[phenixbb] REMARK 3 NCS

Jeff Headd jjheadd at lbl.gov
Thu Oct 3 07:11:41 PDT 2013


Hi Luca,

Thanks for pointing this out. It looks like I introduced a bug when I
refactored some of the torsion NCS code. I'll work up a fix today which
will be available in the next nightly release.

Jeff


On Thu, Oct 3, 2013 at 3:58 AM, Luca Pellegrini <lp212 at cam.ac.uk> wrote:

> Hi Pavel,
>
> Yes, I am using torsion angle NCS in phenix.refine. I don't mean the NCS
> matrices, but the torsion NCS details. Here's an example of the REMARK 3
> NCS that Phenix 1.8.2-1309 used to write in the PDB header and that have
> disappeared from the PDB header with Phenix 1.8.3-1479 and 1.8.4-1496:
>
> REMARK   3  TORSION NCS DETAILS.
> REMARK   3   NUMBER OF NCS GROUPS : 1
> REMARK   3   NCS GROUP : 1
> REMARK   3     SELECTION          : chain 'A'
> REMARK   3     SELECTION          : chain 'B'
> REMARK   3     RESTRAINED TORSIONS: 4042
> REMARK   3     BELOW LIMIT RMSD   : 0.620
> REMARK   3     ALL RESTRAINT RMSD : 4.081
> REMARK   3    Histogram of differences under limit:
> REMARK   3       0.000 -    1.500: 3932
> REMARK   3       1.500 -    3.000: 87
> REMARK   3       3.000 -    4.500: 5
> REMARK   3       4.500 -    6.000: 4
> REMARK   3       6.000 -    7.500: 1
> REMARK   3       7.500 -    9.000: 0
> REMARK   3       9.000 -   10.500: 0
> REMARK   3      10.500 -   12.000: 0
> REMARK   3      12.000 -   13.500: 1
> REMARK   3      13.500 -   15.000: 0
> REMARK   3    Histogram of differences over limit:
> REMARK   3      15.000 -   22.400: 0
> REMARK   3      22.400 -   29.800: 0
> REMARK   3      29.800 -   37.200: 0
> REMARK   3      37.200 -   44.600: 0
> REMARK   3      44.600 -   52.000: 1
> REMARK   3      52.000 -   59.400: 3
> REMARK   3      59.400 -   66.800: 0
> REMARK   3      66.800 -   74.200: 0
> REMARK   3      74.200 -   81.600: 4
> REMARK   3      81.600 -   89.000: 4
>
> Luca
>
> On 3 Oct 2013, at 00:39, Pavel Afonine wrote:
>
> > Hi Luca,
> >
> > when NCS is enabled phenix.refine uses torsion angle NCS by default..
> This may explain why you don't get NCS matrices in your PDB file. Is that
> the case?
> >
> > Pavel
> >
> > On 10/2/13 1:26 AM, Luca Pellegrini wrote:
> >> Hello,
> >>
> >> I have noticed that Phenix 1.8.4-1496 (as well as 1.8.3-1479) appears
> to have stopped writing the REMARK 3 NCS in the PDB header. Is this so? It
> is useful to have that info when it comes to depositing the coordinates.
> >>
> >> Many thanks,
> >> Luca
> >>
> >> Luca Pellegrini
> >> Department of Biochemistry
> >> University of Cambridge
> >> 80 Tennis Court Road
> >> Cambridge CB2 1GA - UK
> >>
> >> Email: lp212 at cam.ac.uk
> >> Tel: 0044-1223-760469
> >> Fax: 0044-1223-766002
> >> Sanger building, room 3.59
> >>
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
> Luca Pellegrini
> Department of Biochemistry
> University of Cambridge
> 80 Tennis Court Road
> Cambridge CB2 1GA - UK
>
> Email: lp212 at cam.ac.uk
> Tel: 0044-1223-760469
> Fax: 0044-1223-766002
> Sanger building, room 3.59
>
>
>
>
>
>
>
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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
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