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'
 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 and temporary.com.bak in the folder and there is only difference, except that
in 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


resolve_giant: Error in label assignments
</pre>


</html>


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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