- modeller_usage - salilab.org

normalized DOPE - expected values vs quality of template?
by Daniel Rigden 20 Nov '08

20 Nov '08

Dear all I expect this is more a question for the developers, but perhaps other users have relevant experiences to share. With 9v5 we have the very useful Z scores from a normalized DOPE assessment. The manual says that +ve scores are bad, and that anything less than -1 or so is 'native-like'. Presumably the best achievable Z score will depend very much on the available templates - we should be able to do much better with 70% identical templates than with 30% identical templates. Has anyone got a feel for what kind of figures we should be happy with (and be able to quote in a paper as supporting the quality of our model) in different ranges of template % sequence identity? Thanks in advance Dan -- 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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Loop model refinement level
by Mauricio Carrillo Tripp 17 Nov '08

17 Nov '08

In the example taken from http://salilab.org/modeller/manual/node32.html, the loop refinement level is set to "fast" a.loop.md_level = refine.fast # Loop model refinement level What other levels of refinement do I have access to? I've seen in other examples something like the following for complete models: # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Very thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e8 Would this also apply for loops? Would it make much difference in terms of final model/loop quality (DOPE score maybe)? Thanks again for all your help. -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | 0 |

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dopehr_loopmodel crashed
by Mauricio Carrillo Tripp 17 Nov '08

17 Nov '08

I'm trying to do a loop refinement calculation with the dopehr_loopmodelclass, modeller 9v4. Here's the python script I'm using: from modeller import * from modeller.automodel import * log.verbose() # request verbose output env = environ() # directories for input atom files env.io.atom_files_directory = ['./', 'PDB/'] a = dopehr_loopmodel(env, alnfile='TTN.ali', knowns='2g8gOligo', sequence='1s58', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 a.loop.ending_model = 1 a.loop.md_level = refine.fast a.make() After a few hours of running, it stop. Here's the last part of the log: ... randomi_498_> Atoms,selected atoms,random_seed,amplitude: 36972 36056 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 327553569 319876.531 312.379 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 554709537 541708.562 529.012 preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. >> Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- 1s58.B99990001.pdb 75059.09375 -361379.46875 0.78559 >> Summary of failed loop models: 1s58.BL00010001.pdb check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. Dynamically allocated memory at finish [B,KiB,MiB]: 549216697 536344.438 523.774 Starting time : 2008/10/24 10:37:24 Closing time : 2008/10/24 12:51:48 Total CPU time [seconds] : 8018.72 The model part went OK, but when it tried to do the loop refinement it went crazy (the coordinates in1s58.BL00010001.pdb are all messed up). I'm also testing the other two classes (loopmodel and dope_loopmodel) and they've been running for a long while now, so I don't know if they'll work or not. I'd just like to know if I'm doing something wrong or I just ran into some kind of glitch or bug in the dopehr algorithm. Thanks! -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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Visuvalise
by nagaraju ngaraju 17 Nov '08

17 Nov '08

Dear caretaker I want to know how to visulized the protein structrue after completing the "plotprofile.py" . Thank you I.Nagaraju Sugen Life Sciences Tirupati 9949860196 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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model a peptide without moving a part of it
by Omar Piña 14 Nov '08

14 Nov '08

I need to bound two peptides and mantain one of them without moving. I looked for restraint but I don´t find how to do it. Sorry If my cuestion is too basic. Omar

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Heme
by Bo Yang 12 Nov '08

12 Nov '08

Dear Modeller: I have heme modeled into my target using Modeller. When I try to visualize the model, the Fe is not shown. I check the pdb file of the model, Fe is there. I couldn't understand what could be wrong. Why can't "Fe" be visuallized? I use Modeller 8v1. The program used for structure visuallization are Chimera and VMD. Thank you for your advice. Bo

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How to install pylab in modeller?
by vidhya ganesh 12 Nov '08

12 Nov '08

Hi, In Model evaluation, I installed matplotlib inorder to build the plot between my template and model , but I can't find pylab, which I think is a submodule under matplotlib. All of the documentation for matplotlib starts with "from pylab import *", but this of course doesn't work. Is pylab included in the distribution? If not, is there a use for matplotlib _without_ pylab? Thanks Vidhya

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Re: [modeller_usage] modeller_why ther is know gui.
by Jayashankar 12 Nov '08

12 Nov '08

Dear developers, Why still there is no gui for modeller. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Thu, Nov 13, 2008 at 12:00 AM, <modeller_usage-request(a)salilab.org>wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: interpolating missing residues (Modeller Caretaker) > 2. Re: modeling of phosphorylated polypeptide (Modeller Caretaker) > 3. Re: modeling of phosphorylated polypeptide (Modeller Caretaker) > 4. How to install pylab in modeller? (vidhya ganesh) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Nov 2008 20:38:24 -0800 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] interpolating missing residues > To: BIN ZHANG <zhngbn(a)gmail.com> > Cc: modeller_usage(a)salilab.org > Message-ID: <491A5DC0.2090509(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1 > > BIN ZHANG wrote: > > I was trying to add missing residues in pdb file according to the page: > > > > http://salilab.org/modeller/wiki/Missing%20residues > > > > But, one thing I don't understand is how can I get the "alignment.ali" > file? > > You have to create it manually. You can add the missing residues by > reading the REMARK lines in the PDB to figure out which ones are > missing, and then perhaps the SEQRES lines to figure out what the > residue types are. > > > Aslo, it seems to me the command complete_pdb() can also do the job? > > http://salilab.org/modeller/manual/node403.html > > Is this true? If so, what's the difference between these 2? > > No - complete_pdb does not add missing residues. It adds any missing > *atoms* for any residue - for example, if your input PDB contains only > CA coordinates, it will add (using internal coordinates) the rest of the > backbone and sidechain. But it won't add any residues that aren't in the > PDB in the first place. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Tue, 11 Nov 2008 22:32:20 -0800 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] modeling of phosphorylated polypeptide > To: xpzhang(a)ucdavis.edu > Cc: modeller_usage(a)salilab.org > Message-ID: <491A7874.6010100(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1 > > Xiao-Ping Zhang wrote: > > Many proteins are phosphorylated in vivo and and the status of their > > phosphorylation correlate to their function. The residues which are > > phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry. > > I wonder how to build a phosphorylated model directly or how to apply a > > patch on a model to get a phosphorylated model in Modeller? > > Sure - you could build a comparative model in the usual way (assuming > you have a template) and phosphorylate the residues you're interested in > by applying a suitable patch in the special_patches method. If a > suitable patch does not exist, you'll have to add a new one to the > topology file - see the FAQ or the CHARMM forums. > > If your intention is to take an existing PDB and use Modeller to > phosphorylate some residues, Modeller is perhaps not the best package > for the job - you'd be better off using a dedicated MD program. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 3 > Date: Tue, 11 Nov 2008 22:36:13 -0800 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] modeling of phosphorylated polypeptide > To: Dibyabhaba Pradhan <dbpinfo(a)gmail.com> > Cc: modeller_usage(a)salilab.org > Message-ID: <491A795D.10104(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1 > > Dibyabhaba Pradhan wrote: > > I modelled number of proteins by basic modelling. After basic > > modelling during procheck evaluation the residues in most favorable > > region is generally above 90% but after loop refinement the residues > > in most favorable region comes below 90%. Please kindly inform me what > > may be the region for this. > > > > Also after energy minimization the the percentage of residue in most > > favorable region decreses. > > I'm not sure what this has to do with phosphorylation, but there is > certainly no guarantee that a single minimization will give a "better" > model. You'd be better off building several models to get a reasonable > sampling of the energy landscape and then picking the best cluster or > single model. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 4 > Date: Wed, 12 Nov 2008 14:33:40 -0800 (PST) > From: vidhya ganesh <vidhya_81in(a)yahoo.com> > Subject: [modeller_usage] How to install pylab in modeller? > To: modeller_usage(a)salilab.org > Message-ID: <499646.88880.qm(a)web34203.mail.mud.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > In Model evaluation, I installed matplotlib inorder to build the plot > between my template and model , but I can't find pylab, which I > think is a submodule under matplotlib.? All of the > documentation for matplotlib starts with "from pylab import *", but > this of course doesn't work. > > Is pylab included in the distribution? > If not, is there a use for matplotlib _without_ pylab? > > Thanks > > Vidhya > > > > >

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Re: [modeller_usage] modeling of phosphorylated polypeptide
by Xiao-Ping Zhang 11 Nov '08

11 Nov '08

Dear Alden, Thank you for your reply and your information. My idea is very similar to the idea presented in this nice paper. But the the approaches they used are beyond the limit of my knowledge. I hope some one can implement their results into a public available program (for example, Modeller, PyMol or Deep Viewer). Direct homology modeling of phosphorylated polypeptide may not make any sense if the template used is not phosphorylated because the conformational change. But if a molecular modeling program allows to add the phosphate group on a model (similar to adding S-S bridge in Modeller) followed by MD simulation, the final model could make sense (Groban et al's paper is very encouraging). I noticed that in the topological library of Modeller9v4, there are information for "converting (patching?) tyrosine to monoanionic phosphotyrosine (PRES TP1)", but no information on converting Thr, Ser and Asp. I wonder if any body tried to patch a model from Tyrosine to phosphotyrosine with Modeller. Is there any possibility to implement information for other residues for patching purpose? Is there any other free program which has this functionality? Thank you for your comments and suggestions. Best regards, Xiao-Ping At 02:16 AM 10/29/2008, you wrote: >Perhaps homology modelling is not the best method. This might help: > >http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1440919 > >Best of luck. > >~alden > > >Xiao-Ping Zhang wrote: > > Hi, > > > > Many proteins are phosphorylated in vivo and and the status of their > > phosphorylation correlate to their function. The residues which are > > phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry. > > I wonder how to build a phosphorylated model directly or how to apply a > > patch on a model to get a phosphorylated model in Modeller? > > > > Thank you advance for your suggestions. > > > > Xiao-Ping Zhang > > > > > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > https://salilab.org/mailman/listinfo/modeller_usage > > > >

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modeling of phosphorylated polypeptide
by Xiao-Ping Zhang 11 Nov '08

11 Nov '08

Hi, Many proteins are phosphorylated in vivo and and the status of their phosphorylation correlate to their function. The residues which are phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry. I wonder how to build a phosphorylated model directly or how to apply a patch on a model to get a phosphorylated model in Modeller? Thank you advance for your suggestions. Xiao-Ping Zhang

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