Hello to all,
I am having problems to use the user distance restraints, they are ignored completely by Modeller 6v1/6v2latest, Windows and Linux- versions: at first I thought they were not met entirely, but then I ran some tests, with and without the restraints:
The 50 models I get when using the restraints are identical to those that are modeled using no restraints at all...
Modeller really reads the commands (because using a "0.0" as standard deviation crashes it), but it does not seem to incorporate the distances into the model.
Changing the form of the restraints (gaussian, LJ, cosine etc) or using different atoms (CA instead of OG) did not help.
My goal is to model the n-terminus of a protein that's available as pdb with the help of measured distances from Electron Spin Resonance.
Could you please tell me whether I am doing something wrong (syntax?) or
if there is a bug of some kind? I would be very grateful for an answer.
Thanks again for listening, Thorsten Schweikardt University of Mainz
My 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'
#eg. Distance Serine-OH AA3 to Serine-OH AA169: 30Angstrom SET ATOM_IDS = 'OG:3' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 1.0
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
Hi Thorsten,
at least with the SGI version of modeller6v2 the addition of restraints by redifining the 'special_restraints' subroutine leads to different optimization traces. I started the calculation of a model with and without additional restraints and inspected the time course of the optimization in the *.D* file. At a certain point during the VTFM optimization the optimization traces start to diverge.
Please let me know what you find out about the Linux and Windows versions of modeller.
Schoene Gruesse nach Mainz, Oliver
Thorsten Schweikardt wrote: > Hello to all, > > I am having problems to use the user distance restraints, they are > ignored completely by Modeller 6v1/6v2latest, Windows and Linux- > versions: at first I thought they were not met entirely, but then > I ran some tests, with and without the restraints: > > The 50 models I get when using the restraints are identical to those > that are modeled using no restraints at all... > > Modeller really reads the commands (because using a "0.0" as standard > deviation crashes it), but it does not seem to incorporate the distances > into the model. > > Changing the form of the restraints (gaussian, LJ, cosine etc) or using > different atoms (CA instead of OG) did not help. > > My goal is to model the n-terminus of a protein that's available > as pdb with the help of measured distances from Electron Spin Resonance. > > > Could you please tell me whether I am doing something wrong (syntax?) or > > if there is a bug of some kind? I would be very grateful for an answer. > > > Thanks again for listening, > Thorsten Schweikardt > University of Mainz > > > > > My 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' > > #eg. Distance Serine-OH AA3 to Serine-OH AA169: 30Angstrom > SET ATOM_IDS = 'OG:3' 'OG:169' > ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 1.0 > > 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 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage
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Oliver Hucke -
Thorsten Schweikardt