[phenixbb] constrain insertion codes to unit occupancy?

van den Bedem, Henry vdbedem at slac.stanford.edu
Wed Oct 19 21:47:42 PDT 2016

Hi Pavel,

Thanks! Yes, several others privately also pointed me to the newsletter. It’s precisely our scenario. Dropping the insertion codes solved my problem.


From: Pavel Afonine <pafonine at lbl.gov>
Date: Tuesday, October 18, 2016 at 4:53 AM
To: Christian Roth <christianroth034 at gmail.com>, "van den Bedem, Henry" <vdbedem at slac.stanford.edu>, "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] constrain insertion codes to unit occupancy?

Hi Henry,

first off you don't need to use insertion codes to do what you are trying to do.

Second, it looks like this scenario is described in section 5 here (page 42):

"13 typical occupancy refinement scenarios and available options in phenix.refine"

Please let me know if this is not your case, or it is still not clear, or you need help with this anyway..

Good luck,
On 10/17/16 11:05, Christian Roth wrote:

Hi Henry,

have you created a proper constraint group including both compounds as described in the manual under special cases for occupancy refingement? That should work, I presume.



Am 15.10.2016 um 22:15 schrieb van den Bedem, Henry:

I’m refining a site where there’s two compounds, each at partial occupancy. I modeled that using alt codes and insertion codes combined, like this

ATOM   6500  CA ACYS B 101B
ATOM   6490  CA BXXX B 101A

How can I constrain the occupancies so that they sum to unity? I tried several option, but the distinct insertions seem to refine independently. Sorry if a similar question has been posted before, but I could not find a solution searching phenixbb.



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20161020/d0f17db7/attachment.htm>

More information about the phenixbb mailing list