You make similar file like ali using your sequence and a homologus structure(s) and follow the steps as explained in the modeller manual. There is a modeller users form. You please mail your quary to them. I am copieing this e-mail to them.
Best .../BVB
| Boojala V. B. Reddy Ph. D. | | Assistant Research Scientist | | University of California, San Diego Fax: (858)-822-0873 | | San Diego Supercomputer Center(SDSC) Voice: (858)-822-0860 | | Chemistry Research Bulding (CRB-166) | | 9500 Gilman Drive, e-mail: breddy@sdsc.edu | | La Jolla, CA 92093-0537 http://www.sdsc.edu/~breddy |
---------- Forwarded message ---------- Date: Mon, 18 Feb 2002 14:23:15 +0530 (GMT+5:30) From: Gowthaman R gowtham@icgeb.res.in To: Boojala Reddy breddy@sdsc.edu Subject: Re: starting problem
hi reddy this is gowtham a graduate student doing phd at ICGEB New delhi.
im planning to do some 3d predictions using the modeller
i installed adn the tutorial is running fine.
now i would like to use some malarial protiens but i donot kow how to get the input files like .ali files ...... im unable to start my work.
can u help me out in this regard.........and it is bit urgent.
i would be thankful to u verymuch
waiting for ur reply regards gowtham
Hi,
Please modify the script accordingly. Also consult the manual.
#################################### # pdb2ali.top # This script reads file in PDB format, extracts the sequence, # and writes it out in a PIR format. PDB file needs to be in the # same directory as this top file.
SET OUTPUT_CONTROL = 1 1 1 1 1
READ_MODEL FILE = 'name.pdb' , MODEL_FORMAT = 'PDB' SEQUENCE_TO_ALI ALIGN_CODES = 'name' , ATOM_FILES = 'name' WRITE_ALIGNMENT FILE = 'name.ali' , ALIGNMENT_FORMAT = 'PIR'
STOP ####################################
Happy modeling, Bozidar
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Boojala Reddy Sent: Monday, February 18, 2002 10:33 AM To: gowtham@icgeb.res.in Cc: modeller_usage@salilab.org Subject: Re: starting problem (fwd)
You make similar file like ali using your sequence and a homologus structure(s) and follow the steps as explained in the modeller manual. There is a modeller users form. You please mail your quary to them. I am copieing this e-mail to them.
Best .../BVB
| Boojala V. B. Reddy Ph. D. | | Assistant Research Scientist | | University of California, San Diego Fax: (858)-822-0873 | | San Diego Supercomputer Center(SDSC) Voice: (858)-822-0860 | | Chemistry Research Bulding (CRB-166) | | 9500 Gilman Drive, e-mail: breddy@sdsc.edu | | La Jolla, CA 92093-0537 http://www.sdsc.edu/~breddy |
---------- Forwarded message ---------- Date: Mon, 18 Feb 2002 14:23:15 +0530 (GMT+5:30) From: Gowthaman R gowtham@icgeb.res.in To: Boojala Reddy breddy@sdsc.edu Subject: Re: starting problem
hi reddy this is gowtham a graduate student doing phd at ICGEB New delhi.
im planning to do some 3d predictions using the modeller
i installed adn the tutorial is running fine.
now i would like to use some malarial protiens but i donot kow how to get the input files like .ali files ...... im unable to start my work.
can u help me out in this regard.........and it is bit urgent.
i would be thankful to u verymuch
waiting for ur reply regards gowtham
participants (2)
-
Boojala Reddy -
Bozidar BJ Jerkovic