Forwarding to list.
----- Forwarded message from Denis Volkov email@example.com -----
Date: Thu, 11 Sep 2003 14:15:18 +0400 From: Denis Volkov firstname.lastname@example.org X-Mailer: The Bat! (v1.52f) Organization: IBCH To: email@example.com Subject: Re: model_refinement
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
I have inserted my comments in your text:
Modeller Caretaker wrote:
>Forwarding to list. > >----- Forwarded message from Denis Volkov firstname.lastname@example.org ----- > >Date: Thu, 11 Sep 2003 14:15:18 +0400 >From: Denis Volkov email@example.com >X-Mailer: The Bat! (v1.52f) >Organization: IBCH >To: firstname.lastname@example.org >Subject: Re: model_refinement > >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. > You can run procheck on all 4 templates to get a feeling for the best quality you can expect from your model. Why not? How did you check the alignment. My experience is that, if the sequence alignment suggests an alignment of a segment of the target sequence with all templates, it is important that the template structures are really very similar for this segment. I.e. you need to check the alignment on basis of the superposed template structures.
>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? > > I would not expect too much of a model based on sequence identity with the templates in the range of 20 percent. Did you do the MD without any restraints? You could apply restraints on the regions of your model which you expect to be correct based on the alignment - in case this makes any sense with respect to the problem you are investigating. I would not expect a stable MD without restraints for a model on basis of 20% identity with the templates. But this actually is only my guess. In general one can usually not expect a homology model to get closer to the actual (experimental) structure by doing a MD simulation (see Proteins 48 (4): 593-604 SEP 1 2002).
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 _______________________________