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I have a CIF file that I downloaded from the PDB, but if I try to use it in Coot, it complains that it is not a complete CIF definition. This page provides a batch script that I may be able to tease apart to suit my needs, but I thought there was a way to do this from within the CCP4 Program Suite GUI/job manager.

Maddeningly, I see in my project job history a couple "dictionary" jobs where I did this, but I utterly forgot how I set them up (forgive the asinine names):

CCP4 dictionary jobs

When I try to use the Monomer Library Sketcher (under Refinement/Restraint Preparation) and open a CIF ("mmCIF") file, nothing happens.

Also under the sketcher, I can severely abuse the "Load Monomer from Library" and it looks like I get the right thing:

load monomer from library dialog

However, when setting up the above, it throws "Error: can't read "monomer_lib(code,n..." warnings, then when running it generates the Geometry file (seemingly successfully) then says that Libcheck failed when trying to create the coordinate file.


If there are other solutions, I'd be interested as well. I've used PRODRG to create CIF files before with its draw tool, but it can be a bit clumsy, it ignores how I drew my double bonds, and it creates new names for all the atoms.

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1 Answer

up vote 2 down vote accepted

Not quite as ideal as I had hoped, but it works:

  1. Get and install CCP4.

  2. Obtain minimal CIF file from PDB or elsewhere. Save to some folder easy to get at with the console.

  3. Launch console and cd to folder with the minimal definition.

  4. Run libcheck by typing it and hitting return

    • If it complains it's not found, the CCP4 bin directory may not be in your PATH environment variable. You can get around this by specifing the full path to the program, e.g.: c:\CCP4-Packages\ccp4-6.1.13\bin\libcheck.exe (may vary with version)
  5. Say "Y" or "A" at the _DOC: prompt for some more files, "N" if you don't care (I generally don't)

  6. At the --> prompts, specify:

    • the input file, e.g.: file_l: ABC.cif
    • the monomer: mon: ABC
    • output file name: file_o: ABC_out
  7. Leave a prompt blank and hit return to start processing.

If it runs successfully it might look something like this:

C:\Users\Nick>libcheck

  --- LIBCHECK --- /Vers 4.2.8   ; 02.06.2009/


  Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/Y/A :
    N - means without DOC-file
    Y - with new contents
    A - means to keep old contents and add new information
        with DOC-file program creates batch file: libcheck.bat
 _DOC:n


 #
 #      Keywords:
 #
 #FILE_L:   < >  - additional library, " " means without this file
 #MON:      < >  - give info about this monomer
 ... (shortened) ...
 #SRCH: <N>/Y/0  - Y - global search, 0 - for MON from PDB_file
 #                 (only with NODIST = N)

 #---  type "keyword   parameters" and/or ---
 #---  press key "CR" to run program      ---
 -->file_l: ABC.cif
 -->mon: ABC
 -->file_o: ABC_out
 -->
 MON   : ABC
 -------------
 Output file   :ABC_comp
 Input user lib:ABC.cif
 _chem_comp.name "DRUG INTERMEDIATE"

          17          55
 "DRUG INTERMEDIATE"

 -------------
 Keywords:
 HFLAG : Y
 COOR  : N
 LCOOR : Y
 SRCH  : 0
 REF   : Y
 NODIST: Y
 ERROR ==> In the loop containing the item_chem_comp.three_letter_code
 ERROR ==> The number of expected items and the number existing items do not match
 ERROR ==> The number of expected items is    7
  NUMBER OF MONOMERS IN THE LIBRARY          :     1
                with complete description    :     0
  NUMBER OF MODIFICATIONS                    :     0
  NUMBER OF LINKS                            :     0
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  I am reading library. Please wait.
      - monomer"s description
  WARNING : monomer:ABC      - has the minimal description.
  now monomer:ABC      - has complete description.
  I will check it.
 * CIFile  : ABC_out_ABC.cif
 * PDBfile : ABC_out_ABC.pdb
 * Plotfile: ABC_out_ABC.ps
  I am writing new description to
  file: ABC_out.lib

C:\Users\Nick>

It yields the following output files:

  • (file_o): looks like a CIF file with lots of whitespace and records stripped out
  • (file_o).lib: the desired, complete definition file
  • (file_o)_(mon).cif: an even more minimal CIF file with only XYZ coords
  • (file_o)_(mon).pdb: a PDB file
  • (file_o)_(mon).ps: a document with a stereo labeled diagram, and lists of bonds, angles, chirality (centers?) and planes. Can convert it to the easier-to-use PDF format using this http://www.ps2pdf.com/convert.htm, or other tools.
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