[phenixbb] phenix autobuild question

Tue Sep 16 06:00:57 PDT 2008

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  <aberndt at mrc-lmb.cam.ac.uk>:
> 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
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
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>
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
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