Will phenix.refine read CNS *.cv files?
Hi all, I'm embarking on a collaboration with someone who is providing me with CNS cross validated data files. They look something like this. NREFlection= 92086 ANOMalous=FALSe { equiv. to HERMitian=TRUE} DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 SIGI= 293.800 TEST= 0 INDE 4 0 0 FOBS= 158.996 SIGMA= 2.329 IOBS= 25279.600 SIGI= 735.200 TEST= 0 INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= 0.242506E+06 SIGI= 17098.000 TEST= 0 INDE 7 0 0 FOBS= 246.492 SIGMA= 3.127 IOBS= 60758.400 SIGI= 1531.800 TEST= 0 INDE 8 0 0 FOBS= 32.790 SIGMA= 0.549 IOBS= 1075.200 SIGI= 35.700 TEST= 1 INDE 9 0 0 FOBS= 426.866 SIGMA= 8.886 IOBS= 0.182215E+06 SIGI= 7507.000 TEST= 0 INDE 10 0 0 FOBS= 411.347 SIGMA= 8.597 IOBS= 0.169206E+06 SIGI= 6999.000 TEST= 0 INDE 11 0 0 FOBS= 87.275 SIGMA= 1.346 IOBS= 7617.000 SIGI= 233.200 TEST= 0 When I try to run phenix.refine --dry_run my_model.pdb my_CNS_cv_file.cv I get the following error: Processing inputs. This may take a minute or two. Sorry: Unknown file format: my_CNS_cv_file.cv Any ideas? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Hi Scott,
When I try to run phenix.refine --dry_run my_model.pdb my_CNS_cv_file.cv
I get the following error:
Processing inputs. This may take a minute or two. Sorry: Unknown file format: my_CNS_cv_file.cv
Any ideas?
Please try this command: iotbx.cns.reflection_reader my_CNS_cv_file.cv Hopefully this will give you a better error message. phenix.refine should read your file if the format is correct. Let me know if this doesn't help. Ralf
Thanks Ralf, I received this error: iotbx.cns.reflection_reader.CNS_input_Error: line 1, word "REMARK": unrecognized keyword I then deleted the 4 lines of remarks from the top of the cv file and now it works! ... automagically, just as I was hoping. Thanks^6, Scott On Jan 14, 2009, at 5:38 PM, Ralf W. Grosse-Kunstleve wrote:
Hi Scott,
When I try to run phenix.refine --dry_run my_model.pdb my_CNS_cv_file.cv
I get the following error:
Processing inputs. This may take a minute or two. Sorry: Unknown file format: my_CNS_cv_file.cv
Any ideas?
Please try this command:
iotbx.cns.reflection_reader my_CNS_cv_file.cv
Hopefully this will give you a better error message.
phenix.refine should read your file if the format is correct.
Let me know if this doesn't help.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iotbx.cns.reflection_reader.CNS_input_Error: line 1, word "REMARK": unrecognized keyword
Doesn't this lead to CNS error messages as well? -- But CNS probably keeps running. You can keep the remarks in the file if you replace REMARK with exclamation marks.
I then deleted the 4 lines of remarks from the top of the cv file and now it works! ... automagically, just as I was hoping.
Great! Ralf
participants (2)
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Ralf W. Grosse-Kunstleve -
Scott Classen