Subject: ** MODELLER SUPPORT ** RE: starting problem (fwd)
From: Bozidar BJ Jerkovic <>
Date: Wed, 20 Feb 2002 13:15:41 -0500
Cc: <>
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:
[">mailto:] On Behalf Of
Boojala Reddy
Sent: Monday, February 18, 2002 10:33 AM
To:
Cc:
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: |
| 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 <>
To: Boojala Reddy <>
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