for "infinite" time. After Ctrl-C it continued and finished installation. I tried to run phenix.autobuild and it hangs ... *and after that it does not quit and seems to be doing nothing new for the rest of the available time.

We had problem reports like this for the last few days, but have been unable to reproduce it on our machines. Could you send me the output of uname -a cat /etc/*-release boost_adaptbx.show_platform_info Ralf

Hi Tatiana, Thanks for trying running the "temporary.com" file directly. The fact that it runs means that your machine has no problem doing this job, at least in principle. The installation problem you had with 1.4-85 is a problem we are currently trying to debug, as Ralf just replied to you about... I am guessing that the run of autobuild has the same problem of deletion of files. Can you try running your exact same job on a single machine with local disk, to see if it will run properly in this case? All the best, Tom T On Jun 5, 2009, at 12:05 PM, Tatyana Sysoeva wrote:

On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger

...

wrote: Hi Tatiana,

This may be a little difficult to debug on a cluster...but here goes.

The error message you got comes from

AutoBuild_run_1_/TEMP0/ AutoBuild_run_1_/TEMP0/temporary.com

You can see exactly what happens with that command file if you can log on to a machine in the cluster:

cd AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0

then copy temporary.com to test.com and edit test.com to replace all the material at the top of the file after #!/bin/csh -f (something like this below) all the way down to "outputdir":

delete all this: ------------- setenv CCP4_OPEN UNKNOWNsetenv SOLVEDIR /Users/terwill/unix/PHENIX/phenix-1.4-67/solve_resolve/ext_ref_files setenv SYMOP /Users/terwill/unix/PHENIX/phenix-1.4-67/solve_resolve/ext_ref_file s/symop.lib /Users/terwill/unix/PHENIX/phenix-1.4-67/build/mac-intel-osx/ solve_resolve/exe/r esolve <<EOD > AutoBuild_run_1_/TEMP0/image.log access_file mirima.dat workdir AutoBuild_run_1_/TEMP0 outputdir /Users/Shared/unix/transfer/shiven/AutoBuild_run_6_ -------------

replace with:

phenix.resolve --huge <

and then run ./test.com ....it should bomb and tell you what is wrong.

It is possible that the size of your problem is too big for even the 8 GB of memory on your machine, but that would imply a pretty big cell and moderate or high resolution. Hopefully the output of that test will tell you...

Just to be sure, you might also go to the phenix web site and download a recent "nightly build" to make sure that there is not some other type of problem going on.

All the best, Tom T

Good afternoon!

Thank you so much for the reply. I edited temporary.com and ran it, it reported no error.

when I'm installing phenix 1.4-85, it stops at ................................. converting reflection_file_tools.html to reflection_file_tools.raw converting reflection_statistics.html to reflection_statistics.raw converting xtriage_gui.html to xtriage_gui.raw converting raw HTML files, creating tables-of-contents, and indexing

for "infinite" time. After Ctrl-C it continued and finished installation. I tried to run phenix.autobuild and it hangs

in gui-output.log - STEP: ImportRawData_output_files Run 1 List of files to convert to mtz format: File 1: e239a.hkl

in autobuild_run1.log - ImportRawData_output_files ImportRawData Run 1 Thu Jun 4 21:54:11 2009 summary of input files: hklin : /home2/tas354/phenix_runs/20090603/e239a.hkl input labels:["FOBS", "SIGMA"] OUTPUT FILE NAME: /home2/tas354/phenix_runs/20090603/ ImportRawData_run_1_/e239a_PHX.mtz SPACE GROUP NAME: P 21 21 2 CELL: [251.209, 242.58600000000001, 40.703000000000003, 90.0, 90.0, 90.0]

and after that it does not quit and seems to be doing nothing new for the rest of the available time.

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

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

Hi Tatyana, I think we have the autobuild and PHENIX installation hanging problem figured out now. There was a problem in deleting system files (.nfsxxxxxx) in temporary directories that caused PHENIX to hang. Now we are able to either ignore them or delete them and it seems to work fine on a system where we could make this problem happen. The next nightly build (tonight) should have this fix in it. Thanks very much to all those reporting the problems and I hope that this will fix it! All the best, Tom T On Jun 5, 2009, at 12:05 PM, Tatyana Sysoeva wrote:

On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger

...

wrote: Hi Tatiana,

This may be a little difficult to debug on a cluster...but here goes.

The error message you got comes from

AutoBuild_run_1_/TEMP0/ AutoBuild_run_1_/TEMP0/temporary.com

You can see exactly what happens with that command file if you can log on to a machine in the cluster:

cd AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0

then copy temporary.com to test.com and edit test.com to replace all the material at the top of the file after #!/bin/csh -f (something like this below) all the way down to "outputdir":

delete all this: ------------- setenv CCP4_OPEN UNKNOWNsetenv SOLVEDIR /Users/terwill/unix/PHENIX/phenix-1.4-67/solve_resolve/ext_ref_files setenv SYMOP /Users/terwill/unix/PHENIX/phenix-1.4-67/solve_resolve/ext_ref_file s/symop.lib /Users/terwill/unix/PHENIX/phenix-1.4-67/build/mac-intel-osx/ solve_resolve/exe/r esolve <<EOD > AutoBuild_run_1_/TEMP0/image.log access_file mirima.dat workdir AutoBuild_run_1_/TEMP0 outputdir /Users/Shared/unix/transfer/shiven/AutoBuild_run_6_ -------------

replace with:

phenix.resolve --huge <

and then run ./test.com ....it should bomb and tell you what is wrong.

It is possible that the size of your problem is too big for even the 8 GB of memory on your machine, but that would imply a pretty big cell and moderate or high resolution. Hopefully the output of that test will tell you...

Just to be sure, you might also go to the phenix web site and download a recent "nightly build" to make sure that there is not some other type of problem going on.

All the best, Tom T

Good afternoon!

Thank you so much for the reply. I edited temporary.com and ran it, it reported no error.

when I'm installing phenix 1.4-85, it stops at ................................. converting reflection_file_tools.html to reflection_file_tools.raw converting reflection_statistics.html to reflection_statistics.raw converting xtriage_gui.html to xtriage_gui.raw converting raw HTML files, creating tables-of-contents, and indexing

for "infinite" time. After Ctrl-C it continued and finished installation. I tried to run phenix.autobuild and it hangs

in gui-output.log - STEP: ImportRawData_output_files Run 1 List of files to convert to mtz format: File 1: e239a.hkl

in autobuild_run1.log - ImportRawData_output_files ImportRawData Run 1 Thu Jun 4 21:54:11 2009 summary of input files: hklin : /home2/tas354/phenix_runs/20090603/e239a.hkl input labels:["FOBS", "SIGMA"] OUTPUT FILE NAME: /home2/tas354/phenix_runs/20090603/ ImportRawData_run_1_/e239a_PHX.mtz SPACE GROUP NAME: P 21 21 2 CELL: [251.209, 242.58600000000001, 40.703000000000003, 90.0, 90.0, 90.0]

and after that it does not quit and seems to be doing nothing new for the rest of the available time.

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

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

phenix.print_sequence phenix.* has a lot of good utils I didnt know about until I tab completed it. FR On Jun 8, 2009, at 9:17 AM, chern wrote:

Hi everybody,

I am building a model of protein and the sequence has wrong parts. I want to compare it to the original sequence side-by-side. How can I extract a one-letter sequence from the pdb file? This information should be easily generated by auto build. I mean, I give the pdb and get the fasta format sequence.

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

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

Hi Maia, it would be helpful if you can send us the PDB file so we can reproduce and fix this problem (send it to my address, not to the whole bb). Pavel. On 6/10/09 11:06 AM, Maia Cherney wrote:

Thank you Francis and Sabine for your help.

phenix.print_sequence worked fine. The only problem I had with one pdb, for some reason the sequence of each subunit was doubled. There was no such problem with the pdbset.

Maia

Maia

Francis E Reyes wrote:

...

phenix.print_sequence

phenix.* has a lot of good utils I didnt know about until I tab completed it.

FR

On Jun 8, 2009, at 9:17 AM, chern wrote:

...

Hi everybody,

I am building a model of protein and the sequence has wrong parts. I want to compare it to the original sequence side-by-side. How can I extract a one-letter sequence from the pdb file? This information should be easily generated by auto build. I mean, I give the pdb and get the fasta format sequence.

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

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

------------------------------------------------------------------------

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