Specification of chain of output atom files.

[Richard Friedman <>]

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.