Error in phenix.autobuild

Tanner, John J.

27 Jun 2012 27 Jun '12

1:25 p.m.

Can anyone shed light on the error below? The situation is that I have a ~90% complete model from refinement (r_work = 0.2415, r_free = 0.3167), and I want phenix.autobuild to build the rest of the structure. I issued this command: phenix.autobuild data=../ccp4/DrPRODH3-6_1_scala2.6Ang.mtz model=Refine_9/DrPRODH_refine_9.pdb seq_file=../seq/DrPRODH-noMet1.fasta rebuild_in_place=False nproc=3 I got this error: [tannerjj@europa AutoBuild_run_2_]$ tail -n20 AutoBuild_run_2_1.log Output space group: P 1 21 1 (No. 4) Columns of data in AutoBuild_run_2_/refinement_PHX.mtz: H K L FreeR_flag F_DrPRODH3-6 SIGF_DrPRODH3-6 Unit cell: (46.806, 95.875, 70.504, 90, 107.733, 90) Space group: P 1 21 1 (No. 4) Using AutoBuild_run_2_/refinement_PHX.mtz for refinement Correcting data file /titan/tanner/DrPRODH/ccp4/DrPRODH3-6_1_scala2.6Ang.mtz for anisotropy and writing to AutoBuild_run_2_/aniso_data_PHX.mtz Getting overall aniso B from datafile... *************ERROR ENDING ******************* **************************************** AutoBuild Input failed iotbx InternalError: /net/longnose/scratch2/phenix/phenix-1.7.3-928/cctbx_project/iotbx/mtz/dataset.cpp(97): IOTBX_ASSERT(strlen(label) < sizeof(column_ptr->label)) failure. **************************************** *************ERROR ENDING *******************

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Terwilliger, Thomas C

27 Jun 27 Jun

1:43 p.m.

Hi John, I'm sorry, that error certainly needs fixing. Presumably there is something slightly unusual in your data that triggered it...might it be possible to send me that data file off-list ([email protected]) and I'll have a look? All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Tanner, John J. [[email protected]] Sent: Wednesday, June 27, 2012 10:25 AM To: PHENIX user mailing list Subject: [phenixbb] Error in phenix.autobuild Can anyone shed light on the error below? The situation is that I have a ~90% complete model from refinement (r_work = 0.2415, r_free = 0.3167), and I want phenix.autobuild to build the rest of the structure. I issued this command: phenix.autobuild data=../ccp4/DrPRODH3-6_1_scala2.6Ang.mtz model=Refine_9/DrPRODH_refine_9.pdb seq_file=../seq/DrPRODH-noMet1.fasta rebuild_in_place=False nproc=3 I got this error: [tannerjj@europa AutoBuild_run_2_]$ tail -n20 AutoBuild_run_2_1.log Output space group: P 1 21 1 (No. 4) Columns of data in AutoBuild_run_2_/refinement_PHX.mtz: H K L FreeR_flag F_DrPRODH3-6 SIGF_DrPRODH3-6 Unit cell: (46.806, 95.875, 70.504, 90, 107.733, 90) Space group: P 1 21 1 (No. 4) Using AutoBuild_run_2_/refinement_PHX.mtz for refinement Correcting data file /titan/tanner/DrPRODH/ccp4/DrPRODH3-6_1_scala2.6Ang.mtz for anisotropy and writing to AutoBuild_run_2_/aniso_data_PHX.mtz Getting overall aniso B from datafile... *************ERROR ENDING ******************* **************************************** AutoBuild Input failed iotbx InternalError: /net/longnose/scratch2/phenix/phenix-1.7.3-928/cctbx_project/iotbx/mtz/dataset.cpp(97): IOTBX_ASSERT(strlen(label) < sizeof(column_ptr->label)) failure. **************************************** *************ERROR ENDING ******************* _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Tanner, John J.

5:51 p.m.

Seeing "IOTBX_ASSERT(strlen(label)" in the error message with fresh eyes this afternoon prompted me to shortened the data labels to F and SIGF. Now it works. Go figure...

...

From: Chemistry Department Reply-To: PHENIX user mailing list Date: Wed, 27 Jun 2012 16:25:13 +0000 To: PHENIX user mailing list Subject: [phenixbb] Error in phenix.autobuild

Can anyone shed light on the error below? The situation is that I have a ~90% complete model from refinement (r_work = 0.2415, r_free = 0.3167), and I want phenix.autobuild to build the rest of the structure.

I issued this command:

phenix.autobuild data=../ccp4/DrPRODH3-6_1_scala2.6Ang.mtz model=Refine_9/DrPRODH_refine_9.pdb seq_file=../seq/DrPRODH-noMet1.fasta rebuild_in_place=False nproc=3

I got this error:

[tannerjj@europa AutoBuild_run_2_]$ tail -n20 AutoBuild_run_2_1.log

Output space group: P 1 21 1 (No. 4) Columns of data in AutoBuild_run_2_/refinement_PHX.mtz: H K L FreeR_flag F_DrPRODH3-6 SIGF_DrPRODH3-6 Unit cell: (46.806, 95.875, 70.504, 90, 107.733, 90) Space group: P 1 21 1 (No. 4) Using AutoBuild_run_2_/refinement_PHX.mtz for refinement

Correcting data file /titan/tanner/DrPRODH/ccp4/DrPRODH3-6_1_scala2.6Ang.mtz for anisotropy and writing to AutoBuild_run_2_/aniso_data_PHX.mtz

Getting overall aniso B from datafile...

*************ERROR ENDING *******************

**************************************** AutoBuild Input failed iotbx InternalError: /net/longnose/scratch2/phenix/phenix-1.7.3-928/cctbx_project/iotbx/mtz/dataset .cpp(97): IOTBX_ASSERT(strlen(label) < sizeof(column_ptr->label)) failure. **************************************** *************ERROR ENDING *******************

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

Nathaniel Echols

5:57 p.m.

On Wed, Jun 27, 2012 at 1:51 PM, Tanner, John J. wrote:

...

Seeing "IOTBX_ASSERT(strlen(label)" in the error message with fresh eyes this afternoon prompted me to shortened the data labels to F and SIGF. Now it works. Go figure...

I suspected it might be something like this, but I think there is potentially a problem in our code if a valid MTZ file is causing Phenix to crash. What were the original data labels? I'd like to try replicating the crash with simple test data. thanks, Nat

Tanner, John J.

6 p.m.

H K L FreeR_flag F_DrPRODH3-6 SIGF_DrPRODH3-6

...

From: Nathaniel Echols Reply-To: PHENIX user mailing list Date: Wed, 27 Jun 2012 13:57:37 -0700 To: PHENIX user mailing list Subject: Re: [phenixbb] Error in phenix.autobuild

On Wed, Jun 27, 2012 at 1:51 PM, Tanner, John J. wrote:

...
Seeing "IOTBX_ASSERT(strlen(label)" in the error message with fresh eyes this afternoon prompted me to shortened the data labels to F and SIGF. Now it works. Go figure...

I suspected it might be something like this, but I think there is potentially a problem in our code if a valid MTZ file is causing Phenix to crash. What were the original data labels? I'd like to try replicating the crash with simple test data.

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

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Nathaniel Echols
Tanner, John J.
Terwilliger, Thomas C