Hi Tom, thanks for your answer. I just checked the phenix version I used and it is version-1.3-final. Please find attached the .log file you asked for. I just realised that resolve apparently had a problem with the .mtz label assignment. I never had this problem before. Now that I mention that I have to confess that this is not entirely true. All the phenix tutorials I have looked through so far state that you can use ccp4s mtz the way they are. Yet, this is not entirely true. Say I want to have an analysis from phenix.xtriage by typing 'phenix.xtriage latest.mtz'. So phenix will give me the error message: Multiple equally suitable arrays of observed xray data found. Possible choices: ab_xds_pointless_scala5.mtz:IMEAN_XDSdataset,SIGIMEAN_XDSdataset ab_xds_pointless_scala5.mtz:I_XDSdataset(+),SIGI_XDSdataset(+),I_XDSdataset(-),SIGI_XDSdataset(-),merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. Sorry: Multiple equally suitable arrays of observed xray data found. Is there a way a way to avoid going back to ccp and sorting the labels accordingly. What would be the 'scaling.input.xray_data.obs_labels' command in the xtriage command line? Anyway, Tom, many thanks for your answer in advance! I reaaly like working with phenix. I just need to learn loads more ... Best, Alex
Hi Alex,
I'm sorry for both the failure and the lack of a clear message here! I will try to fix both.
Is this running phenix-1.3-final? (If not, could you possibly run with that version so we are on the same version.)
Can you possibly send me the end of the output in
/someplace/home/someuser/ work/someproject/phenix2/AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/AutoBuild_run_1_1.log
which I hope will have an actual error message to look at?
The reason for the subdirectories is this: phenix.autobuild runs several jobs in parallel (if you have set nproc ) or one after the other (if you have not set nproc). These subdirectories contain those jobs...which are then combined together to give the final results in your overall AutoBuild_run_1_/ directory.
I don't know the answer to the phenix.refine question...perhaps Pawel or Ralf can answer that one.
All the best, Tom T
Dear phenix community,
I started an AutoBuild run using the phenix GUI (ver 1.3 rc4) on a linux cluster. It worked okay and all the refinement looked pretty decent. However, after quite a while I obtained the following error message (see below). Would anyone please tell me what to do to prevent this error and get phenix get its job finished?
Also, I don't understand why phenix AutoBuild creates 5 (or whatever number) AutoBuild_run_x in the AutoBuild-run_1/TEMP0 directory and not two dirs up in the tree. In other words in my /someplace/home/someuser/ work/someproject/phenix2/AutoBuild_run_1_/TEMP0 directory are more AutoBuild_run_x_ directories (with x=1 to 5). It is a bit confusing to me.
A final question: I realised that the phenix.refine drastically increases the number of outliers. I know that thare is a weighting term someplace ... but what was it again?
Many thanks in advance, Alex
warnings Failed to carry out AutoBuild_multiple_models: Sorry, subprocess failed...message is: ******************************************************************************** phenix.autobuild \
write_run_directory_to_file=/someplace/home/someuser/work/someproject/ phenix2/AutoBuild_run_1_/TEMP0/INFO_FILE_1
Reading effective parameters from /someplace/home/someuser/work/ someproject/phenix2/AutoBuild_run_1_/TEMP0/PARAMS_1.eff
Sending output to AutoBuild_run_1_/AutoBuild_run_1_1.log
********************************************************************************
Failed to carry out AutoBuild_build_cycle:
failure
********************************************************************************
********************************************************************************
work_pdb_file "AutoBuild_run_1_/edited_pdb.pdb" working_directory "/someplace/home/someuser/work/someproject/phenix2" worst_percent_res_rebuild 2.0
--------------------------------------------------- Alex Berndt MRC-Laboratory of Molecular Biology Hills Road Cambridge, CB2 0QH U.K.
phone: +44 (0)1223 402113 ---------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb