Re: [phenixbb] running geometry regularization on side chains only

On 07/28/2011 03:39 AM, Nathaniel Echols wrote:

On Tue, Jul 26, 2011 at 11:48 PM, Francois Berenger wrote:

...

Thanks for the workaround Pavel. However, I just wanted to know if it could be done using geometry only with phenix.pdbtools. If it was possible and fast, I or some colleague may have needed to wrap the functionality into some code as a compiled library.

Maybe I should rather look for some tool that can add sidechains to a backbone model (without introducing clashes in the process).

Try PULCHRA (http://www.pirx.com/pulchra/index.shtml) - since it is open-source, we distribute it with Phenix (phenix.pulchra). My guess is it won't be able to avoid all clashes for a poor starting structure, but it is incredibly fast,

I like to encounter such tools: 0.049s to rebuild side-chains of 1M6T as a test case. That's really fast yes. :)

and it can even start from C-alpha coordinates alone. It appears to only work with a single chain at a time, but a little bit of scripting will fix that problem.

Thanks for the suggestion Nathaniel. Regards, Francois.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb