modeller_usage September 2003

modeller_usage@salilab.org

5 participants
15 discussions

Re: model_refinement
by Modeller Caretaker 08 Sep '03

08 Sep '03

Forwarding to list. ----- Forwarded message from Denis Volkov <themelon(a)yandex.ru> ----- Date: Mon, 8 Sep 2003 17:41:54 +0400 From: Denis Volkov <themelon(a)yandex.ru> To: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: Fwd: Re: model_refinement Hello Modeller, Thursday, September 04, 2003, 12:16:20 AM, you wrote: MC> ----- Forwarded message from Oliver Hucke <ohucke(a)u.washington.edu> ----- MC> Date: Tue, 02 Sep 2003 10:03:00 -0700 MC> From: Oliver Hucke <ohucke(a)u.washington.edu> MC> To: Modeller Care <modeller-care(a)salilab.org> MC> Subject: Re: model_refinement MC> Hi Denis, MC> did you compare the quality of the structure calculated with modeller MC> with that of the template(s)? MC> If the quality of the model is really worse something might be wrong MC> with your alignment. Did you do the manual adjustment of the input MC> alignment on basis of the analysis of the quality of the first models? MC> This usually helps a lot. MC> I do not think that it is necessary to use charmm or another external MC> molecular mechanics package to improve the quality of your model. MC> Modeller actually uses (an older version of) the charmm force field for MC> the molecular mechanics part of the optimization. MC> Best, MC> Oliver MC> Modeller Care wrote: >>------ Forwarded Message >> >>From: Denis Volkov <D.Volkov(a)artcustoms.ru> >>X-Mailer: The Bat! (v1.52f) >>Reply-To: Denis Volkov <D.Volkov(a)artcustoms.ru> >>X-Priority: 3 (Normal) >>Message-ID: <43123585810.20030902125313(a)artcustoms.ru> >>To: modeller <modeller_usage(a)salilab.org> >>Subject: model_refinment >> >> >>Hello everyone, >>I successfully used Modeller to model unknown protein. Now I'd like >>to sent my model to Protein Data Bank. So i checked my structure >>using Procheck and find some problems, namely some bad contacts,etc. >>In order to clean a structure i used Charmm program for energy >>minimization. But after it i obtain structure with bad angles and >>bond lengths. Can anybody know how to clean a structure well for >>PDBank and what programs should be use for it. >>Thanks in advance >>Denis Volkov >> >>Enzyme Laboratory,IBCH RAS >> >> >> >> Hello,Oliver Thank you for fast answering! :) No i didn't test a quality of templates course i used 4 structures as a templates so its difficult to do it. Alignment I manually adjust so it's not a origin of fault. I look at the model again and think it's not so bad as I said. But a problem is more global: A similarity with templates is no more than 20%. A great deal of mismatches are in loop origin so it's not so bad...but can i do a good model with so low similarity? As I said I use Charmm, I used it to investigate protein-protein interactions. I used Modeller model to investigate enzyme-substrate and enzyme-inhibitor interaction. But after MD a structure was a great deal disturbed. Is it a problem of low similarity or as you said its not good to use MD with models maid by Modeller? Also I've another question: earlier I used Windows version of Modeller and everything was OK, but now I run Modeller on Linux and have some problem. When I used sequence-search routine it runs for some time (~30-40 min) but then terminated. In log file there is nothing interesting: chains libraries were opened two times. First times it takes 20Mb of memory, second time ~200 Mb and then it terminated. So the problem is a memory usage as I think. I looked through archive and find out that it's a common problem. I checked my top-files and system config (stack size) and everything is good. I've got 500 Mb RAM but half of it utilized by X-Windows. So may be i should run some Modeller routines without running X ? Thanks in advance Denis Volkov Enzyme Laboratory,IBCH RAS -- Best regards, Denis mailto:themelon@yandex.ru ----- End forwarded message -----

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Fwd: can't write the model structure
by Modeller Caretaker 05 Sep '03

05 Sep '03

Forwarding to list. ----- Forwarded message from Sherin Yang <sherin(a)sina.com> ----- From: "Sherin Yang" <sherin(a)sina.com> To: <modeller-care(a)salilab.org> Subject: can't write the model structure Date: Sat, 6 Sep 2003 02:17:46 +0800 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Hi, all I have write a TOP script and want to align a sequence with a structure using ALIGN2D. but I can't get the proper alignment result. The structure's sequence isn't contained in the alignment file. And the log file didn't inform any error information. The following is the TOP scrip, and the attachment is the PDB file. The 1CF8 contains two chains, L and H. Maybe there is something wrong in "MODEL_SEGMENT='1:L' 'X:L' "? ######################################################## READ_MODEL FILE = '1CF8.pdb', MODEL_SEGMENT='1:L' 'X:L' SEQUENCE_TO_ALI ALIGN_CODES = '1CF8L' READ_ALIGNMENT FILE = query_mod.ali', ALIGN_CODES = 'query' ALIGN2D WRITE_ALIGNMENT FILE = 'align2d.ali', ALIGNMENT_FORMAT = 'PIR' ########################################################### Thank you ! Sherin ----- End forwarded message -----

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Fwd: Re: model_refinement
by Modeller Caretaker 03 Sep '03

03 Sep '03

----- Forwarded message from Oliver Hucke <ohucke(a)u.washington.edu> ----- Date: Tue, 02 Sep 2003 10:03:00 -0700 From: Oliver Hucke <ohucke(a)u.washington.edu> To: Modeller Care <modeller-care(a)salilab.org> Subject: Re: model_refinement Hi Denis, did you compare the quality of the structure calculated with modeller with that of the template(s)? If the quality of the model is really worse something might be wrong with your alignment. Did you do the manual adjustment of the input alignment on basis of the analysis of the quality of the first models? This usually helps a lot. I do not think that it is necessary to use charmm or another external molecular mechanics package to improve the quality of your model. Modeller actually uses (an older version of) the charmm force field for the molecular mechanics part of the optimization. Best, Oliver Modeller Care wrote: >------ Forwarded Message > >From: Denis Volkov <D.Volkov(a)artcustoms.ru> >X-Mailer: The Bat! (v1.52f) >Reply-To: Denis Volkov <D.Volkov(a)artcustoms.ru> >X-Priority: 3 (Normal) >Message-ID: <43123585810.20030902125313(a)artcustoms.ru> >To: modeller <modeller_usage(a)salilab.org> >Subject: model_refinment > > >Hello everyone, >I successfully used Modeller to model unknown protein. Now I'd like >to sent my model to Protein Data Bank. So i checked my structure >using Procheck and find some problems, namely some bad contacts,etc. >In order to clean a structure i used Charmm program for energy >minimization. But after it i obtain structure with bad angles and >bond lengths. Can anybody know how to clean a structure well for >PDBank and what programs should be use for it. >Thanks in advance >Denis Volkov > >Enzyme Laboratory,IBCH RAS > > > > -- ____________________________________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific Ave Seattle, WA 98195 T:(206)685-7046 _______________________________ ----- End forwarded message -----

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modeling membrane protein loops
by Modeller Care 02 Sep '03

02 Sep '03

------ Forwarded Message From: Lucy Forrest <lrf2103(a)columbia.edu> Subject: modeling membrane protein loops Hi, In my experience (see ref below) the membrane does not affect modeling loops to any great extent. However, when comparing different loop conformations energetically, if you treat the loop environment as vacuum then will get a much worse prediction than if you use solvation energy terms also. Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions Proteins: Structure, Function, and Genetics Volume 52, Issue 4, Date: September 2003, Pages: 492-509 Lucy R. Forrest, Thomas B. Woolf I can discuss this in more detail if anybody wishes, Lucy Lucy Forrest Honig Lab Department of biochemistry Columbia University New York, NY 10032 >Date: 27 Aug 2003 11:37:52 -0400 >From: Andras Fiser <afiser(a)aecom.yu.edu> >Subject: Re: loop modeling > >Hello, > >It is right. Or as good as it gets, for two reasons, because Modeller >does not account for the environment explicitly anyway and loop modeling >will effect only the loop regions while keeping the rest of the >structure intact, irrespectively of how properly the rest was built. > >You will find a web interface to loop modeling in Modeller at >http://alto.compbio.ucsf.edu/modloop//modloop.html >that may help. > > >best wishes,Andras > >On Wed, 2003-08-27 at 02:32, Moshe Amitay wrote: > > >>Hi all, >>I whuld like your advice: >>I build a model of a membrane protein and I want now to do "loop modeling" >>to few extra cellular and intra-cellular loops. >> I wonder if this protocol of modeller is the right >>choice since the model doesn't contain the membrane and I actually ignore >>the influence of the polar heads. >> thank's >> Moshe Amity. >> >> >> >> >> ------ End of Forwarded Message

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model_refinement
by Modeller Care 02 Sep '03

02 Sep '03

------ Forwarded Message From: Denis Volkov <D.Volkov(a)artcustoms.ru> X-Mailer: The Bat! (v1.52f) Reply-To: Denis Volkov <D.Volkov(a)artcustoms.ru> X-Priority: 3 (Normal) Message-ID: <43123585810.20030902125313(a)artcustoms.ru> To: modeller <modeller_usage(a)salilab.org> Subject: model_refinment Hello everyone, I successfully used Modeller to model unknown protein. Now I'd like to sent my model to Protein Data Bank. So i checked my structure using Procheck and find some problems, namely some bad contacts,etc. In order to clean a structure i used Charmm program for energy minimization. But after it i obtain structure with bad angles and bond lengths. Can anybody know how to clean a structure well for PDBank and what programs should be use for it. Thanks in advance Denis Volkov Enzyme Laboratory,IBCH RAS -- Best regards, Denis mailto:D.Volkov@artcustoms.ru ------ End of Forwarded Message

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modeller_usage September 2003