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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