Hi, Try this (substring matching in action): phenix.xtriage ab_xds_pointless_scala5.mtz obs_labels=+ or phenix.xtriage ab_xds_pointless_scala5.mtz obs=M HTH P 2008/9/15 :

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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

-- ----------------------------------------------------------------- P.H. Zwart Beamline 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 CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

sorry, i just realised what EW meant, sorry, yeah, EW ;)) a

Hi, Is it the Dortmund Alex from AG EW? :) Cheers, Partha

On Mon, Sep 15, 2008 at 7:11 PM, Alex Berndt wrote:

...

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

-- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [email protected] Phone: + 44 208 816 2515 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb