RE: Specification of chain of output atom files.

["Andrej Sali" <>]

There are two MODELLER commands that allow some manipulkation of chain ids:
RENAME_SEGMENTS and TRANSFER_RES_NUMB.

Andrej

--
Andrej Sali, Professor
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and 
    California Institute for Quantitative Biomedical Research
Mission Bay Genentech Hall
600 16th Street, Suite N472D
University of California, San Francisco
San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier)
Tel +1 (415) 514-4227; Fax +1 (415) 514-4231
Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232,  4233, 4239
Email ; Web http://salilab.org


> -----Original Message-----
> From:  
> [">mailto:] On Behalf Of 
> Richard Friedman
> Sent: Thursday, March 13, 2003 9:08 AM
> To: 
> Subject: Specification of chain of output atom files.
> 
> 
> 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-RGTITGKHGYSVKVDLTFDKVN
> PEE-FDALVLPGG
> RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG
> -VEWVDAEVVVDG
> NWVSSRVPADLYAWMREFVKLLK----------------*
> >P1;prk7
> sequence:prk7:1    :A:189  :A:park7:human: 2.00:-1.00
> MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAK
> KEGPYDVVVLPGG
> NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGG
> HYTYSENRVEKDG
> 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.
> 
>