stuck with phenix refine
Hi I am working with a twinned data set having R32 space group. when i tried to refine with phenix refine using the twin option it got stuck after some time. There is no error message showing up and the refinemnet donot progresses further. I have used the twin law suggested by Xtriage program in Phenix. Kindly help me out. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
please send me xtriage logfile and refinement logs off list so I can
help you further.
P
On 19 August 2010 00:05, intekhab alam
Hi I am working with a twinned data set having R32 space group. when i tried to refine with phenix refine using the twin option it got stuck after some time. There is no error message showing up and the refinemnet donot progresses further. I have used the twin law suggested by Xtriage program in Phenix. Kindly help me out.
Regards
-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
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-- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------
On Thu, Aug 19, 2010 at 12:05 AM, intekhab alam
I am working with a twinned data set having R32 space group. when i tried to refine with phenix refine using the twin option it got stuck after some time. There is no error message showing up and the refinemnet donot progresses further. I have used the twin law suggested by Xtriage program in Phenix. Kindly help me out.
GUI or command line, and which version? There are a few cases in which errors are not handled correctly when run from the GUI - this would result in the behavior you describe. I think I've fixed them all now, but this may not be the case in the version you're using. -Nat
Hi try to unstuck it. Pavel. PS> Sending a log file or more details about what exactly is happening and what exactly you did would more likely result in a more useful reply -:) On 8/19/10 12:05 AM, intekhab alam wrote:
Hi I am working with a twinned data set having R32 space group. when i tried to refine with phenix refine using the twin option it got stuck after some time. There is no error message showing up and the refinemnet donot progresses further. I have used the twin law suggested by Xtriage program in Phenix. Kindly help me out. Regards
-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Intekhab, thanks for sending the files. Your log file shows you are refining at 2.7A resolution and the R-factors are 24/26% (which is not bad!), and the parameters you use are main { fix_rotamers = True simulated_annealing_torsion = True number_of_macro_cycles = 5 max_number_of_resolution_bins = 10 use_experimental_phases = False } . Try this instead: main { number_of_macro_cycles = 5 ordered_solvent=true } ordered_solvent { mode = *every_macro_cycle } Does phenix.model_vs_data confirms the need to use twin-target: phenix.model_vs_data model.pdb data.mtz ? Pavel. On 8/19/10 12:05 AM, intekhab alam wrote:
Hi I am working with a twinned data set having R32 space group. when i tried to refine with phenix refine using the twin option it got stuck after some time. There is no error message showing up and the refinemnet donot progresses further. I have used the twin law suggested by Xtriage program in Phenix. Kindly help me out. Regards
-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
I tried with the steps suggested by Pavel and it seems working, !!
Thank You guys for your interest!!
Regards
Intekhab Alam
On Fri, Aug 20, 2010 at 1:18 AM, Pavel Afonine
Hi Intekhab,
thanks for sending the files.
Your log file shows you are refining at 2.7A resolution and the R-factors are 24/26% (which is not bad!), and the parameters you use are
main { fix_rotamers = True simulated_annealing_torsion = True number_of_macro_cycles = 5 max_number_of_resolution_bins = 10 use_experimental_phases = False } .
Try this instead:
main { number_of_macro_cycles = 5 ordered_solvent=true } ordered_solvent { mode = *every_macro_cycle }
Does phenix.model_vs_data confirms the need to use twin-target:
phenix.model_vs_data model.pdb data.mtz
?
Pavel.
On 8/19/10 12:05 AM, intekhab alam wrote:
Hi I am working with a twinned data set having R32 space group. when i tried to refine with phenix refine using the twin option it got stuck after some time. There is no error message showing up and the refinemnet donot progresses further. I have used the twin law suggested by Xtriage program in Phenix. Kindly help me out.
Regards
-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
_______________________________________________ phenixbb mailing list [email protected]http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
participants (4)
-
intekhab alam -
Nathaniel Echols -
Pavel Afonine -
Peter Zwart