- modeller_usage - salilab.org

Modeling multiple domains
by randalla＠uci.edu 03 Nov '05

03 Nov '05

Hello- Is there a way to force/encourage Modeller to join domains in a manner with few or no clashes/atom overlaps between domains? My first test modeling a multiple domain protein, just as in the example from FAQ #1, resulted in a model with many clashes between the CAs and other atoms of the domains. I realize that Modeller cannot correctly predict domain orientation, but I hope there is a way to strongly discourage inter-domain clashes. Thanks, Arlo Randall University of California, Irvine

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error
by sankari thirumal 03 Nov '05

03 Nov '05

Dear all, I'm not able to solve the following error. i get the same error even when i tired with the known pdbs. how to rectify this problem.please do suggest me. ERROR msg C:\mod\sanmod>mod8v1 model-default.py Traceback (most recent call last): File "model-default.py", line 18, in ? a.make() # do the actual homology modelling File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", line 331, in homcsr aln.check() File "C:\Program Files\Modeller8v1\modlib\modeller\alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v1\modlib\modeller\util\top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args)_modeller.error: check_a_337E> Structure not read in: 1 with regards sankari --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click.

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Refinement of part of model
by Matt wagner 02 Nov '05

02 Nov '05

I was curious to know if I could refine only part of my model. I want to make a 12 amino acid segment from a loop into an alpha helix without changing the rest of the model. What I am trying to do is only make certain parts of the model less solvent accessible. Thanks for any help, Matt Wagner Cleveland State University

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add new residue type
by Hai-long Wang 02 Nov '05

02 Nov '05

Hi, Modeller I am trying to add a ligand as new residue type. My ligand is acetylcholine. I found its topology in CHARMM /toppar/top_all27_port_lipid.rtf as ACHO. This is how I did: I copy the part from CHARMM file for ACHO to the end of $MODLIB/top_heav.lib. Then add a line at the end of $MODLIB/restyp.lib 142 | ACH | # | ACHO | acetylcholine I use # in the alignment file I have the following in my top file: SET TOPLIB = '$(LIB)/top_heav.lib' SET PARLIB = '$(LIB)/par.lib' SET HETATM_IO = 'ON' However, mod7v7 still indicate that I have unknown residue type. Where I was wrong? Thank you Hailong

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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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