- modeller_usage - salilab.org

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 07 Jul '02

07 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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what is wrong?
by Yoram Devary 25 Jun '02

25 Jun '02

Hi ! i have a some problems with this result : in log file Kind, OS, HostName, Kernel, Processor: 4, IRIX bioinfo-2 6.5 IP32 Date and time of compilation : 04/26/2002 20:34:09 Job starting time (YY/MM/DD HH:MM:SS): 2002/06/24 19:53:32.102 fullfn__230E> File not found: `TVLDH.ALI` Directories: Extensions : :.chn Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148. 909 2.099 Starting time : 2002/06/24 19:53:32. 102 Closing time : 2002/06/24 19:53:40. 908 Total CPU time [seconds] : 0.00 some question: 1) i write non-capital , and when i run , the program see that is capital why? 2)why i receveid file not found? i put in same directory? 3)why items Directory are empty? 4)how i really need to give the name of file in top sricpt ps: i run the tutorial example , and wotk, when i write my examples didn't wotk i dont know why ;-( best regads, yoram devary

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win-modeller
by Shamshad Zarina 24 Jun '02

24 Jun '02

Hi modllers, I am trying to use win version of modeller. I have two problems: 1. Although example files run fine, I get this error message with my proteins: check_337E>structure not read in 2. I have failed to get a log/out file. Any help will be appreciated. Regards, S. Zarina __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com

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MPAIRS problem - 6.2 vs 6a
by Daniel John Rigden 20 Jun '02

20 Jun '02

Hi I'm having a problem with a simple modelling task in 6.2. I get the following error pick_re_612_> Number of MODEL atoms, selected restraints; 1440 13788 TOP_________> 393 234 OPTIMIZE pair2___223E> Array too small. Increase MPAIRS current maximum, current need: 4320 4320 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I see that this problem has been reported twice before but I didn't find any answer. What's new in this case is that I can run the same task file (on a different machine) with Modeller 6a with no problems. Any thoughts as to what's going on? Thanks in advance. Daniel PS Attaching the top and alignment files. +-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel(a)cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +-------------------------------------------------------------------------+

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Error in win distribution
by Andras Fiser 20 Jun '02

20 Jun '02

-- dear windows version users of modeller, there was a wrong environment variable definition in the distribution package of modeller, effecting only the windows distribution. 2 ways to correct it: ###################################### please visit http://salilab.org/modeller/download_installation.shtml and download/reinstall the full mod6v2.zip windows version again, or alternatively, ###################################### you can download and replace only the faulty file in your distribution, called mod.bat, you will find it in /bin/mod.bat. To get this file: anonymous ftp salilab.org cd andras get mod.bat ###################################### Thanks for Jaroslaw Pillardy to pointing out this problem. Andras -------------------- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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helix axis of alfa-helix
by Michael Petersen 19 Jun '02

19 Jun '02

Hi, Does anyone on the list have a script to calculate the helix axis of an alfa-helix? Regards, __________________________________ Michael Petersen Nucleic Acid Center Department of Chemistry University of Southern Denmark, Odense University Campusvej 55 5230 Odense M Denmark e-mail: mip(a)chem.sdu.dk Tel: +45 65 50 25 30 Fax: +45 66 15 87 80

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