Unix command line program for molecular replacement.

When you run the program, please give a log file name like the following

Epmr [options] files > epmr.log

All the statistic information will be recorded in the log file.


The command to extract information is:

pdb_extract –e MR –m epmr –ilog epmr.log -o test.mmcif



    1. Programs for heavy atom position location and protein phasing


The whole issue of protein crystallography may be the phase problem. Heavy atom phasing is performed at earlier stage of structure determination. Some log files generated from phasing step contain important statistic information (don’t throw them away). The pdb_extract program can be used to extract the following information from log files.



      1. Using CNS/XPLOR (http://cns.csb.yale.edu/v1.1/)


CNS is a complete software system for protein crystallography. The scripts for heavy atoms location and phasing refinement are ‘mad_phase.inp’ or ‘ir_phase.inp’. When you run these scripts, you will get the output files like ‘phase_final.summary’, ‘phase_final.sdb’ or ‘mad_phase.fp’.

The output file phase_final.summary has all the phasing statistics. The output file phase_final.sdb has all the heavy atom coordinates, occupancies and B factors. The output file mad_phase.fp has refined f_prime and f_double_prime.


(Note: The refined heavy atom coordinates and the B factors and the occupancies can be found in a file like ‘phase_final.sdb’. If you prefer to convert to the PDB format, you can run the script sdb_to_pdb.inp. You will get a file ‘phase_final.pdb’ with PDB format.)


To extract phasing information, you need the following description:

pdb_extract -o test.mmcif –e MAD –p CNS \

–iLOG phase_final.summary phase_final.sdb mad_phase.fp


or, if you have the heavy atom coordinates in PDB format:

pdb_extract -o test.mmcif –e MAD –p CNS \

–iLOG phase_final.summary mad_phase.fp \

–iPDB phase_final.pdb


      1. Using MLPHARE (http://www.ccp4.ac.uk/dist/html/INDEX.html)


MLPHARE is a program in the CCP4 suit. It is used for refining heavy atom parameters:


If you use the CCP4i graphical interface or the script mode, you need to ask the program to write a harvesting file. Select the data harvest button, when you use the CCP4i interface. Do not give command word NOHARV, when you use script. After you finished running this program, you will get a file (e.g. name.mlphare) which is in mmCIF format. It contains statistics information for heavy atom phasing refinement.


For extracting the wavelength information, you need to run program REVISE in the CCP4 (version 4.1-4.2). You may get a file (like prephadata.log which is in LOG format)


To extract phasing information, you need the following description:

pdb_extract -o test.mmcif –e method –p MLPHARE \

–iCIF name.mlphare –iLOG prephadata.log



      1. Using SOLVE (http://www.solve.lanl.gov/)


Solve is a popular program for finding heavy atom and refining heavy atom parameters. The summary information will be written to a file called “solve.prt” (default name used by the program). The program also exports the heavy atom coordinates, called “ha.pdb”.


The pdb_extract program works for any one of the following situations:


To extract phasing information, you need the following descriptions:

pdb_extract –e method –p SOLVE –iLOG solve.prt -ipdb ha.pdb -o test.mmcif


      1. Using SHARP (http://babinet.globalphasing.com/sharp/)


SHARP is a program for finding heavy atom positions and refining heavy atom parameters. When you run SHARP or autoSHARP, the log files containing useful information are normally in the directory sharpfiles/logfiles_local/dirs, where dirs are all the subdirectories for your various structures. One should be advised that the location of generated log files might depend on how the program is installed!


SHARP produces many output files. You need to get the following files:

For version 1.3.x:


For version 2.0 or above:


The easiest way to obtain these files is to run the program from the SUSHI interface. Review all the log files from the internet browser and save the files as plain txt (or html) files.


To extract phasing information, you need the following description:

pdb_extract -o test.mmcif –e method –p SHARP –iPDB heavy.pdb \

–iLOG FOMstats.html Otherstat.html Name.sin



      1. Using SnP (http://www.hwi.buffalo.edu/SnB/)


SnB is graphic interface software using the Shake-and-Bake algorithm. It has no heavy atom parameter refinement, and it has no corresponding statistics. However, SnB gives the heavy atom or substructure coordinates (e.g. heavy.pdb) in PDB format.


You can use the following command to extract the heavy atom PDB coordinates:

pdb_extract -o test.mmcif –e method –p SNB –iPDB heavy.pdb


Note: Sometimes the coordinates and other parameters can be refined by other programs like MLPHARE or CNS. Therefore, the heavy atom phasing information as well as the heavy atom coordinates will be extracted from MLPHARE or CNS instead of SnB even though SnB may have been used to find the initial heavy atom positions.

      1. Using BnP (http://www.hwi.buffalo.edu/BnP/)


BnP is a combination of program SnB and Phases by Furry. The heavy atom positions are located by SnB and the heavy atom parameters will be refined by Phases.


The log file (for example auto.log) can be found from the directory ~/PHASES/*. Log file normally contains phasing power for each phasing set.


You can use the following command to extract the heavy atom PDB coordinates:

pdb_extract -o test.mmcif –e method –p BnP –ilog auto.log –iPDB heavy.pdb

or

pdb_extract -o test.mmcif –e method –p phases –ilog auto.log –iPDB heavy.pdb


      1. Using SHELXD or SHELXS (http://shelx.uni-ac.gwdg.de/SHELX/)


They are pretty much the same as SnB. Only heavy atom or substructure coordinates are produced in PDB format (e.g. heavy.pdb).


You can use the following command to extract the heavy atom PDB coordinates:

pdb_extract -o test.mmcif –e method –p SHELXD –iPDB heavy.pdb

or

pdb_extract -o test.mmcif –e method –p SHELXS –iPDB heavy.pdb


      1. Using PHASES (http://imsb.au.dk/~mok/phases/phases.html)


PHASES is a package developed by Furry. It can be used to located heavy atom positions and refine the heavy atom parameters.


The log file (for example name.log) can be found from the directory ~/PHASES/*. Log file normally contains phasing power for each phasing set.


You can use the following command to extract the heavy atom PDB coordinates:

pdb_extract -o test.mmcif –e method –p Phases –ilog name.log –iPDB heavy.pdb


    1. Programs for density modification


Density modification is normally applied after obtaining phase (or heavy atom coordinates). If you use density modification in you structure determination, you can apply the pdb_extract program to extract some statistics from the generated log files.


The following items may be extracted:


      1. Using CNS/XPLOR (http://cns.csb.yale.edu/v1.1/)


The CNS user may need to run the input script like ‘density_modify.inp’. You will get

a log file called ‘density_modify.list’.


The command to extract density modification statistics is:

pdb_extract -o test.mmcif –e method –d CNS –iLOG density_modify.list



      1. Using DM (http://www.ccp4.ac.uk/dist/html/INDEX.html)


DM is a popular density modification program in the CCP4 suit. When you run DM either by using the CCP4i graphic interface or the script, you will get a log file like ‘dm.log’.


The command to extract density modification statistics is:

pdb_extract -o test.mmcif –e method –d DM –iLOG dm.log


      1. Using SOLOMON (http://www.ccp4.ac.uk/dist/html/INDEX.html)


SOLOMON is also a popular density modification program CCP4 suit. When you run DM either by using the CCP4i graphic interface or the script, you will get a log file like ‘Solomon.log’.


The command to extract density modification statistics is:

pdb_extract -o test.mmcif –e method –d SOLOMON

–iLOG solomon.log


      1. Using RESOLVE (http://www.solve.lanl.gov/)


RESOLVE is a density modification program in the solve/resolve package. Normally it runs together with SOLVE, but one can run it separately. When you run RESOLVE, (resolve ? > resolve.log) you will get a log file like ‘resolve.log’.


The command to extract density modification statistics is:

pdb_extract -o test.mmcif –e method –d RESOLVE –iLOG resolve.log


      1. Using SHARP (http://babinet.globalphasing.com/sharp/)


Density modification used in SHARP is actually the DM (version 2.2) or solomon. When you run density modification in SHARP, you will get a log file like ‘dm.log’.


The command to extract density modification statistics is:

pdb_extract -o test.mmcif –e method –d SHARP –iLOG dm.log

or

pdb_extract -o test.mmcif –e method –d dm –iLOG dm.log




    1. Programs for final structure refinement


The structure refinement is performed at the end of structure determination. Normally the atom coordinates are generated in PDB format and the statistics are generated in log files. The pdb_extract program can be applied to extract the following information:




      1. Using CNS/XPLOR (http://cns.csb.yale.edu/v1.1/)


CNS is a popular program for final structure refinement. After you finish the structure refinement, you need to run script (deposit_mmcif.inp). It produces a file (e.g. deposit.mmcif) in CIF format. This file contains rich statistic information.


The command to extract refinement statistics and model details is:

pdb_extract -o test.mmcif –e method –r CNS –iCIF deposit.mmcif

      1. Using REFMAC5 (http://www.ccp4.ac.uk/dist/html/INDEX.html)


REFMAC5 is a popular program for structure refinement (also supported in the CCP4 suite). If you run this program using CCP4i or the script, you need to ask the program to write a harvesting file. When you use the CCP4i interface, select the data harvest button. When you use script mode, do not give command word NOHARV. After you finish running this program, you will get a file (e.g. name.refmac) which is in CIF format. It contains all the information for structure refinement. You will also get a PDB file (e.g. name.pdb). This file contains all the atom coordinates, Bfactors, etc.

The command to extract refinement statistics and model details is:

pdb_extract -o test.mmcif –e method –r REFMAC5 –iCIF \

name.refmac –iPDB name.pdb


      1. Using SHELXL (http://shelx.uni-ac.gwdg.de/SHELX/)


SHELXL is a sub_program in the SHELX package. It is used for structure refinement.

After you finish structure refinement, you need to run the shelxpro interactive program and use option B. After going through the shelxpro, you will get a PDB file (e.g. name.pdb) with header information.


The command to extract refinement statistics and model details is:

pdb_extract -o test.mmcif –e method –r SHELXL –iPDB name.pdb



      1. Using TNT (http://www.uoxray.uoregon.edu/tnt/welcome.html)


TNT is a crystal structure refinement program. Data from this program can be extracted from the output PDB file and some LOG files. You can use the to_pdb command to convert coordinates in TNT format (name.cor) to the PDB format (name.pdb).


The command is: to_pdb name.cor


After finishing refinement, you must use command rfactor to generate a log file (e.g. rfactor.log) which contains the refinement statistics.


The command is: rfactor name.cor > rfactor.log


To extract the symmetry information, user must provide the symmetry file (e.g. p6122.dat). The information is in the control file name.tnt


The complete command to extract information from TNT should be the following:

pdb_extract –r TNT –iLOG p6122.dat rfactor.log –iPDB name.pdb


      1. Using ARP/wARP (http://www.embl-hamburg.de/ARP/)


ARP/wARP is an automatic program for structure solution and refinement. REFMAC5 is used for the structure refinement step.


The new version (6.0) can use CCP4i as graphic interface. You can run this program either by CCP4i or by script. You will get a log file (for example warpNtrace_refine.log). You also get a PDB file like warpNtrace.pdb.


To extract phasing information, you need the following description:

pdb_extract -o test.mmcif –e method –r WARP –iLOG warpNtrace_refine.log \

–iPDB warpNtrace.pdb



      1. Using RESTRAIN (http://www.ccp4.ac.uk/dist/html/INDEX.html)


RESTRAIN is a program for structure refinement (also used in the CCP4 suite). Do not give command word NOHARV, when you use script mode. After you finish running this program, you will get a file (e.g. name.restrain) which is in CIF format. It contains all the information for structure refinement. You will also get a PDB file (e.g. name.pdb). This file contains the atom coordinates, Bfactors, etc.

The command to extract refinement statistics and model details is:

pdb_extract -o test.mmcif –e method –r RESTRAIN –iCIF name.restrain \

–iPDB name.pdb



  1. Program argument description


There are three components (pdb_extract, pdb_extract_sf, and extract) for the program.


    1. Unix argument description and options for pdb_extract


NAME pdb_extract

SYNOPSIS pdb_extract [OPTIONs]... [FILEs]...


DESCRIPTION

PDB_EXTRACT is used to extract information about data processing, heavy atom phasing, molecular replacement, density modification, and final structure refinement from the output files produced by many X-ray crystallographic applications, and merges the information into macromolecular Crystallographic Information File (mmCIF) data files.


User can get help by typing ‘pdb_extract –h or pdb_extract –help’ to get information how to do extractions and deposition to PDB


OPTIONS

-o Followed by a given output file name.


For example: -o outfile.mmcif


NOTE: if you do not give this description, the default output file name (pdb_extract.mmcif) will be used.

-e Followed by one of the following experimental methods:


example: -e MAD


Note: If your experiment is solved by combinations of above methods (e.g. MR with MAD), you may extract things from both methods (e.g. -e MR –m program_mr –ilog Log_file –e MAD –p program_mad –ilog file_name)


-m Followed by the one of following programs for molecular replacement:

For example: -m amore

-p Followed by the one of following program names for phasing:

For example: -p CNS


Note: if the program that you used for phasing is not in the above list, you may still give the program name. Some information (like heavy atom coordinates) may still be extracted, if the produced file is in PDB or mmCIF format. (use –p program_name )

-d Followed by the one of following program names for density modification:


For example: -d CNS

-r Followed by one of the following program names for final structure refinement.

For example: -r CNS


Note: if the program that you used for final structure refinement is not in the above list, you may still give the program name. Some information (like atom coordinates) may still be extracted, if the produced file is in PDB or CIF format. (use –r program_name )


-s Followed by one of the following programs for data scaling (for refinement):

For example: -s HKL


Note: The –s option here is only used to get statistics from data reduction. The reflection data must be used to the final structure refinement.


-sp Followed by one of the following programs for data scaling (for refinement):

For example: -sp HKL


Note: The option is similar to –s, but it is used to extract statistics from multiple data reductions. The reflection data sets must be used to protein phasing solutions (SAD, MAD, SIR, MIR …). Normally, there are multiple data sets.



-iPDB Followed by a input file with PDB format.

For example: -iPDB test1.pdb


NOTE: The PDB files are usually generated from heavy atom phasing (heavy atom coordinates) or the final structure refinement.


-iCIF Followed by a input file with CIF format.


For example: -iCIF deposit_cns.cif


NOTE: This file can be produced during crystal structural determination. For instance: if you use MLPHARE for locating heavy atom position and do heavy atom phasing refinement, a file in mmCIF format will be generated. This file will contain statistics for heavy atom phasing. Another instance, if you use CNS for final structure refinement, running the deposit.inp macro will produce a CIF file containing the model coordinates and refinement statistics.

-iLOG Followed by one or more input LOG files

For example: -iLOG mad_sdb.dat mad_summary.dat


NOTE: Log files are usually generated during crystal structural determination. The format depends on the program used. They may contain phasing statistics or heavy atom coordinates. For instance, when people use CNS for heavy atom phasing, they will generate a file (e.g. mad_sdb.dat) which contains the heavy atom coordinates and a file (e.g. mad_summary.dat) which contains phase refinement statistics.


-iENT Followed by the either a mmCIF file or the pdb_extract generated plain text file.


For example: -iENT data_template.text or -iENT entity-poly.mmcif


NOTE: This file should be generated by the program extract. It contains the full chemical sequence and related information to be filled for each macromolecule in the solved structure. The format is either mmCIF (entity-poly.mmcif) or a plain text (data_template.text). The chemical sequences are grouped in each molecular entity which is defined as a unique monomer in asymmetric unit. For example, if there are several copies (chain A, B, ..) of a molecule in asymmetric unit (e.g. dimmer, trimmer ..), the molecular entity is only one. This file can be found in each example. For details of the definition, please see the website: http://pdb.rutgers.edu/mmcif.


The file (data_template.text or entity-poly.mmcif) have to be editored or modified (as necessary) before it is used with pdb_extract.


For convenience, user can use the following commands to generate the file “entity-poly.text” from either your PDB file or your mmCIF file.


extract –pdb pdb_file_name (coordinate file in PDB format)

or

extract –cif cif_file_name (coordinate file in mmCIF format (e.g. CNS))



    1. Examples for using pdb_extract options


Note: you can extract statistics separately from each step of structure determination applications (data processing, heavy atom phasing, density modification, molecular replacement and final structure refinement), or you can put all the steps together, which is a complete deposition.


Command for extracting information about heavy atom phasing:

(The experimental_method must be given for this step)

pdb_extract -e experimental_method -p program_name_phasing \

-iPDB pdb_files –iLOG log_files \

–iCIF mmCIF_files -o output_file_name


Command for extracting information about density modification (output from this program is normally the LOG file):

pdb_extract -d program_name_for_dm –iLOG log_files -o output_file_name


Command for extracting information about molecular replacement (output from this program is normally the LOG file):

pdb_extract -m program_name_for_mr –iLOG log_files -o output_file_name


Command for extracting information from final structure refinement:

pdb_extract -r program_name_for_refinement -iPDB pdb_files \

–iLOG log_files –iCIF mmCIF_files -o output_file_name


Command for extracting information from data scaling LOG files (for refinement):

pdb_extract -s program_name_scaling –iLOG log_file -o output_file_name


Note: HKL/SCALEPACK does not export <I/SimgaI>, but it is needed in the PDB deposition.

pdb_extract can calculate this for you when providing the data for refinement. The command is

pdb_extract -s program_name_scaling –iLOG log_file -o output_file_name \

-idat reflection_data_file



Command for extracting information from data scaling LOG files (for phasing):

pdb_extract -sp program_name_scaling –iLOG log_file1 log_file2 -o output_file_name



Command for extracting information for a complete structure:

pdb_extract -e experimental_method -r rogram_name_for_refinement \

-iPDB pdb_files –iLOG log_files –iCIF mmCIF_files \

-p program_name_for_phasing -iPDB pdb_files \

–iLOG log_files –iCIF mmCIF_files \

-d program_name_for_dm –iLOG log_files \

-s program_name_for_scaling –iLOG log_files \

-sp program_name_for_scaling –iLOG log_files \

-iENT data_template.text -o output_file_name



    1. Unix argument description and options for pdb_extract_sf


NAME pdb_extract_sf

SYNOPSIS pdb_extract_sf [OPTIONs]... [FILEs]...


DESCRIPTION

This program can be used to capture

1. Reflection data used for final structure refinement.

2. Multiple reflection data (eg. MAD, MIR …) processed by the software at the data collection site.


OPTIONS

-o Followed by an output file name.


For example: -o outfile.cif


NOTE: if you do not specify an output file, a default output file name (pdb_extract­_sf.mmcif) will be used.

-dt Data type for initial data processing (normally intensity).

It is followed by F (Amplitude) or I (Intensity)


For example: -dt I

-dp Data format for initial data processing.

It is followed by one of the following program names:

HKL/SCALEPACK, DTREK, SAINT, XPREP, 3DSCALE, SCALA, OTHER.

For example: -dp HKL

NOTE1: If the program for data scaling is not in the above list, please give OTHER. Then you must provide either a plain text file with reflection data in the order of H, K, L, (F or I), (sigmaF or sigmaI) separated by spaces in each row, or a mmCIF file: e.g. –dt I –dp OTHER –idat file_name

NOTE2: If the output data is in mtz format (processed by MOSFILM and SCALA), you must convert the data either to CNS format or scalepack format or mmCIF format. If it is CNS format, you will use -dp CNS –idat file-name. If it is scalepack format, you will use -dp HKL –idat file-name. If it is mmCIF format, you can use -dp SCALA –idat file-name.


-c crystal index.

It is followed by crystal number (integers, like 1,2,3, ..)


Example: -c 2

(It means the reflection was from the second crystal).


-w wavelength index.

It is followed by wavelength number (integers, like 1, 2, 3)

Example: -w 2

(This means the data was collected from the crystal using the second

wavelength).


-idat reflection data file

It is followed by data file name

Example: -idat scalepack.sca


NOTE: You should always give the combination –c i, -w j –idat file_name in the right order! Here i is the crystal index, j is wavelength index, and file_name is the file name containing the reflections.


-rt data type used for final structure refinement.

It is followed by F (Amplitude) or I (Intensity)


For example: -dt F


-rp data format in the final structure refinement.

It is followed by the data format name: CNS/XPLOR, REFMAC5, SHELX, TNT, HKL/SCALEPACK, DTREK, SAINT, XPREP, 3DSCALE, SCALA,


Example: -rp CNS


NOTE: If you used REFMAC5 to do final structure refinement, you need convert the MTZ file to mmCIF format or CNS format.


If it is converted to mmCIF format, you can use the command

pdb_extract_sf –rt I –rp REFMAC5 –idat data-file-name


If it is converted to CNS format, you can use the command

pdb_extract_sf –rt I –rp CNS –idat data-file-name



NOTE1: If the program for refinement is not in the above list, please give OTHER. Then you must provide either a plain text file with reflection data in the order of H, K, L, (F or I), (sigmaF or sigmaI) separated by spaces in each row, or a mmCIF file: e.g. –rt F –rp OTHER –idat file_name


-imgCIF file name for imgCIF format.

It is followed by the input file name:


Example: -imgCIF example.cbf

NOTE: Only the head information of the imgCIF file can be extracted!



    1. Examples for using pdb_extract_sf options


Extracting reflection data used for final structure refinement:

pdb_extract_sf -rt data-type -rp data-format-for-refinement \

-idat data-file-name –o output-file-name


NOTE: Normally, there is only one data set. If you have several data set used for final refinement, you need to merge all the data in one file.


Extracting reflection data from initial data process (e.g. scaling …):

pdb_extract_sf -dt data_type -dp program_name_for_scaling \

-c crystal_number_1 -w wavelength_number_1 -idat data_file_name_1 \

-c crystal_number_2 -w wavelength_number_2 -idat data_file_name_2 \

…

–o output_file_name


NOTE: Normally, there are several data sets (e.g. in MAD, MIR …). These reflections are used for protein phasing. The formats are from the initial data process.



Converting all the reflection data in one mmCIF file (just combine the above two steps):


pdb_extract_sf -rt data-type_refine -rp data-format-for_refine \

-idat data-file-name_refine -dt data_type_scaling \

-dp program_name_for_scaling\

-c crystal_number_1 -w wavelength_number_1 -idat data_file_name_1 \

-c crystal_number_2 -w wavelength_number_2 -idat data_file_name_2 \

…

–o output_file_name



The output_file_name contains the reflections for refinement and the reflections for protein phasing.


    1. Unix argument description and options for extract


NAME extract

SYNOPSIS extract [OPTIONs] [FILE]


DESCRIPTION

This program can be used to do the following:

1. Generate the plain text file (data_template.text) used with pdb_extract.

Generated the plain text file (log_script.inp) used by extract itself.

2. Run all the commands in the script input file (log_script.inp).


OPTIONS

-pdb Followed by the coordinate PDB file name

example -pdb pdb_file_name


NOTE: it will generate two plain text files (data_template.text and log_script.inp) with the chemical sequences extracted from the coordinate PDB file.


-cif Followed by the coordinate mmCIF file name

example -cif mmCIF_file_name


NOTE: it will generate two plain text files (data_template.text and log_script.inp) with the chemical sequences extracted from the coordinate mmCIF file.


-ext Followed by the generated file log_script.inp

example -ext log_script.inp


NOTE: you just fill the LOG files and some additional information to the log_script.inp. Then use ‘extract –ext log_script.inp ’ to get a complete mmCIF file and structure file.



    1. Examples for using extract options


Obtain the input file entity-poly.inp

extract -pdb pdb_file_name or extract -cif cif_file_name


Get a complete mmCIF file for deposition


extract -ext log_script.inp


  1. Tables


    1. Unix command options


Unix command line options for the three components of PDB_EXTRACT. pdb_extract_sf is used to capture structure factors, and pdb_extract is used to capture the details of molecular replacement, heavy atom phasing, density modification and structure refinement, and extract is used to generate entity-poly.text and entity-poly.inp.

pdb_extract_sf [OPTION]... [FILE]...

Option

Argument descriptions

-o

output file name (default name is pdb_extract_sf.mmCIF).

-dt

data type (I or F) after data processing at beam line.

-dp

program for processing data (e.g. HKL/Scalepack, D*Trek, SCALA).

-rt

data type (I or F) used for final structure refinement.

-rp

program for structure refinement (e.g. CNS|REFMAC5|SHELX|TNT).

-c

crystal number (like 1, 2, 3 …) for diffraction.

-w

wavelength number (like 1, 2, 3 …) for diffraction.

-idat

data file name used for phasing or structure refinement.

-ilog

log file name obtained from data processing.

-icif

file name obtained from data processing (in mmCIF format).


pdb_extract [OPTION]... [FILE]...

Option

Argument descriptions

-o

output file name (default name is pdb_extract.mmcif)

-e

experimental method (eg. MR|SAD|MAD|SIR|MIR|SIRAS|MIRAS)

-m

program for molecular replacement

(e.g. CNS|AMORE|MOLREP|EPMR)

-p

program for heavy atom phasing

(e.g. CNS|MLPHARE|SOLVE|SHARP|SHELXD|SnB|BnP)

-d

program for density modification

(e.g. CNS|DM|SOLOMON|RESOLVE)

-r

program for final structure refinement

(e.g. CNS|REFMAC5|RESTRAIN|SHELXL|TNT|WARP)

-s

program for reflection data scaling (only for refinement)

(e.g. HKL/Scalepack, D*Trek, SAINT, SCALA, 3DSCALE).

-sp

program for reflection data scaling (only for phasing)

(e.g. HKL/Scalepack, D*Trek, SAINT, SCALA, 3DSCALE).

-ilog

the input file with format corresponding to the program used.

-ipdb

the input file with PDB format.

-icif

the input file with mmCIF format.

-ient

the input file entity-poly.text. (for complete sequence.)


extract [OPTION] [FILE]

Option

Argument descriptions

-pdb

input coordinate file name (PDB format)

-cif

input coordinate file name (mmCIF format)

-ext

input script file name entity-poly.inp


    1. Crystallographic software list


Crystallographic software applications supported by PDB_EXTRACT.

Category

Software

Versions

Authors

Data collection and

reduction

HKL/SCALEPACK

1.30 - 1.96

Otwinowski & Minor (1997)

d*TREK

7.0SSI

Pflugrath (1997)

SAINT

V6.35A

Siemens (1994)

SCALA

3.1.4 - 3.2.3

Evans (1997)

Molecular

replacement

CNS

0.9 - 1.1

Brunger et al. (1998)

Amore

CCP4 (4.0 - 5.0)

Navaza (1994)

Morep

7.5.01

Vagin & Teplyakov (1997)

EPMR

2.5

Kissinger et al. (1999)

Heavy atom

phase

determination

CNS

0.9 - 1.1

Brunger et al. (1998)

SOLVE

2.0 - 2.06

Terwilliger & Berendzen. (1999)

MLPHARE

CCP4 (4.0 - 5.0)

CCP4 (1994)

SHARP/autoSHARP

1.3.x - 2.02

Fortelle & Bricogne (1997)

SHELXD/SHELXS

97

Sheldrick (1997)

PHASES

95

Furry (1997)

SnB

2.0 - 2.2

Weeks & Miller (1999).

BnP

0.93 - 0.94

Weeks et al. (2002)

Density

modification

CNS

0.9 - 1.1

Brunger et al. (1998)

DM

2.0 - 2.1

Cowtan (1994)

Solomon

CCP4 (4.0 - 5.0)

Abrahams & Leslie (1996)

RESOLVE

2.0 - 2.06

Terwilliger (2000)

SHELXE

97

Sheldrick (1997)

Structure

refinement

CNS

0.9 - 1.1

Brunger et al. (1998)

REFMAC5

5.0 - 5.2

Murshudov (1997)

RESTRAIN

4.7.7

CCP4 (1994)

SHELXL

97

Sheldrick (1997)

TNT

5F

Tronrud (1997)

WARP

5.0 - 6.0

Lamzin & Wilson, (1997)




  1. References


H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne(2000), "The Protein Data Bank". Nucleic Acids Research, 28 235-242


P.W. Haebel, V.L. Arcus, E.N. Baker, and P. Metcalf(2001). Acta Cryst. D57, 1341-1343


M. Harris and T.A. Jones(2002). Acta Cryst. D58, 1889-1891


Z. Otwinowski and W. Minor, " Processing of X-ray Diffraction Data Collected in Oscillation Mode ", Methods in Enzymology, Volume 276: Macromolecular Crystallography, part A, p.307-326, 1997


Pflugrath JW (1999). "The finer things in X-ray diffraction data collection." Acta Cryst. Section D-Biological Crystallography. 55 1718-25


Evens, P. R. (1997). "the Scala” Joint CCP4 and ESF-EACBM Newsletter 33, 22-24


Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, N., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., and Warren, G.L. (1998). Crystallography and NMR

system (CNS): A new software system for macromolecular structure determination, Acta Cryst. D54, 905-921.


Terwilliger, T.C. and J. Berendzen. (1999) "Automated MAD and MIR structure solution". Acta Crystallographica D55, 849-861.


COLLABORATIVE COMPUTATIONAL PROJECT, NUMBER 4. 1994. ``The CCP4 Suite: Programs for Protein Crystallography''. Acta Cryst. D50, 760-763


E. de La Fortelle & G. Bricogne (1997) "Maximum-Likelihood Heavy-Atom Parameter Refinement for the Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods" Methods in Enzymology 276 472-494


Abrahams J. P. and Leslie A. G. W., Acta Cryst. D52, 30-42 (1996)


K. Cowtan (1994), Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, p34-38.


Terwilliger, T. C. (2000) "Maximum likelihood density modification," Acta Cryst. D56, 965-972.


Weeks, C.M. & Miller, R. (1999). 'The design and implementation of SnB v2.0', J. Appl. Cryst.32, 120-124.


Tronrud, D, E., (1997). " The TNT Refinement Package" in Macromolecular Crystallography, Part B, Methods Enzymol. 277, 306-318


Lamzin, V.S. & Wilson, K.S. (1997). "Automated refinement for protein crystallography", Methods Enzymol. (Carter, C. & Sweet, B. eds.) 277, 269-305


G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method" Acta Cryst. D53, 240-255.


Weeks, C.M., Blessing, R.H., Miller, R., Mungee, S., Potter, Rappleye, A., Simith, G.D. Xu, H., Furey, W. (2002), "Towards automated protein structure determination: BnP, the SnB-PHASES Interface ". Z. Kristallogr. 217, 686-693


Furey, W. & Swaminathan, S. (1997), " PHASES-95: A Program Package for the Processing and Analysis of Diffraction Data from Macromolecules". Methods in Enzymology, 277, 590-620


Sheldrick G. (1997) "The SHELX-97 homepage" http://shelx.uni-ac.gwdg.de/SHELX/


Navaza J. (1994) "AMoRe: an Automated Package for Molecular Replacement", Acta. Cryst. 50, 157-163.


Vagin A. , Teplyakov A. (1997) , “ MOLREP: an automated program for molecular replacement” J. Appl. Cryst. 30, 1022-1025.


Charles R. Kissinger, Daniel K. Gehlhaar & David B. Fogel, (1999) "Rapid automated molecular replacement by evolutionary search", Acta Cryst. , D55, 484-491


  1. Frequently asked questions


1. Question: What should I do, if the program that I used for solving a structure is not checked by pdb_extract?


Answer: If the program exports log files in mmCIF format or the PDB format for atomic coordinates, you just give the program name, some information will be extracted. However, if the unknown program only generates LOG file which is neither mmCIF no PDB format, please send us [email protected] the log file and the program name. We will add the program to our list.


2. Question: If it takes really long time between each crystallographic step (like from phasing to refinement), I may not keep the old log files.


Answer: I suggest you apply the pdb_extract program as soon as you finished this step. Then, you will generate one mmCIF file for this step. You may only keep this mmCIF file somewhere in your disk. Finally, you just use the same program to merge all the steps together. (Your options should all be –icif cif_file_name …).


3. Question: How do I know that I obtained the correct mmCIF file?


Answer: Normally the program gives a warning message. But it is a good idea to check if the mmCIF file has the right PDB coordinates (_atom_site. ?). If you encounter an error when running the program, please take a look if you used the correct options. Otherwise, send a message to [email protected]


4. Question: I have installed the CCP4 suit. do I have to install the pdb_extract again.


Answer: You do not have to install the standalone version of pdb_extract, if you prefer to do validation by the ADIT server. In addition to using the CCP4i interface, you can also do all the Unix command line option under the CCP4 environment.






  1. Appendix (data_template.text)



++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

THE DATA_TEMPLATE.TEXT FILE

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


NOTES AND REMINDER

The data template file contains data entries for unique chemical sequences

present in the structure and other non-electronically captured information.


PLEASE CHECK CATEGORIES 1 & 2: Before proceeding any further, make necessary

corrections here so that all information in these categories are complete

and correct.


You may choose to fill in CATEGORIES (3-19) either here or later in ADIT.


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


GUIDELINES FOR USING THIS FILE

1. Only strings included between the 'lesser than' and 'greater than'

signs (<.....>) will be parsed for evaluation by the program. Therefore,

DO NOT write either on the left or right of the 'less than' and 'greater

than' signs respectively.


2. All alphanumeric values or strings that you include in the different

categories should be within double-quotes. Blank spaces or carriage

returns within a pair of double quotes are ignored by the program.

DO NOT use double quotes (") within strings that you enter.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

~~~~~~~~~~~~~~~~~~~~~~~~~~~~START INPUT DATA BELOW~~~~~~~~~~~~~~~~~~~~~~~


================CATEGORY 1: Crystallographic Data=======================

Enter crystallographic data


<space_group = " C 2"> (use International Table conventions)

<space_group_number = "? ">


<unit_cell_a = " 108.742 " >

<unit_cell_b = " 61.679 " >

<unit_cell_c = " 71.652 " >

<unit_cell_alpha = " 90.00 " >

<unit_cell_beta = " 97.15 " >

<unit_cell_gamma = " 90.00 " >



================CATEGORY 2: Sequence Information =======================

Enter one letter sequence for each polymeric entity in asymmetric unit


--------------------------------------------------------------------------

SOME DEFINITIONS

An ENTITY is defined as any unique molecule present in the asymmetric

unit. Each unique biological polymer (protein or nucleic acids) in the

structure is considered an entity. Thus, if there are five copies of

a single protein in the asymmetric unit, the molecular entity is still

only one. Water and non-polymers like ions, ligands and sugars are

also entities.


Here we only consider the sequences of polymeric entities (protein or

nucleic acid).


GUIDELINES FOR COMPLETING THIS CATEGORY

* In a PDB or mmCIF format file, all residues of a single polymeric

entity should have one chain ID. Multiple copies of the same entity

should each be assigned a unique chain ID. The multiple chain IDs

should be separated by commas as 'A,B,C,...'. If incorrect chain IDs

are used the entity groups extracted by this program will not be

correct. To avoid this, make necessary corrections in the PDB or mmCIF

file used to generate the data_template file and regenerate the

data_template.text file. Alternatively, edit the extracted sequence

in this file to correctly represent the sequence and chain IDs of each

polymeric entity.


* In addition to chain IDs, this program uses distance geometry to

asses if there are any breaks in the polymer sequence. These breaks

may occur due to missing residues (not included in the model due to

missing electron density) or due to poor geometry. Four question marks

'????' are used to denote these chain breaks. Replace these question

marks with the sequence of residues missing from the coordinates. Also

add any residues missing from the N- and/or C-termini here.


* If there are non-standard residues in the coordinates, this program

lists them according to the three letter code used in the coordinate

file as (ABC). If all the residues in your sequence are nonstandard,

check and edit the sequence manually to represent it correctly in this

file.


* If any residue was modeled as Ala or Gly due to lack of the side-chain

density, the sequence extracted here will represent them as A or G

respectively. Correct this to the original sequence that was present in

the crystal.

----------------------------------------------------------------------------


Below is the one letter chemical sequence extracted from your PDB

coordinate file. The molecular entities are grouped and listed

together.


PLEASE CHECK THE SEQUENCE of each entity carefully and modify it, as necessary.

Make sure that you REVIEW THE FOLLOWING:

* chain breaks due to missing residues,

* missing residues in the N- and/or C-termini,

* non-standard residues and

* cases of residues modeled as Ala or Gly due to missing side-chain density.


<molecule_entity_id="1" >

<molecule_entity_type="polypeptide(L)" >

<molecule_one_letter_sequence="

SKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL" >

< molecule_chain_id="1,2,3,4,5,6" >


<molecule_entity_id=" " >

<molecule_entity_type=" " >

<molecule_one_letter_sequence=" " >

<molecule_chain_id=" " >




================CATEGORY 3: Contact Authors=============================

Enter information about the contact authors.


Information about the Principal investigator (PI) should be given.


For principal investigator

<contact_author_PI_name = " "> (Surname, F.M.)

<contact_author_PI_email = " ">

<contact_author_PI_phone = " ">

<contact_author_PI_fax = " ">

<contact_author_PI_address = " ">


For other contact authors

<contact_author_name_1 = " ">

<contact_author_email_1 = " ">

<contact_author_phone_1 = " ">

<contact_author_fax_1 = " ">

<contact_author_address_1 = " ">


<contact_author_name_2 = " ">

<contact_author_email_2 = " ">

<contact_author_phone_2 = " ">

<contact_author_fax_2 = " ">

<contact_author_address_2 = " ">


...(add more if needed)...


================CATEGORY 4: Release Status==============================

Enter release status for the coordinates, constraints and sequence


Status should be chosen from one of the following:

(release now, hold for publication, hold for 6 weeks, hold for 6 months,

hold for 1 year)


<Release_status_for_coordinates = " ">

<Release_status_for_structure_factor = " ">

<Release_status_for_sequence = " ">


================CATEGORY 5: Title=======================================

Enter the title for the structure


<structure_title = " ">


================CATEGORY 6: Citation Authors============================

Enter citation authors (e.g. Surname, F.M.)


The primary citation is the article in which the deposited coordinates

were first reported. Other related citations may also be provided.


For the primary citation

<primary_citation_author_name_1 = " ">

<primary_citation_author_name_2 = " ">

<primary_citation_author_name_3 = " ">

<primary_citation_author_name_4 = " ">

<primary_citation_author_name_5 = " ">

...add more if needed...


For other related citations (if applicable)

<citation_1_author_name_1 = " ">

<citation_1_author_name_2 = " ">

<citation_1_author_name_3 = " ">

<citation_1_author_name_4 = " ">

<citation_1_author_name_5 = " ">

...add more if needed...


<citation_2_author_name_1 = " ">

<citation_2_author_name_2 = " ">

<citation_2_author_name_3 = " ">

<citation_2_author_name_4 = " ">

<citation_2_author_name_5 = " ">

...add more if needed...


...(add more citations if needed)...


================CATEGORY 7: Citation Article============================

Enter citation article (journal, title, year, volume, page)


If the citation has not yet been published, use 'To be published'

for the category 'journal_abbrev'. The order of citations in this

category should correspond to that is CATEGORY 6.


For primary citation

<primary_citation_journal_abbrev = " ">

<primary_citation_title = " ">

<primary_citation_year = " ">

<primary_citation_journal_volume = " ">

<primary_citation_page_first = " ">

<primary_citation_page_last = " ">


For other related citation (if applicable)

<citation_1_journal_abbrev = " ">

<citation_1_title = " ">

<citation_1_year = " ">

<citation_1_journal_volume = " ">

<citation_1_page_first = " ">

<citation_1_page_last = " ">


<citation_2_journal_abbrev = " ">

<citation_2_title = " ">

<citation_2_year = " ">

<citation_2_journal_volume = " ">

<citation_2_page_first = " ">

<citation_2_page_last = " ">


...(add more citations if needed)...


================CATEGORY 8: Molecule Names==============================

Enter the name of the molecule for each entity


The name of molecule should be obtained from the appropriate

sequence database reference, if available. Otherwise the gene name or

other common name of the entity may be used.

e.g. HIV-1 integrase for protein

RNA Hammerhead Ribozyme for RNA

The number of entities should be the same as in CATEGORY 1.


<molecule_name_1 = " "> (entity 1)

<molecule_name_2 = " "> (entity 2)

<molecule_name_3 = " "> (entity 3)


...(add more if needed)...



================CATEGORY 9: Molecule Details============================

Enter additional information about each entity


Additional information would include details such as fragment name

(if applicable), mutation, and E.C.number.


For entity 1

<Molecular_entity_id_1 = " "> (e.g. 1, 2, ...)

<Fragment_name_1 = " "> (e.g. ligand binding domain, hairpin)

<Specific_mutation_1 = " "> (e.g. C280S)

<Enzyme_Comission_number_1 = " "> (if known: e.g. 2.7.7.7)


For entity 2

<Molecular_entity_id_2 = " ">

<Fragment_name_2 = " ">

<Specific_mutation_2 = " ">

<Enzyme_Comission_number_2 = " ">


For entity 3

<Molecular_entity_id_3 = " ">

<Fragment_name_3 = " ">

<Specific_mutation_3 = " ">

<Enzyme_Comission_number_3 = " ">


...(add more if needed)...



================CATEGORY 10: Genetically Manipulated Source=============

Enter data in the genetically manipulated source category


If the biomolecule has been genetically manipulated, describe its

source and expression system here.


For entity 1

<Manipulated_entity_id_1 = " "> (e.g. 1, 2, ...)

<Source_organism_scientific_name_1 = " "> (e.g. Homo sapiens)

<Source_organism_gene_1 = " "> (e.g. RPOD, ALKA...)

<Expression_system_scientific_name_1 = " "> (e.g. Escherichia coli)

<Expression_system_strain_1 = " "> (e.g. BL21(DE3))

<Expression_system_vector_type_1 = " "> (e.g. plasmid)

<Expression_system_plasmid_name_1 = " "> (e.g. pET26)

<Manipulated_source_details_1 = " "> (any other relevant information)


For entity 2

<Manipulated_entity_id_2 = " ">

<Source_organism_scientific_name_2 = " ">

<Source_organism_gene_2 = " ">

<Expression_system_scientific_name_2 = " ">

<Expression_system_strain_2 = " ">

<Expression_system_vector_type_2 = " ">

<Expression_system_plasmid_name_2 = " ">

<Manipulated_source_details_2 = " ">


For entity 3

<Manipulated_entity_id_3 = " ">

<Source_organism_scientific_name_3 = " ">

<Source_organism_gene_3 = " ">

<Expression_system_scientific_name_3 = " ">

<Expression_system_strain_3 = " ">

<Expression_system_vector_type_3 = " ">

<Expression_system_plasmid_name_3 = " ">

<Manipulated_source_details_3 = " ">


...(add more if needed)...


================CATEGORY 11: Natural Source=============================

Enter data in the natural source category


If the biomolecule was derived from a natural source, describe

it here.


For entity 1

<natural_source_entity_id_1 = " "> (e.g. 1, 2, ...)

<natural_source_scientific_name_1 = " "> (e.g. Homo sapiens)

<natural_source_details_1 = " "> (any other relevant information

e.g. organ, tissue, cell ..)


For entity 2

<natural_source_entity_id_2 = " ">

<natural_source_scientific_name_2 = " ">

<natural_source_details_2 = " ">


for entity 3

<natural_source_entity_id_3 = " ">

<natural_source_scientific_name_3 = " ">

<natural_source_details_3 = " ">


...(add more if needed)...


================CATEGORY 12: Keywords===================================

Enter a list of keywords that describe important features of the deposited

structure.


For example, beta barrel, protein-DNA complex, double helix,

hydrolase, structural genomics etc.


<structure_keywords = " ">


================CATEGORY 13: Biological Assembly========================

Enter data in the biological assembly category


Biological assembly describes the functional unit(s) present in the

structure. There may be part of a biological assembly, one or more

than one biological assemblies in the asymmetric unit.

Case 1

* If the asymmetric unit is the same as the biological assembly

nothing special needs to be noted here.

Case 2

* If the asymmetric unit does not contain a complete biological unit.

Please provide symmetry operations including translations required

to build the biological unit.

(example:

The biological assembly is a hexamer generated from the dimer

in the asymmetric unit by the operations: -y, x-y-1, z-1 and

-x+y, -x-1, z-l.)

Case 3

* If the asymmetric unit has multiple biological units

Please specify how to group the contents of the asymmetric unit into

biological units.

(example:

The biological unit is a dimer. There are 2 biological units in the

asymmetric unit (chains A & B and chains C & D).


For biological unit 1

<biological_assembly_1 = " ">


For biological unit 2

<biological_assembly_2 = " ">


....(add more if needed)....


================CATEGORY 14: Crystals===================================

Enter the number of crystals used for diffraction


<number_of_crystals = " ">


================CATEGORY 15: Methods and Conditions=====================

Enter the crystallization conditions for each crystal


For crystal 1:

<crystal_number_1 = " "> (e.g. 1, 2, ...)

<crystallization_method_1 = " "> (e.g. vapor diffusion, hanging drop)

<crystallization_pH_1 = " "> (e.g. 7.5 ...)

<crystallization_temperature_1 = " "> (e.g. 100) (in Kelvin)

<crystallization_components_1 = " "> (e.g. PEG 4000, NaCl etc.)


For crystal 2:

<crystal_number_2 = " ">

<crystallization_method_2 = " ">

<crystallization_pH_2 = " ">

<crystallization_temperature_2 = " ">

<crystallization_components_2 = " ">


...(add more if needed)...


================CATEGORY 16: Crystal Property===========================

Enter solvent content, Matthews coefficient

These values were calculated based on the sequence as shown in

CATEGORY 2. If there are missing residues, you need to add the

missing residues and re-run the program to get accurate values.

(The command to re-run is 'extract -sol data_template.text')


For crystal 1:

<crystals_number_1 = " 1 "> (e.g. 1, 2, ...)

<crystals_solvent_content_1 = "52.2 ">

<crystals_matthews_coefficient_1 = "2.6 ">

<crystals_mosaicity_1 = " "> (e.g. 0.5 ...)


...(add more if needed)...


================CATEGORY 17: Radiation Source===========================

Enter the details of the source of radiation, the X-ray generator,

and the wavelength for each diffraction.


For experiment 1:

<radiation_experiment_1 = " "> (e.g. 1, 2, ...)

<radiation_source_type_1 = " "> (e.g. rotating-anode, synchrotron ...)

<radiation_source_name_1= " "> (e.g. Rigaku RU200, CHESS Beamline A1 ...)

<radiation_wavelengths_1= " "> (e.g. 1.502 ...)

<radiation_protocol_1= " "> (e.g. MAD, SINGLE WAVELENGTH ...)

<radiation_detector_type_1 = " "> (e.g. CCD, IMAGE PLATE ...)

<radiation_detector_name_1= " "> (e.g. SIEMENS-NICOLET, RIGAKU RAXIS ...)


For experiment 2:

<radiation_experiment_2 = " ">

<radiation_source_type_2 = " ">

<radiation_source_name_2 = " ">

<radiation_wavelengths_2 = " ">

<radiation_protocol_2= " ">

<radiation_detector_type_2 = " ">

<radiation_detector_name_2= " ">


....(add more if needed)....


================CATEGORY 18: Collection Temperature=====================

Enter the temperature for data collection (in Kelvin)


<collection_temperature_crystal_1 = " "> (for crystal 1:)

<collection_temperature_crystal_2 = " "> (for crystal 2:)


....(add more if needed)....



================CATEGORY 19: Structure Genomics=========================

If it is the structure genomics project, give the information


<SG_project_id = " 1">

<SG_project_name = " ">

<full_name_of_SG_center = " ">

<initial_of_SG_center = " ">


=====================================END==================================

  1. Appendix (log_script.inp)


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

THE LOG_SCRIPT.INP FILE

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


NOTES AND REMINDER

This script file is used to enter the names of the crystallographic

software used for structure determination and the log, PDB, mmCIF or

text files generated by them.


PLEASE COMPLETE the ENTRY FIELDS according to the type of your experiment

and use the command 'extract -ext log_script.inp' to obtain the completed

structure data ready for validation and deposition.


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

GUIDELINES FOR USING THIS FILE

1. Only strings included between the 'lesser than' and 'greater than'

signs (<.....>) will be parsed for evaluation by the program. Therefore,

DO NOT write either on the left or right of the 'less than' and 'greater

than' signs respectively.


2. All alphanumeric values or strings that you include in the different

categories should be within double-quotes. Blank spaces or carriage

returns within a pair of double quotes are ignored by the program.

DO NOT use double quotes (") within strings that you enter.

3. Log files used for generating the deposition should be generated from

the best (usually the last) trial for each crystallographic software.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


~~~~~~~~~~~~~~~~~~~~~~~~~~~~START INPUT DATA BELOW~~~~~~~~~~~~~~~~~~~~~~~


===============PART 1: Structure Factor for Final Refinement==============

Enter reflection data file used for final structure refinement

NOTE:

* Usually the highest resolution or best data set is used for the

refinement. Use that structure factor file here.

* In some cases, it may not be possible to collect a complete dataset

from a single crystal. Thus, multiple data sets have to be scaled

and merged together for refinement. Use the merged reflection file

here.


* If the reflection data format is not one of those listed below,

please use OTHER for the data format, and provide an ASCII file

that has at least five values [H, K, L, I (or F), sigmaI (or sigmaF)]

for each reflection and seperate each item by one or more spaces.

Include the test flags as the sixth column in the file (if available).


* If the reflection file is in mtz format (e.g. using REFMAC5), convert

it to mmCIF format using the mtz2various application provided by CCP4.


Reflection data format:

CNS|SHELX|TNT|REFMAC5|HKL|SCALEPACK|DTREK|SAINT|SCALA|3DSCALE


<reflection_data_type = "F" > [enter I (intensity) or F (amplitude)]

<reflection_data_format = "CNS" >

<reflection_data_file_name = " input_data/gere-nat.cv" >


==============PART 2: Structure Factors for Protein Phasing================

Enter reflection data files used for heavy atom or MAD phasing


NOTE:

* Enter this category if you have more than one complete reflection

file (e.g. in the case of MAD,SIRAS, MIR). The LOG files generated

from data scaling software for all these data sets are also needed.


* If the scaling program is not one of those listed below

(HKL|SCALEPACK|DTREK|SAINT|3DSCALE), enter OTHER for the program

name and provide an ASCII file with five values

[H, K, L, I (or F), sigmaI (or sigmaF)] for each reflection and

seperate each item by a space


* If the same crystal was used for collecting multiple data sets, the

crystal number will remain '1' as the wavelength numbers change.

However, if multiple crystals were used, for the data collections,

the corresponding crystal numbers should be used for each data set.


* IT IS IMPORTANT THAT THE LOG FILE AND DATA FILE COME FROM THE

SAME PROGRAM.


<scale_data_type = "I" > [enter I (intensity) or F (amplitude)]

<scale_program_name = "HKL" >


For data set 1:

<crystal_number = "1" >

<diffract_number = "1" >

<scale_data_file_name = " input_data/w1.sca" >

<scale_log_file_name = " " >


For data set 2:

<crystal_number = "1" >

<diffract_number = "2" >

<scale_data_file_name = "input_data/w2.sca " >

<scale_log_file_name = " " >


For data set 3:

<crystal_number = "1" >

<diffract_number = "3" >

<scale_data_file_name = "input_data/w3.sca " >

<scale_log_file_name = " " >


==================PART 3: Statistics for Indexing=====================

Enter log file and software name for data indexing


NOTE:

* This is only for the data of final structure refinment.


Software for indexing is one of the following:

(HKL|DENZO|DTREK|MOSFLM)


<data_indexing_software = "HKL" >

<data_indexing_LOG_file_name = " " >

<data_indexing_CIF_file_name = " " > (if mmCIF format)


==================PART 4: Statistics for Data Scaling=====================

Enter log file and software name for data scaling


NOTE:

* The log file included here should have scaling statistics of

the file used for the final structure refinement. If multiple data

sets were scaled and merged for refinement (as described in Part 1

above) use the log file generated during merging of the data sets.


Software for scaling is one of the following:

(HKL|SCALEPACK|DTREK|SAINT|3DSCALE|SCALA)


<data_scaling_software = "HKL" >

<data_scaling_LOG_file_name = "input_data/sclepack1.log " >

<data_scaling_CIF_file_name = " " > (if mmCIF format)


==============PART 5: Statistics for Molecular Replacement================

Enter log files and software name for molecular replacement


NOTE:

Software is one of the following:

(CNS|AMORE|MOLREP|EPMR|PHASER)

The log file should be from the best trial of MR.


<mr_software = " " >

<mr_log_file_LOG_1 = " " >

<mr_log_file_LOG_2 = " " >


=================PART 6: Statistics for Protein Phasing===================

Enter log files and software name for heavy atom phasing


NOTE:

The phasing method should be one of (SAD|MAD|SIR|SIRAS|MIR|MIRAS).

Software is one of the following:

(CNS|MLPHARE|SOLVE|SHELXS|SHELXD|SNB|BNP|SHARP|PHASES)

The log file should be from the best trial of phasing.


<phasing_method = "MAD" > (SAD|MAD|SIR|SIRAS|MIR|MIRAS)

<phasing_software = "CNS" >


<phasing_log_file_LOG_1 = "input_data/mad_sdb.dat " >

<phasing_log_file_PDB_1 = " " > (in PDB format (heavy atom coordinates))

<phasing_log_file_CIF_1 = " " > (in mmCIF format)


<phasing_log_file_LOG_2 = "input_data/mad_summary.dat " >

<phasing_log_file_PDB_2 = " " >

<phasing_log_file_CIF_2 = " " >


<phasing_log_file_LOG_3 = "input_data/mad_fp.dat " >

<phasing_log_file_PDB_3 = " " >

<phasing_log_file_CIF_3 = " " >


... add more if needed ...


===============PART 7: Statistics for Density Modification================

Enter log files and software name for density modification


NOTE:

Software is one of the following:

(CNS|DM|RESOLVE|SOLOMON|SHELXE)

The log file should be from the best trial of density modification.


<dm_software = "CNS " >

<dm_log_file_LOG_1 = " input_data/density_modify.dat" >

<dm_log_file_CIF_1 = " " > (in mmCIF format)


===============PART 8: Statistics for Structure Refinement================

Enter log files and software name used for final structure refinement


NOTE:

Software is one of the following:

(CNS|REFMAC5|SHELXL|TNT|PROLSQ|NUCLSQ|RESTRAIN)

The log file should be from the final trial of structure refinement.


<refine_software = "CNS" >


<refine_log_file_PDB_1 = " " > (coordinate file in PDB format)

<refine_log_file_CIF_1 = "input_data/deposit_cns.mmcif " > (mmCIF file containing refinement statistics)

<refine_log_file_LOG_1 = " " >




=======================PART 9: Data Template File=========================

Enter file name of the data template file


NOTE:

This file 'data_template.text' was generated by using the

command 'extract -pdb pdb_file' or 'extract -cif cif_file'. It

contains the sequences of all unique polymers (protein or nucleic

acid) present in the structure. It also contains other

non-electronically captured information. Please complete the

data template file before running pdb_extract.


<data_template_file = "input_data/data_template.text" >



==========================PART 10: Output Files============================

Enter the output file names


NOTE:

If you do not give the output file names, the default names

pdb_extract_sf.mmcif containing structure factors and

pdb_extract.mmcif containing coordinates will be assigned

by the program



<sf_output= " script_example_1_sf.cif" > (for structure factors)

<statistics_output= "script_example_1.cif " > (for coordinates and statistics)


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