side-chains like in template
Hello,
I want to create a model based on two templates. How can I constraint few selected positions, so they would preserve (if possible) side-chain conformation of one of the templates?
Thanks for hints, sdh
On 5/31/10 8:25 AM, sdh wrote: > I want to create a model based on two templates. How can I constraint > few selected positions, so they would preserve (if possible) side-chain > conformation of one of the templates?
Modeller doesn't really work this way for sidechains, particularly when you have multiple templates. The restraints don't act to make the sidechains look like the templates, merely to keep them in an appropriate class (energy well). But if you want to keep a certain sidechain in a certain conformation, you can add your own restraints to do that.
Ben Webb, Modeller Caretaker
On Tue, 2010-06-01 at 10:32 -0700, Modeller Caretaker wrote: > On 5/31/10 8:25 AM, sdh wrote: > > I want to create a model based on two templates. How can I constraint > > few selected positions, so they would preserve (if possible) side-chain > > conformation of one of the templates? > > Modeller doesn't really work this way for sidechains, particularly when > you have multiple templates. The restraints don't act to make the > sidechains look like the templates, merely to keep them in an > appropriate class (energy well). But if you want to keep a certain > sidechain in a certain conformation, you can add your own restraints to > do that. >
Thank you for the answer. Could you tell me which functions should I use? (function names will be enough, I just want to know where to start)
Best wishes, Staszek
On 6/1/10 10:40 AM, sdh wrote: > On Tue, 2010-06-01 at 10:32 -0700, Modeller Caretaker wrote: >> On 5/31/10 8:25 AM, sdh wrote: >>> I want to create a model based on two templates. How can I constraint >>> few selected positions, so they would preserve (if possible) side-chain >>> conformation of one of the templates? >> >> Modeller doesn't really work this way for sidechains, particularly when >> you have multiple templates. The restraints don't act to make the >> sidechains look like the templates, merely to keep them in an >> appropriate class (energy well). But if you want to keep a certain >> sidechain in a certain conformation, you can add your own restraints to >> do that. >> > > Thank you for the answer. Could you tell me which functions should I > use? (function names will be enough, I just want to know where to start)
Override the special_restraints method: http://salilab.org/modeller/9v8/manual/node27.html
Ben Webb, Modeller Caretaker
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