- modeller_usage - salilab.org

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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interpolating missing residues
by BIN ZHANG 11 Nov '08

11 Nov '08

Hi, All: 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? 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? Thanks a lot. Bin ------------------------------------------------------------- The tree of liberty must be refreshed from time to time with the blood of patriots and tyrants.

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automodel vs loopmodel
by Mauricio Carrillo Tripp 11 Nov '08

11 Nov '08

When I run the automodel or the loopmodel classes, either way I get a target.B99990001.pdb for the structure of the final model. From the documentation, I understand that in the case of the loopmodel, an extra pdb file will be produced with refined loops. My question is: Should the models in files target.B99990001.pdb be the same whether I use automodel or loopmodel? (provided I'm using the same optimizations and all, I'm just changing the class name in the python script) 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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adding two residues of different peptides
by prasun kumar 11 Nov '08

11 Nov '08

Dear users, There is a PATCH for adding sulfide bridge among two sulfur atom in a peptide.Can we use this concept for adding two residues of two different peptides at a certain angle........... please give me some suggestions thanx in advance -- PRASUN (ASHOKA)

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Error massage
by nagaraju ngaraju 11 Nov '08

11 Nov '08

Dear Sir/Madam I took the example given in your tutorial page: "Modeling lactate dehydrogenase from Trichomonas vaginalis based on a single template. When I run compare.pr file I am getting the error massage like below pdbnam_____E> Filename for PDB code not found: 1b8p Directories: Extensions : ;.atm;.pdb;.ent;.crd (Also tried prepending 'pdb', and looking for .Z, .gz, .bz2, .7z) Can you please suggest me to run compare.py. Thanking you I.Nagaraju Tirupati 9949860196 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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adding two proteins
by prasun kumar 11 Nov '08

11 Nov '08

Dear users, I am trying to add two proteins by means of making bond between the residues of both the proteins.Can we do this using modeller. this question came into my mind because of the DISULFIDE bond that we can make using modeller. if there is any method then please help me thanx in advance -- PRASUN (ASHOKA)

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