Re: Specification of chain of output atom files.

[Richard Friedman <>]

Dear Peter,

	My template is a homotrimer, not a monomer. I am modelling a
sequence against each of the monomers in the template. I would then like
to merge the 3 target monomers into a homotrimer of the target. I want
to be able to write chain designations in the monomer pdb files.

	I have done this with vi global change commands but hope that
there is a faster way with Modeller.

Thanks and best wishes,
Rich



On Thu, 13 Mar 2003, Peter C. Lai wrote:

> 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/
>
>

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