- modeller_usage - salilab.org

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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Ideal helices
by Dan Thomas Major 18 Jun '02

18 Jun '02

Hi, I'm modelling G-protein coupled receptors using rhodopsin as a template. When I compare the Ramachandran plot of the models vs that of rhodopsin, the models have much more ideal helices than the rhodopsin X-ray structure (2.8 A). Is this because: 1) The homology is relatively low (20-30%) and the distance constraints receive a low weight in the pdf function?? 2) The helices in rhodopsin are less regular than the globular proteins used in the pdf parametrization?? 3) None of the above... Sincerely, Dan -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel Phone: 972-3-5317785 Fax: 972-3-5348730

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user_distance, group restraints
by Karl Gruber 18 Jun '02

18 Jun '02

Dear Modeller team, I have got a couple of questions about the more uncommon restraint types that are available in Modeller (v62). There is a rather big loop in my target structure for which no homology derived restraints can be defined and which tends to protrude into the vacuum in the resulting models. I wanted to try 'user_distance' in order to get a more compact model but failed in producing a correct restraints file. test input file: ----- . . set atom_types = 'CA' pick_atoms pick_atoms_set=2, selection_segment='2:' '3:' pick_atoms pick_atoms_set=3, selection_segment='10:' '11:' set restraint_parameters = 3 1 1 27 2 2 0 0.0 0.010 make_restraints restraint_type='user_distance' . . ----- restraints file: ----- MODELLER5 VERSION: MODELLER FORMAT R 3 1 1 27 2 2 0 11 0 0.0000 0.0100 R 3 1 1 27 2 2 0 11 0 0.0000 0.0100 R 3 1 1 27 2 2 0 20 0 0.0000 0.0100 R 3 1 1 27 2 2 0 20 0 0.0000 0.0100 . . ----- It appears to be a problem of pick-set 3. The numbers of atoms and restraints are correct (also in more realistic examples) but the second set of atom indices gets lost somewhere along the way. My second bunch of questions concerns restraint feature 5 (distance between gravity centers). What is the exact format of this restraint? How are 'groups of atoms' defined in the rsr-file? Is it equivalent with defining the gravity centers as pseudo-atoms and restraining the distance between them? Thanks a lot in advance! Best wishes, Karl --------------------------------------------------------------------- Karl Gruber Institute of Chemistry KFU Graz Heinrichstrasse 28 e-mail: karl.gruber(a)uni-graz.at A-8010 Graz phone: (+43 316) 380-5483 AUSTRIA fax: (+43 316) 380-9850 ---------------------------------------------------------------------

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array too small problem
by Tommy Wang 15 Jun '02

15 Jun '02

What do I do with the following problem? Thanks. Kind, OS, HostName, Kernel, Processor: 4, Linux orion.ima.org.sg 2.4.18-4custom i686 Date and time of compilation : 05/24/2002 09:27:23 Job starting time (YY/MM/DD HH:MM:SS): 2002/06/15 17:09:13.786 check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- 210 1 165 170 F K 8.143 270 1 229 245 V G 11.690 END OF TABLE delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 22885 20618 pair2___223E> Array too small. Increase MPAIRS current maximum, current need: 7593 7593 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 15765545 15396.040 15.035 Starting time : 2002/06/15 17:09:13.786 Closing time : 2002/06/15 17:10:18.222 Total CPU time [seconds] : 31.71

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