[phenixbb] REMARK 3 NCS

[Luca Pellegrini]

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
>> 
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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