Hi all, I seem to be having a problem specifying the labels for the Hires dataset for an Autobuild run. Here is my input script: input_data_file sharp.mtz input_labels 'Fdm' 'SIGFPsha' 'PHIdm' 'FOMdm' 'HLAdm' 'HLBdm' 'HLCdm' 'HLDdm' 'FreeR_flag' input_pdb_file ab.pdb input_seq_file seq.dat input_hires_file output.native.sca Here is the error from the AutoBuild.log file: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************ I've tried to use the mtz file from the ImportRawData_run directory and specify the columns by substituting the last line in my input script file with: input_hires_file output_PHX.mtz input_hires_labels 'output.native' 'SIGoutput.native' which are the only labels I could find from mtzdump and that doesn't work either. What am I missing here? Any suggestions would be greatly appreciated. Thanks, Troy
Hi Troy, I'm sorry for this problem! This sounds like my problem, not yours...but first can you make sure that you have the most recent version of PHENIX? If you type phenix.version it should say something like; Version: 1.3b Release tag: rc3 If that is ok (or if it still does this when you use that version), then I have to fix something. I tried to make something very similar on my machine: input_data_file fobs.mtz input_labels 'FP' 'SIGFP' 'PHIM' 'FOMM' 'HLAM' 'HLBM' 'HLCM' 'HLDM' 'FreeR_flag' input_pdb_file coords.pdb input_seq_file seq.dat input_hires_file w1.sca and this worked fine with the command: phenix.runWizard AutoBuild test.inp If all this does not solve the problem, can you possibly send me the input files and I'll try to duplicate the problem here? Thanks! -Tom T
Hi all,
I seem to be having a problem specifying the labels for the Hires dataset for an Autobuild run.
Here is my input script: input_data_file sharp.mtz input_labels 'Fdm' 'SIGFPsha' 'PHIdm' 'FOMdm' 'HLAdm' 'HLBdm' 'HLCdm' 'HLDdm' 'FreeR_flag' input_pdb_file ab.pdb input_seq_file seq.dat input_hires_file output.native.sca
Here is the error from the AutoBuild.log file: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************
I've tried to use the mtz file from the ImportRawData_run directory and specify the columns by substituting the last line in my input script file with: input_hires_file output_PHX.mtz input_hires_labels 'output.native' 'SIGoutput.native'
which are the only labels I could find from mtzdump and that doesn't work either. What am I missing here? Any suggestions would be greatly appreciated.
Thanks, Troy _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi, this was discussed some time ago (a few years?) on ccp4: is there a way (even a fudge) to restrain a refinement at low resolution to an existing (much) higher resolution model? The scenario: you have a 1.9A structure, beautiful etc. You do a ligand soak, get 2.6A data, and only really want to see what's in the active site. This requires refinement (to improve phases), but most of the structure shouldn't change (often the case, especially if it's the the same crystal form). So you only want things to change that really are different. Thanks phx
Hi Frank, this is not available in phenix.refine but it sounds like very easy to do implement. I will put it in my to-do list. Pavel Frank von Delft wrote:
Hi, this was discussed some time ago (a few years?) on ccp4: is there a way (even a fudge) to restrain a refinement at low resolution to an existing (much) higher resolution model?
The scenario: you have a 1.9A structure, beautiful etc. You do a ligand soak, get 2.6A data, and only really want to see what's in the active site. This requires refinement (to improve phases), but most of the structure shouldn't change (often the case, especially if it's the the same crystal form). So you only want things to change that really are different.
Thanks phx _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
I guess that you could do it the with the tools that are available,
but would require some scripting to get it going, and will be
relatively slow and possibly not recommended.
phenix.refine allows the possibility to add distance restraints
between any atom specified:
http://www.phenix-online.org/documentation/refinement.htm#anch281
what you could do, is take the high resolution structure you have,
find all 1-4 distances that you think should (not around the active
site) be invariant (this is the scripting bit) and write them out as a
custom bond with an appropriate sigma and feed this into
phenix.refine. This scheme is similar to the NCS restraints in shelx i
belive.
Again, this is possible, but not sure if recommended.
There are probably other (possibly better) ways of doing it as well.
Peter
2007/10/11, Frank von Delft
Hi, this was discussed some time ago (a few years?) on ccp4: is there a way (even a fudge) to restrain a refinement at low resolution to an existing (much) higher resolution model?
The scenario: you have a 1.9A structure, beautiful etc. You do a ligand soak, get 2.6A data, and only really want to see what's in the active site. This requires refinement (to improve phases), but most of the structure shouldn't change (often the case, especially if it's the the same crystal form). So you only want things to change that really are different.
Thanks phx _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (5)
-
Frank von Delft -
Pavel Afonine -
Peter Zwart -
Thomas C. Terwilliger -
Troy E Messick