Dears:

I already tried the modeller6a in the RedHat 6.2. However, it still stoped in some step. I mailed the sequence and the log files to you.

friendly, Jack ----- Original Message ----- From: "Andrej Sali" sali@mail.rockefeller.edu To: "Azat Badretdinov" azat@accelrys.com; "Tsu-Sheng Wang" g894284@life.nthu.edu.tw Cc: modeller_usage@salilab.org Sent: Thursday, November 15, 2001 12:33 AM Subject: RE: Crash in running the SEQUENCE_SRCH

if still a problem, would you please try it with the pre-release of modeller 6 (ask bozidar@rockefeller.edu). if still a problem, would you please email us the input files.

thanks, andrej

-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org]On Behalf Of Azat Badretdinov Sent: Wednesday, November 14, 2001 9:56 AM To: Tsu-Sheng Wang Cc: modeller_usage@salilab.org Subject: Re: Crash in running the SEQUENCE_SRCH

At 03:38 PM 11/14/01 +0800, Tsu-Sheng Wang wrote: >Dears: > > When I run below program, it will be crash. > >INCLUDE >SET OUTPUT_CONTROL = 1 1 1 1 1 >SET ATOM_FILES_DIRECTORY = '/usr/local/lib/pdb' >SET OUTPUT = 'SHORT' # 'LONG' >SET SIGNIF_CUTOFF = 8 3 >SET SEARCH_RANDOMIZATIONS = 10 >SET STOP_ON_ERROR = 2 >CALL ROUTINE = 'sequence_srch', SEGFILE = 'ny10.chn', SEQUENCE = 'ny10' > > I want to use this program to get the alignment and using the alignment >to get the template sequence and get the model by homology modelling. > The ny10.chn is one chain protein with 68 a.a. , and I set the >ATOM_FILES_DIRECTORY is the all PDB files in my server. This program will >be crash after abour the 45 min. I don't know what's wrong. My server is >RedHat Linux 7.1 with PIII 1G cpu and 512Mb ram.

7.1 is notorious for its bugs. It crashes randomly blastpgp jobs too at certain conditions. I would advise you to reproduce it on 6.2.

>Your friendly, >Jack Wang > >

-- Azat Badretdinov, Accelrys