RE: Specification of chain of output atom files.

[Richard Friedman <>]

Dear Andrej and Everybody,

	The only  place I was able to find RENAME_SEGMENTS in the Modeller
manual, December 21, 2001, was on page 85, where it is used implictly.
Is it documented elsewhere in detail?

	The top program that I wrote based upon my best understanding of
the command was

READ_MODEL FILE = 'park7a'
RENAME_SEGMENTS SEGMENT_IDS = 'A' 'I', RENUMBER_RESIDUES = 1 1
WRITE_MODEL FILE = 'park7i.atm'

It wrote a file park7i.atm but did not change the chain ID.
Any suggestions would be appreciated.

Thanks and best wishes,
Rich



On Thu, 13 Mar 2003, Andrej Sali wrote:

> 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.
> >
> >
>
>

--------------------------------------------------------------
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.