Re: Specification of chain of output atom files.

["Peter C. Lai" <>]

Don't specify chain IDs in the alignments for PDBs that don't have chain IDs.
Similarly, to return to a system with no chain IDs at all, strip
the chain IDs out of any PDB that have chain IDs (by looking for 
<space>CHAINID<space>). Note that this will only work with monomeric PDBs,
which is apparently what you are working with so it should work. (It worked
for me).

Adding the chain ID to a pdb is tricky, but can be done with some clever
perl tricks (read a line, explode the line into an array using whitespace
as the delimiter, insert <space>A<space> into the appropriate element,
serialize the array and write the resulting line into your new file,
read next line, etc).

On Thu, Mar 13, 2003 at 12:07:53PM -0500, Richard Friedman wrote:
> Dear Modellers,
> 
> 	How can I write a pdb file containing a chain specification?
> 
> My top file is
> 
> # Homology modelling by the MODELLER TOP routine 'model'.
> 
> INCLUDE                             # Include the predefined TOP routines
> 
> SET OUTPUT_CONTROL = 1 1 1 1 2      # uncomment to produce a large log
> file
> SET ALNFILE  = 'monomer3.ali'      # alignment filename
> SET KNOWNS   = '1g2i'               # codes of the templates
> SET SEQUENCE = 'prk7'               # code of the target
> SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom
> files
> SET STARTING_MODEL= 1               # index of the first model
> SET ENDING_MODEL  = 1               # index of the last model
>                                     # (determines how many models to
> calculate)
> 
> CALL ROUTINE = 'model'              # do homology modelling
> 
> My ali file is:
> 
> C; alignment
> >P1;1g2i
> structureX:1g2i:1    :A:166  :A:Protease:Pyrococcus Horikosh: 2.00:-1.00
> M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVNPEE-FDALVLPGG
> RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG-VEWVDAEVVVDG
> NWVSSRVPADLYAWMREFVKLLK----------------*
> >P1;prk7
> sequence:prk7:1    :A:189  :A:park7:human: 2.00:-1.00
> MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGG
> NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGGHYTYSENRVEKDG
> LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD*
> 
> I was hoping that inclusion of the chain designators in the prk7
> sequence  file, would produce a pdb file with the chain designators
> included, but that is not what had happened. How can I be sure that the
> output file includes the chain designation 'A' on every atom line?
> 
> Thanks and best wishes,
> Rich
> 
> 
> 
> 
> --------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist
> Herbert Irving Comprehensive Cancer Center
> Oncoinformatics Core
> Lecturer
> Department of Medical Informatics
> Box 95, Room 130BB or P&S 1-420C
> Columbia University
> 630 W. 168th St.
> New York, NY 10032
> (212)305-6901 (5-6901) (voice)
> 
> http://cancercenter.columbia.edu/~friedman/
> 
> "You don't have ot do any more work to write a book. You
> already wrote a book. Your course notes are a book. I've
> seen them lying on the floor of your office. I've seen
> course notes used for books on everything from Math to
> Origami. Just hand your course notes in. Make sure you
> hand in the ones  with the apple juice spilled on it."
> -Isaac Friedman, age 13
> 
> Upon Isaac's attainment of his majority I am discontinuing
> the quotes from him.
> 
> 

-- 
Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology
Yale University School of Medicine
SenseLab | Research Assistant
http://cowbert.2y.net/