[Chimera-users] dock

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 23 10:20:24 PDT 2013


I forgot to mention:

You can check for clashes with "Find Clashes/Contacts" (in menu under Tools... Structure Analysis) or its command version "findclash":
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

Similarly, you could look at H-bonds using "FindHBond" (or command "findhbond"), although this will not update automatically:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>

There are examples of using Find Clashes/Contacts and FindHBond in the "structure analysis and comparison" tutorial:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

You can save the two models to a single PDB file using "File... Save PDB" and choosing the appropriate options in the save dialog.  If you needed them to be in a single model, you would first need to make a new model containing both those structures using the "combine" command, then save the new model as PDB.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

Elaine

On Apr 23, 2013, at 10:02 AM, Elaine Meng wrote:

> Dear LW,
> Chimera does not do docking calculations.   It is often used to view the results (output) from  docking programs.   You might try asking on a more general molecular-modeling forum such as ccl.net  about which docking program(s) might be good for your situation.
> 
> In Chimera, you could try positioning the structures manually by freezing one in place and moving the other with the mouse, but it can be difficult, and you would have to judge the result simply by eye.  For more details about how to move one structure at a time with the mouse, see:
> 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Apr 22, 2013, at 6:53 PM, LW wrote:
> 
>> Dear all,
>> As attached, I have a structure of Saposin C in the presence of SDS micelle solved using NMR. I took the first model out of its 20-structure ensemble and generated SapC_one_model.pdb. I also have a PDB file(as attached )built to model SDS micelle surrounded by water. Does Chimera allow people to dock these two molecules and generate a combined PDB file for further analysis? While the structure of Saposin C in the presence of SDS micelle, NMR data indicate that the open hydrophobic core is in contact with SDS micelle. Is it possible to use Chimera to determine the relative orientation of the two molecules where (i), they are in intimate contact, (ii), there is no clash, (iii), the shape complementarity is at its optimal?
>> Any clue would be much appreciated.
>> Levi




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