modeller_usage July 2002

modeller_usage@salilab.org

24 participants
27 discussions

complete set of execs for repaired 6v2
by Bozidar Yerkovich 09 Jul '02

09 Jul '02

Hi all, You can now access all 7 executables for the repaired 6v2, including windows version. >From now on there should be no MPAIRS errors/crashes. Happy modeling, Bozidar

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the alignment problem
by Margot Ernst 09 Jul '02

09 Jul '02

thanks for all who replied to my original posting. The bottom line appears to be that various groups have been using a "user-driven" approach to iterative alignment - model optimization, but no generally recommended or automated protocol appears to be in use. thanks once more, margot

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Some problems with respect to non-standard residues
by Kong Lesheng 08 Jul '02

08 Jul '02

It seems there are some differences with respect to non-standard residues between Modeller4 and Modeller6v2. I'm working on conotoxin. Some conotoxin sequences include non-standard residues. (such as 1OMC.pdb includes HYP) When I used Modeller4 before, I modified the template file("HETATM" into "ATOM "), then did alignment and modelling. The non-standard residues were read as "B". I'm currently using Modeller6v2. When I did the same things, these residues were read as "G". So the program always complain "the sequence is different with structure." Maybe a dirty solution is : modify the template file, delete surplus atoms, change the non-standard residue into standard residue. But non-standard residues are important for the function of conotoxin. Is there a better way to deal with non-standard residues? It seems that "SET HETATM_IO=ON" can not solve this problem. Thank you very much! With best regards, Kong Lesheng -- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6774 7149 Fax: (65)6778 2466

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The sequence of template was wrongly read!
by Kong Lesheng 08 Jul '02

08 Jul '02

Hi, I'm currently using Modeller6v2. It is very strange that in the alignment, the sequence from the template is wrong. The 17th residue should be "NH2", c-terminal amidation. But in the alignment file, it is replaced by "G". I attached my top file and log file? Is there any mistake in it? Thank you very much! With best regards, Kong Lesheng -- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6774 7149 Fax: (65)6778 2466

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E> Array too small. Increase MPAIRS, 6v2 executable update July 4th 2002.
by Bozidar Yerkovich 04 Jul '02

04 Jul '02

Hi all, Several of you reported the problem of MODELLER crashing with the following error: E> Array too small. Increase MPAIRS. It seems that all of those problems were due to the scaling factor in natm2mpairs function in MODELLER code. I have changed the value and tested it with those problematic top files. I hope that others will find it stable too. What you need to do if you had this problem: reinstall 6v2, that's the only solution, since the problem was in the source code. Sorry ;-( For advanced users: you only need to replace the "sick' executable with the "repaired" one from our web site, and put it in your {MODINSTALL6v2}/bin/modeller6v2/bin directory. If some of you still experience this problem please let me know. New executables will be available sometime later today. Happy modeling, Bozidar

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Re: the alignment problem
by Paul＠pdchem.demon.co.uk 04 Jul '02

04 Jul '02

In message <200207041335.49310.margot.ernst(a)univie.ac.at> Margot Ernst writes: > > Hi Modeller developers and friends, > > in Sanchez and Sali 1997 Curr Opin Struct Biol 7:206-214 > I read that a possible way to improve on homology modeling below 30 PID could > be "iterative changes in the alignment during caluclation" > My question is: Is this a great idea that has been realized already and I > just missed where and how, is it work in progress or has it been discarded > again due to technical problems? I believe this iterative approach to homology modelling is used routinely. See for example Burke et al (1999), Proteins Suppl 3:55-60. A three-dimensional alignment of a model with the template(s) is made, and the implied linear alignment is adjusted so as to preserve local structural features that might be expected to be conserved. The new alignment is then used to build an improved model, and so on. I do not know whether the full procedure has been automated successfully. -Paul -- -------------------------------------------------------------------- Paul Davis paul(a)pdchem.demon.co.uk

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the alignment problem
by Margot Ernst 04 Jul '02

04 Jul '02

Hi Modeller developers and friends, in Sanchez and Sali 1997 Curr Opin Struct Biol 7:206-214 I read that a possible way to improve on homology modeling below 30 PID could be "iterative changes in the alignment during caluclation" My question is: Is this a great idea that has been realized already and I just missed where and how, is it work in progress or has it been discarded again due to technical problems? Could one, alternatively, if only one template is availble, use this template several times with different alignment variants (home-made version of modeling on several templates, so to speak) so that different homology derived restraints go into the same VTF, or is it, at present knowledge, better to go for ensembles of models and then try to construct one or more "best" consensus models? Any and all information and ideas are much appreciated! margot -- Dr. Margot Ernst Abteilung Prof. Sieghart Institut f. Hirnforschung Spitalgasse 4 A-1090 WIEN margot.ernst(a)univie.ac.at visit brainresearch: www.univie.ac.at/brainresearch

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modeller_usage July 2002