[phenixbb] Selection of Torsion NCS restraint groups

Pavel Afonine pafonine at lbl.gov
Sat Oct 3 21:10:16 PDT 2015


could you please send me the PDB file so I can reproduce what you 


On 10/3/15 09:40, Victor Xiao wrote:
> Hi All,
> I just have tried to run phenix.refine after designating the NCS 
> groups, and it actually worked as I expected. So only is the display 
> not correct (all chains are shown in every NCS groups) when I re-open 
> ''Detect NCS Groups'. Maybe it is a bug?
> Xiao
> 2015-10-02 22:23 GMT-07:00 Victor Xiao <victor41187 at gmail.com 
> <mailto:victor41187 at gmail.com>>:
>     Dear all,
>     I have a protein-DNA structure that has six molecules in ASU. All
>     six molecules share the same sequence and very similar structure.
>     However, only three of them bind to DNA and conformations are
>     slightly different from the other three. By default, PHENIX will
>     consider six molecules into the same NCS group. Now I am trying to
>     set up two NCS group, e.g. chain A,B,C are in one group (no-DNA),
>     chain D, E, F are in another group (DNA-bound).
>     So I did the following steps:
>     1. I used PHENIX GUI and go to 'Utilities' -> 'Detect NCS Groups'.
>     2. Put chain A, B, C in 'Torsion NCS restraint group 1'.
>     3. 'Add group' and put chain D, E, F in 'Torsion NCS restraint
>     group 2'.
>     4. Click 'Update and exit'.
>     However, after that, when I re-open  'Utilities' -> 'Detect NCS
>     Groups', I found all six chains A-F are in group 1, and all six
>     chains A-F in group 2.
>     Did I do something incorrectly? Or any other suggestion for my
>     purpose?
>     Thank you!
>     Best,
>     Xiao
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