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: [email protected] Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59
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: [email protected] Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59
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: [email protected] Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: [email protected] Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59
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
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: [email protected] Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK
Email: [email protected] Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Jeff Headd -
Luca Pellegrini -
Pavel Afonine