Forwarding to list.

----- Forwarded message from Denis Volkov themelon@yandex.ru -----

Date: Mon, 8 Sep 2003 17:41:54 +0400 From: Denis Volkov themelon@yandex.ru To: Modeller Caretaker modeller-care@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@u.washington.edu -----

MC> Date: Tue, 02 Sep 2003 10:03:00 -0700 MC> From: Oliver Hucke ohucke@u.washington.edu MC> To: Modeller Care modeller-care@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@artcustoms.ru >>X-Mailer: The Bat! (v1.52f) >>Reply-To: Denis Volkov D.Volkov@artcustoms.ru >>X-Priority: 3 (Normal) >>Message-ID: 43123585810.20030902125313@artcustoms.ru >>To: modeller modeller_usage@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