[phenixbb] running geometry regularization on side chains only

Francois Berenger berenger at riken.jp
Wed Jul 27 22:48:00 PDT 2011

On 07/28/2011 03:39 AM, Nathaniel Echols wrote:
> On Tue, Jul 26, 2011 at 11:48 PM, Francois Berenger<berenger at riken.jp>  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.


> -Nat
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