[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: Problem with SEQUENCE_TO_ALI



One more note:

Karl Gruber wrote:
> 
> Dear all,
> 
> I am a new user of Modeller (vers. 4h, June 16, 1997) and I hope that
> this list is still alive. I have encountered some problems running the
> scripts 'loop' and 'cluster', which I tried both with my own and the
> tutorial files.
> 
> The input and (part of the) output in the case of 'cluster' were as
> follows:
> 
> --------------------
> 
> INCLUDE
> 
> DEFINE_STRING VARIABLES = SEQUENCE MODEL CSRFILE
> 
> SET SEQUENCE = 'pruse1'            # sequence code
> SET MODEL = 'pruse1.B99990002'     # one PDB structure
> SET CSRFILE = 'pruse1.rsr'         # restraints file
> SET ID1 = 2, ID2 = 11            # cluster these models
> 
> CALL ROUTINE = 'cluster'

try to use the clustering script in this form:
#################
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1 

SET ROOT_NAME = 'pruse1'            # sequence code
SET MODEL = 'pruse1.B99990002'     # one PDB structure
SET CSRFILE = 'pruse1.rsr'         # restraints file
SET FILE_EXT  = ' '
SET FILE_ID   = '.B'

SET EXPAND_CONTROL = 0000 0000  2  11  0

CALL ROUTINE = 'cluster'
######################

"expand_control" first two arguments: the starting first 4 and ending first  4
digits in the file extension (from 9999 and to 9999 in your case), the third
and fourth is about the second part of the file extension: from model-2 to
model-11

A "cluster.opt" named coordinate file should appear as a result. It worked for
me, of course the underlying coordinate files were different.

Andras

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras