[phenixbb] prime_and_switch, error in input mtz label assignment

[Pavel Afonine]

Hi Tanya,

a typical suggestion in this case (before trying anything else) is to 
get and install the latest PHENIX which is 1.5-2 (1.3 is horribly old) 
and try to run your command again. Hopefully, the error goes away by 
itself, and please let us (Tom specifically) if updating to the latest 
did not help.

Pavel.


On 10/6/09 10:01 PM, Tatyana Sysoeva wrote:
> Dear all,
>
> I have a question to your kindest attention.
>
> We were trying to run today phenix on distant cluster (phenix-1.3) 
> with next command line
>
> /phenix.autobuild data=data.mtz solvent_fraction=0.6 
> ps_in_rebuild=True   \
> input_pdb_file=model.pdb maps_only=True/
>
> Autobuild failed with these last lines in the Autobuild_run_1_1.log
>
> Failed to carry out AutoBuild_multiple_models:
>
> /Sorry, subprocess failed...message is:
> ********************************************************************************
> phenix.autobuild   \
>
> write_run_directory_to_file=/home/btn1/tn_phenix/refine/final_loops/with_ncs_H/no_wateradd_noH/prime_switch/AutoBuild_run_1_/TEMP0/INFO_FILE_1 
>
> Reading effective parameters from 
> /home/btn1/tn_phenix/refine/final_loops/with_ncs_H/no_wateradd_noH/prime_switch/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
> ********************************************************************************
> /
> in Autobuild_run_1_/TEMP0/Autobuild_run_1_/Autobuold_run_1_1.log the 
> failure message is next:
>
> /Columns of data in AutoBuild_run_1_/TEMP0/TEMP.mtz:
> H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT
> child process stderr output:
>   command: 'AutoBuild_run_1_/TEMP0/temporary.com <http://temporary.com>'
>    resolve_giant:  Error in label assignments
> Failed to run resolve
> ----------------------------------
> TRIED resolve_giant ...but not OK
>
> ********************************************************************************
> Failed to carry out AutoBuild_build_cycle:
>
> failure
> ********************************************************************************
> /
>
> There are temporary.com <http://temporary.com> and temporary.com.bak 
> in the folder and there is only difference, except that
> in temporary.com <http://temporary.com> there is "labin FP=FP 
> FC=FMODEL PHIC=PH2FOFCWT FWT=2FOFCWT"
> in temporary.com.bak there is "labin FP=FP FC=FMODEL PHIC=PHI2FOFCWT 
> FWT=2FOFCWT"
>
> Prime_and_switch.log file ends with
>
> /Reading SG information from
>  TEMP.mtz                                                                       
>
>  
>  Space group name: P21212     Point group: 222      
>  Space group number :          18  Symmetry operators:            4
>  Number of columns:            9
>  H                             K                            
>  L                             FMODEL                       
>  PHIFMODEL                     FP                           
>  SIGFP                         2FOFCWT                      
>  PH2FOFCWT                    
>  
>  ***  Warning
>  From LRASSN : User input label PHI2FOFCWT does not match any file label
>  
> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
>  resolve_giant:  Error in label assignments
> </pre>
> <!--SUMMARY_END--></FONT></B>
> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> </html>
> <!--SUMMARY_END--></FONT></B>/
>
> I checked created TEMP.mtz, it looks like:
> * Column Labels :
>
>  H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT
>
> So the question is next:  Why is prime_and_switch process looking for 
> the "right" labels (PH2FOFCWT), which are present in previously 
> created TEMP.mtz file,  but sees them wrong (PHI2FOFCWT)? Is this 
> possible that we have somewhat wrong inputs or is there problem with 
> the set of commands?
>
>
> Sincerely,
> Tanya
> /
>
> /
> ------------------------------------------------------------------------
>
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