Adding allowed data type to mrannotator

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Need to add relaxation data (T1, etc) to allowed data types.
for STAR and other.

Noted here because I had like to track it thru the different NRG setups.

Original issue reported on code.google.com by jurge...@gmail.com on 11 Sep 2009 at 1:42

[GoogleCodeExporter]

Original comment by jurge...@gmail.com on 11 Sep 2009 at 1:43

• Changed title: Adding allowed data type to mrannotator

[GoogleCodeExporter]

Added line to csv file in revision .

Need to add it to the wattos.jar locally on every setup.
Let's mark this issue as verified when all setups are done.

Original comment by jurge...@gmail.com on 14 Sep 2009 at 1:04

• Changed state: Fixed

[GoogleCodeExporter]

Forgot to fill in revision 124.
Tested on stella now.

Original comment by jurge...@gmail.com on 14 Sep 2009 at 1:20

[GoogleCodeExporter]

Updated tang to r214.
Added a ~dorcr/wattos.runtime.properties with the below settings for tang.

I would like to ask Chris to reannotate 2k9y with the new type. It's not easy 
to do remotely.

#
# Example runtime config file. 
# Override settings from Episode_II/Globabls.java here.
# For NRG servlet: save as wattos.runtime.properties in tomcat user's homedir.
# For mrannotator: override relevant settings, save in annotator's homedir.
#
testing     = false
bmrb_url    = http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=
#db_machine  = localhost
#db_password = 4I4KMS
#db_username = wattos1
dbfs_dir    = /big/jurgen/DB/mrgrid/bfiles/wattos1
#dbfs_root   = /website/admin/wattos
dbfs_root   = /big/jurgen/DB/mrgrid
#mr_dir      = /website/ftp/pub/pdb/data/structures/divided/nmr_restraints
mr_dir      = /dumpzone/pdb/pdb/data/structures/divided/nmr_restraints
#pdb_dir     = /website/ftp/pub/pdb/data/structures/divided/pdb
pdb_dir     = /dumpzone/pdb/pdb/data/structures/divided/pdb
#servlet_molgrap_dir = /servlet_data/molgrap
servlet_molgrap_dir = /../servlet_data/molgrap/molgrap
#servlet_top_dir     = /website/htdocs/servlet_data # OBSOLETE PARAMETER
#mr_anno_dir          = /big/docr/wattosTestingPlatform/Wattos/mr_anno_dir # 
UNUSED except 
MRReclassify.java
mr_anno_progress_dir = /dumpzone/pdb/mr_anno_progress_nrg31
amber_pdb_dir        = /dumpzone/pdb/external/amber_pdb

Original comment by jurge...@gmail.com on 16 Sep 2009 at 8:58

• Changed state: Started

[GoogleCodeExporter]

What _is_ the new type? I used relaxation. This works on tang, but not grunt.

2k9y crashes weeklyDOCR_FRED when reading the mmCIF file. I've looked at the 
file and it seems OK to me. 

What's up?

Original comment by schulte....@gmail.com on 22 Sep 2009 at 3:31

[GoogleCodeExporter]

relaxation,n/a,n/a is indeed what I used.
It's easy to check at: http://code.google.com/p/wattos/source/detail?r=124
Just click the diff link.

Why doesn't it work on grunt? Did you update wattos on grunt?

Is 2k9y crashing on grunt? What's the error?

Original comment by jurge...@gmail.com on 23 Sep 2009 at 8:54

[GoogleCodeExporter]

I didn't touch anything on grunt. I was waiting to see what happened on tang.

As far as 2k9y, the terminal error isn't helpful:
ERROR 2k9y Wattos script 2k9y.wcf failed; not continueing

and no link_dir is created. The star_dir log file does seem to have some info.

See attached:

Original comment by schulte....@gmail.com on 23 Sep 2009 at 1:19

Attachments:

• 2k9y.log
• 2k9y.wcf

[GoogleCodeExporter]

so when you see the below lines in there you can deduce it's encountered before:

ERROR: Failed to find any atom in first model for entity: 2
ERROR: This was found in for instance entry 1j6t for the PO3 group and was 
reported in NRG issue 157
ERROR: No easy work around possible.
ERROR: entry.readmmCIFFormattedFile was unsuccessful. Failed to read nmrstar 
formatted file

Original comment by jurge...@gmail.com on 23 Sep 2009 at 2:02

• Changed state: Duplicate

[GoogleCodeExporter]

Yes. Should it be added to issue 157?  I figured it would be rerun, along with 
everything else, when/if we have a 
major code update. Otherwise, there is not much we can do about it.

I looked at the cif file, and the atoms were there (wrong format?). I don't 
know what the problem would be.

Original comment by schulte....@gmail.com on 23 Sep 2009 at 2:23