- modeller_usage - salilab.org

selection to model
by Alex Brown 13 Sep '07

13 Sep '07

Hi. Only a small problem. Is there any way to convert a selection object to a model object ? I would like to extract the chains from a multi-chain model and use the separate chains as individual models. At the moment, the only way I seem to be able to do this is to write the selection to a file and the read the file into a model object. Cheers, Alex Brown www.mrctechnology.org Medical Research Council Technology is a company limited by guarantee no. 2698321, incorporated in England and a charity registered in England and Wales no. 1015243, and a charity registered in Scotland no. SC037861. Regsistered office 1-3 Burtonhole Lane, Mill Hill, LONDON, NW7 1AD, UK. T: +44 (0)208 906 7100; F: +44(0)208 906 7200. This communication contains confidential information and may be legally privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any disclosure, distribution, copying or use of this communication or the information in it is prohibited and may be unlawful. If you have received this communication by mistake, please notify the sender or contact MRC Technology by telephone on 0208 906 7100 and then delete the e-mail and any copies of it. No representation is made that this email or any attachments are free of viruses. Scanning for the presence of viruses in this e-mail, and any attachments, is highly recommended and is the responsibility of the recipient.

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using DOPE assessment
by saccenti＠cerm.unifi.it 11 Sep '07

11 Sep '07

Hi all, I'm wondering if using DOPE assessment is only possible to evaluate each chains indvidually. Once I get the DOPE score of the two chains, how to combine them to get an unique DOPE score for my complex? Is summing the two (or more) score reasonable? Other way, what If I create my complex as a single chain? Many thanks for suggestion Edo -- Dr Edoardo Saccenti CERM Magnetic Resonance Center University of Florence Fiorgen Foundation Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4574281

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Cu(I) Parameters
by saccenti＠cerm.unifi.it 11 Sep '07

11 Sep '07

Hi all, I'm modleing a complex with a copper ion Cu(1). I searched for copper paramters in the modlib/restyp.lib but I did not find them. Are topology and suitable forcefield parameters available? Many thanks edoardo -- Dr Edoardo Saccenti CERM Magnetic Resonance Center University of Florence Fiorgen Foundation Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4574281

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dope_loopmodel question
by Mike White 10 Sep '07

10 Sep '07

I would like to refine my models of a homopentamer with loop refinement. In the past (Mod8) I would use loopmodel, but noticed that there is an "improved" loop modeling routine dope_loopmodel() which uses (among other things) the DOPE score in the refinement process. In various parts of the manual it mentions that the DOPE score was developed for single-chain models and shouldn't be used as an evaluative tool for multichain models. Does this also meas that the dope_loopmodel() routine shouldn't be used for loop refinement of multichain models? What's the downside of using it for multi-chain models? If so, this would be a shame since there are also other enhancements (Leonard_Jones potentials, etc.) unrelated to DOPE that would be nice to be able to use. Mike White

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align_codes error
by Dave Roe 10 Sep '07

10 Sep '07

I'm receiving the following error on linux with Modeller 9.2: _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = mod2hg42 Here's the alignment line from my python file: aln = alignment(env, file='mod2hg42.fa', align_codes=('mod2hg42')) Here's the contents of mod2hg42.fa (located in the same directory): >mod2hg42 EEKLRRYLKRTVTELDSVTARLREVEHRAGEPIAIVGXACRFPGDVDSPESFWEFVSGGGDAIAEAPADRGWEPD PDARLGGXLAAAGDFDAGFFGISPREALNXDPQQRIXLEISWEALERAGHDPVSLRGSATGVYTGSSTNDYGFLA VSDPDEAHPYAITGTASSVASGRVAYCLGLEGPAXTVDTACSSSLTALHLAXESLRRDECGLALAGGVNVLSTPM VTLGFDSQGGLAADGRIKPFSKAADGYTRSEGAGVLVLQRLSAARREGRPVLAVLRGSAVNQDGASNGLIAPSGP AQQRVIRRALENAGVRAGDVDYVEAHGTGTRLGDPIEVHALLSTYGAERDPDDPLWIGAVKTNVGHLESAAGVAG VXKAVLALRHGEXPRTLHFDEPSPQIEWAVSVVSQARSWPAGERPRRAGVSSFGFGGTNAHVIVEEAPEADEPV I've tried dozens of combinations, but I can't get around this error. Any advice? -- Dave Roe roex0050(a)umn.edu

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Special Considerations in Membrane-bound models?
by Andrew D. Fant 10 Sep '07

10 Sep '07

Good morning, I'm looking at trying to build models of a set of membrane-bound proteins via structural homology, and I was wondering if there are any special caveats that apply to this situation. Thanks, Andy

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Model quality assessment
by saccenti＠cerm.unifi.it 10 Sep '07

10 Sep '07

Which is the best strategy to assess the quality of a model and sort them out of a bunch of many calculated models? I have models a complex of two proteins plus a metal ion. Many Thanks edo -- Dr Edoardo Saccenti CERM Magnetic Resonance Center University of Florence Fiorgen Foundation Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4574281

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modeller.top location?
by DANIEL TAYLOR 07 Sep '07

07 Sep '07

Greetings Forum users I'm a final year Biochemistry undergraduate and am slowly learning the ropes when it comes to computers; I have recently installed modellerv9.2 on my ubuntu system (having used Redhat at Uni) and am having real difficulty in getting started, I've tried to find the modeller.top file and also tried to find a comprehensive instructions to help me setup but a lot of it is too advanced for me? can somebody please point me in the right direction; I'm certain once the modeller.top is up and running I should be able to get it working from then on. Many thanks in advance regards Dan

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Modelling complexes
by saccenti＠cerm.unifi.it 06 Sep '07

06 Sep '07

Hi All, I want to model a complex A1+B1 on a template complex A+B where A and B are proteins. I have only one template available. Does somebody as a warking script to do this? Many thanks Edo -- Dr Edoardo Saccenti CERM Magnetic Resonance Center University of Florence Fiorgen Foundation Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4574281

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setting distance restraints
by Mike White 05 Sep '07

05 Sep '07

I am trying to incorporate some experimentally-derived distance restraints into a homopentamer model, and had a few questions: 1.) the manual says that restraints.make_distance() should be used for setting physical distance restraints. However,in the section on restraints.add() http://salilab.org/modeller/manual/node209.html, an example is given on setting distance restraints with this instead of restraints.make_distance(). Is there any benefit to using one versus the other? Do you use the rsr.add() if you have a lot of restraints to add (as I do- 15 in all)? 2.) restraints.make_distance() uses an analytic model to calculate standard deviations, and the manual says to use model 5 for Calpha-Calpha distances and model 6 for N-O distances. I have not been able to find a description of these models, or which one to use for other atom-pair distances. Does it really make much difference? I did try a quick modeling using restraints.add with the following line in the script: rsr.add(forms.gaussian(group=physical.xy_distance,feature=features.distance(at['ND2:93'],at['NH1:905']),mean=19.3,stdev=0.2)) and got the following error message: ************************************************************************** File "EnforceSymmetryTrim_distance_restraints.py", line 96, in ? a.make() File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py", line 99, in make self.homcsr(exit_stage) File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py", line 423, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py", line 506, in mkhomcsr self.special_restraints(aln) File "EnforceSymmetryTrim_distance_restraints.py", line 37, in special_restraints feature=features.distance(at['ND2:93'], at['NH1:905']), File "/usr/lib/modeller9v2/modlib/modeller/coordinates.py", line 137, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v2/modlib/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v2/modlib/modeller/coordinates.py", line 47, in _indxatm raise KeyError, ("No such atom: %s" % indx) KeyError: 'No such atom: ND2:93' ************************************************************************* which suggests that it can't find the ND2 atom in residue 93 . However, the atom does exist in the *.ini file (as does atom NH1 in residue 905): ATOM 783 ND2 ASN A 93 30.499 39.522 -12.905 ATOM 7622 NH1 ARG E 905 45.372 32.420 -16.993 any ideas as to what is going on here? Thanks Mike White

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