Final reminder: 2008 Crystallographic Computing School
The registration deadline for the 2008 Crystallographic Computing School is in two days: *** July 25 *** The schedule of the program including abstracts from all speakers is available here: http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html This program puts a strong weight on fostering one-on-one interactions. There will be only 16 lectures of 45 minutes each (12 hours total) but more than 20 hours of tutorials and demonstrations. Don't miss this unique opportunity for close interaction with the developer community! On behalf of the organizing committee: A. L. Spek (Utrecht University , Netherlands) R. Grosse-Kunstleve (LBNL, USA) M. Yao (Hokkaido University, Japan) A. Nakagawa (Osaka Institute of Protein, Japan) H. Powell (MRC, UK) L. Cranswick (NRC , Canada)
Hi I have been using a SePeak.hkl file in my refinement (CNS, and then switched to Phenix). This was created from SePeak.sca to SePeak.mtz and then to SePeak.hkl with ccp4i's (scalepack2mtz and mtz2various). I want to try using the group anomalous command to see is my Rfree decrease with the inclusion of the anomolous data. The problem I am encountering is that the SePeak.hkl contains no anomolous inforomation. If I make a new mtz (I have used reflection_file_converter to create a new SePeak#2.mtz from my original SePeak.sca and this does contain + and - columns) I can't find a way to merge the test set from the SePeak.hkl file. And generating a new test set raises othere issue that have been discussed in this bb before. Does this make sense? And is there a way to merge a test set from one file and a F or I obs. Mark
2008/7/23 Mark Collins
Hi I have been using a SePeak.hkl file in my refinement (CNS, and then switched to Phenix).
This was created from SePeak.sca to SePeak.mtz and then to SePeak.hkl with ccp4i's (scalepack2mtz and mtz2various). I want to try using the group anomalous command to see is my Rfree decrease with the inclusion of the anomolous data.
The problem I am encountering is that the SePeak.hkl contains no anomolous inforomation. If I make a new mtz (I have used reflection_file_converter to create a new SePeak#2.mtz from my original SePeak.sca and this does contain + and - columns) I can't find a way to merge the test set from the SePeak.hkl file. And generating a new test set raises othere issue that have been discussed in this bb before.
Does this make sense? And is there a way to merge a test set from one file and a F or I obs.
Mark _______________________________________________
Dear Mark, I believe your could simply define explicitly the columns in your input .def file for phenix.refine, I have done so previously with great succes. I guess the keywords you are looking for is: xray_data.file_name xray_data.labels xray_data.r_free_flags.file_name xray_data.r_free_flags.label And phenix.refine should put it in a nice .mtz file for you :-) Hope this helps. Regards, Folmer
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Hello again, I'm still seem to have a problem with merging these files. I tried this in my .params file but phenix can't use my test set, any suggestions appreciated? input { xray_data { file_name = ../testmtz.mtz labels = "I(+),SIGI(+),I(-),SIGI(-)" r_free_flags { file_name = ../SePeak.hkl label = TEST test_flag_value = 1 }} Sorry: R-free flags not compatible with F-obs array: missing flag for 2 F-obs selected for refinement. This appears to arise from the SePeak.hkl having Number of Miller indices: 9198 but the testmtz.mtz having Number of Miller indices: 9199 (where is the extra reflection coming from?) by converting the SePeak.hkl to an mtz and dumping, I get SePeak.hkl.mtz and testmtz.mtz label #valid %valid min max type H 9198 100.00% 0.00 14.00 H: index h,k,l K 9198 100.00% 0.00 10.00 H: index h,k,l L 9198 100.00% 0.00 135.00 H: index h,k,l hkl 9198 100.00% 0.00 1.00 I: integer H 9199 100.00% 0.00 14.00 H: index h,k,l K 9199 100.00% 0.00 10.00 H: index h,k,l L 9199 100.00% 0.00 135.00 H: index h,k,l I(+) 9199 100.00% -39.40 32280.10 K: I(+) or I(-) SIGI(+) 9199 100.00% -1.00 771.20 M: standard deviation I(-) 6529 70.98% -32.00 16383.20 K: I(+) or I(-) SIGI(-) 6529 70.98% 5.20 293.30 M: standard deviation Thanks Mark
Dear Mark,
I believe your could simply define explicitly the columns in your input .def file for phenix.refine, I have done so previously with great succes.
I guess the keywords you are looking for is: xray_data.file_name xray_data.labels xray_data.r_free_flags.file_name xray_data.r_free_flags.label
And phenix.refine should put it in a nice .mtz file for you :-)
Hope this helps.
Regards, Folmer
phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Folmer Fredslund -
Mark Collins -
Ralf W. Grosse-Kunstleve