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** MODELLER SUPPORT ** RE: starting problem (fwd)



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