------ Forwarded Message From: owner-modeller_usage@salilab.org Date: Fri, 25 Jul 2003 09:31:27 -0700 To: modeller_usage-approval@salilab.org Subject: BOUNCE modeller_usage@salilab.org: Non-member submission from ["Thorsten Schweikardt" thorsten@mail.uni-mainz.de]

Dear all,

I am having a problem with the add_restraints-command: using Modeller6v2 (linux/windows-version), I am trying to model the N-terminus of a protein using experimental distance-data. The rest of the protein is available as pdb-file and serves as template for the C-terminal end.

Using the linux-version does not work well: without implementing the distances or when implementing only the _first_ distance (see below), modeller works fine, but as soon as I want to use another or more than this first distance, modeller crashes with a segmentation fault.

Using the windows-version with the script below, models are produced that have an n-terminus formed like a straight line, as if the distance restraints that were meant to guide the structure are simply ignored or not read in...

I tried to change the corresponding atoms from 'OG' to 'CA' in case this option only works with certain atom types, but this had no effect.

Can someone tell me what I am doing wrong?

Many thanks in advance, Thorsten Schweikardt

Molecular Biophysics University of Mainz

Top-File: ----------------------------- INCLUDE SET ALNFILE = 'alignment.ali' SET KNOWNS = 'protein1' SET SEQUENCE = 'protein1plusnterm' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL= 1 SET ENDING_MODEL = 20

SET LIBRARY_SCHEDULE = 4 SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'model'

SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS = 'OG:3' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 10.0 SET ATOM_IDS = 'OG:116' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 0.0 SET ATOM_IDS = 'CA:42' 'CA:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 1.0 SET ATOM_IDS = 'CA:3' 'CA:42' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 21.0 4.0 SET ATOM_IDS = 'CA:3' 'CA:116' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 50.0 1.0 RETURN END_SUBROUTINE

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