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) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/
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