Subject: RE: Specification of chain of output atom files.
From: "Andrej Sali" <>
Date: Thu, 13 Mar 2003 14:08:46 -0800
Cc: <>
Don't have the ps version of the manual handy right now, but this is the url
to rename_segments
http://salilab.org/modeller/manual/node70.html
Maybe there is a problem with modeller? I'd be happy to try if you email me
a tarball with all the input files.
Thank you,
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: Richard Friedman [">mailto:]
> Sent: Thursday, March 13, 2003 2:06 PM
> To: Andrej Sali
> Cc:
> Subject: RE: Specification of chain of output atom files.
>
>
> 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.
>
>