- modeller_usage - salilab.org

topology for nicotine
by Hai-long Wang 01 Nov '05

01 Nov '05

Hi, Modeller I am using nicotine as ligand in modeller. Does anyone know modeller include the nicotine topology ? How to use it in alignment? I don't want to use it as BLK residue. Thanks Hailong

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Re: model assessment method
by Mensur Dlakic 01 Nov '05

01 Nov '05

Hi, I am interested in the last part of this statement, which is calling external programs. Could you provide a working example of how to call ProsaII and evaluate each model? As it is, I use ProsaII at the end of each Modeller run, but it would be nice if GA341 and ProsaII scores could be obtained in parallel for easier comparison. Also, is there any way to get perl scripts for stand-alone pG calculations? Some time ago Andrej (or Roberto) told me that those scripts were too unrefined to be shared, but maybe that has changed? Many thanks for your patience and explanations, Mensur At 11:27 AM 11/1/2005, you wrote: >Two methods are available by default - assess.GA341 and assess.DOPE - >but these are just ordinary Python functions, so you can define your own >function to generate an assessment score if you so desire (for example, >you could call an external program like Prosa and return the score). > > Ben Webb, Modeller Caretaker ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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Question running script on cluster
by zkatsim＠nimr.mrc.ac.uk 01 Nov '05

01 Nov '05

Hello, I'm trying to do some modelling using 6 templates with very low sequence id (<30), so I wan't to generate as many models as possible. I was thinking 50 in the first instance (unless someone recommends a lot more). I have decided to send the job to a cluster (parallel machines) I have access to in the interest of time, but before doing so I wanted to clarify some things. Am I correct in assuming I need to create 50 diff script files, each with a different STARTING_MODEL and ENDING_MODEL, and in each script setting a different random number seed? ie. script 1 STARTING_MODEL = 1 ENDING_MODEL = 1 script 2 STARTING_MODEL = 2 ENDING_MODEL = 2 .....and so on Also, if I do this, will all models be intercomparable, because I thought you were only able to compare models of the same run. Could someone briefly explain why this is or isn't the case? And also, one last question. Should I be worried about log files over-writing each other, because I think they will all go to the same directory in the cluster? Is there maybe some line I can add to each script do direct the output into its own folder? (As you probably can tell from that question, my background is not in computing!) Thanks in advance. I appreciate any help anyone can give. -Zoe

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model assessment method
by 서주현 01 Nov '05

01 Nov '05

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constrain template secondary structure in energy minimization/loop building
by Frank Peelman 27 Oct '05

27 Oct '05

-- I'm modellling an Immunoglobulin-type domain. When generating the homology models using automodel, the beta sheet structure in the models seems to be disturbed when compared to the template. This is obviously an error in the model as the besta-sheets are conserved in every related family member. As expected, the problem occurs in the loop building and energy minimization steps, as i do not see the loss of beta-sheet structure when using "a.make("exit=2")". What is the best way to avoid loss of beta-sheet structure, e.g. by tethering, restraining sec. structure ...?

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problem with modelling a non-template helix
by Renée Vancraenenbroeck 25 Oct '05

25 Oct '05

dear modellers, I've come to the problem where I have to elongate a helix but the template is absent, I've tried to restrain it into a helixconformation using the following script wich I found in the archive, however it doesn't seem to make any difference. What am I doing wrong? renée vancraenenbroeck renee.vancraenenbroeck(a)student.kuleuven.ac.be from modeller.automodel import * # Redefine the special_restraints routine to include the secondary # structure restraints (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints # An alpha-helix: rsr.make(aln, restraint_type='ALPHA', residue_ids= ('133', '139'), spline_on_site=False) # This is as usual: log.verbose() env = environ() a = automodel(env, alnfile='Lrrk2-mult5.ali', knowns=('2aedA','1byuA'), sequence='Lrrk2roc') a.starting_model = 1 a.ending_model = 5 a.make()

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chain
by PARVINI 22 Oct '05

22 Oct '05

Dear friends I want to have chain name and amino acid numbers for tetramer protein in modeller output file. For example A 1 A 2 ------- A 30 B 1 B 2 ------ B 30 Would you please help me? Sincerely yours parvini

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multiple protein conformations
by jf163201＠ohio.edu 20 Oct '05

20 Oct '05

Hi, I have a single sequence and several structures of different conformations of the same protein. I would like to use this information to create a single alignment that incorporates the data from all the conformations. The structures are all of the same protein, so they have the same sequence. Once I have the single alignment, then I can use this alignment to create a model for each conformation. Also note that because of the different conformations, the alignment of the sequence with structure A is not (necessarily) the same alignment given if I align the sequence with structue B. My main approach has been to append the structures and the sequence to alignment and then run align2d(). The problem I have here is that because all the structures have the same sequence, the returned alignment just has all the protein sequences aligned with no gaps and my single sequence is just added with all the extra residues overhanging(the sequence is a little longer that the protein sequences) the alignment of the proteins. Is there some way to add a weight to the protein sequences so that they don't overpower the single sequence? Since the protein sequences align perfectly, the addition of the single sequence is negligible to the overall alignent. I thought this was what the align_what='BLOCK' argument was supposed to do, but I didn't have any luck with that either--I tried to put the proteins in one block, and the sequence in another. I've also been trying salign() without success. I'm new to Modeller and this problem seems sufficiently different from the tutorials and examples in the manual to leave me at a loss. Would someone give me some guidance about how to approach this? Thank you, Jim Fonseca

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error when trying to set MDT_LIB_FILE and BIN_LIB_FILE
by Daniel Rigden 19 Oct '05

19 Oct '05

Dear all I sometimes need to reconstruct a complete structure from a main chain alone structure derived from dynamic analysis. To do this I have, in the past, used a modified mkhomcsr routine to take main chain constraints from one structure (the main chain alone) and side chain constraints from another (the original crystal structure). In the past this has worked. Now, for some reason, on a different machine but running the same v6.2 of modeller, I get errors. My remodelled routine looks like this --------------------------------------------- SUBROUTINE ROUTINE = 'mkhomcsr' SET MAX_CA-CA_DISTANCE = 30.0 SET MAX_N-O_DISTANCE = 20.0 SET MAX_SC-MC_DISTANCE = 4.5 SET MAX_SC-SC_DISTANCE = 6.0 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS = OFF ### MNCH restraints! READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = 'mc_only' SEQUENCE SET MDT_LIB_FILE = '${LIB}/mnch1.mdt' SET BIN_LIB_FILE = '${LIB}/mnch1.bin' MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_RESTRAINTS = ON etc. --------------------------------------------- but MODELLER gives errors of this type --------------------------------------------- getprog_531W> ROUTINE redefined: mkhomcsr assgn___544E> Variable name not recognized: MDT_LIB_FILE Command line: SET MDT_LIB_FILE = '${LIB}/mnch1.mdt' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: BIN_LIB_FILE Command line: SET BIN_LIB_FILE = '${LIB}/mnch1.bin' etc. --------------------------------------------- Can anyone tell me why Modeller isn't recognising these variable names? It's not a general issue - simpler modelling tasks run fine. Many thanks in advance Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.

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PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP
by Troy Wymore 14 Oct '05

14 Oct '05

************************************************** PITTSBURGH SUPERCOMPUTING CENTER NATIONAL RESOURCE FOR BIOMEDICAL SUPERCOMPUTING WORKSHOP This workshop is funded by a grant to the PSC from the NIH National Center for Research Resources. The grant provides tuition, hotel, supercomputing time, and workshop materials for US academic participants. COMPUTATIONAL BIOPHYSICS WORKSHOP Nov. 28 - Dec. 1 Application Deadline: October 24 Primary Instructor: Prof. Klaus Schulten (UIUC) www.psc.edu/biomed/training/workshops/2005/NAMD/index.html The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. For specific details, including an electronic application form, see: www.psc.edu/biomed/training/workshops/2005/NAMD/index.html Please direct any questions about the workshop to Dr. Troy Wymore (wymore(a)psc.edu)

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