search

google-code-export / nmrrestrntsgrid

Automatically exported from code.google.com/p/nmrrestrntsgrid
0 stars 0 forks source link

Format converter truncates Auth_asym_ID for AMBER files #245

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
This looks like it is mangling chain information. In these cases, 2kh5_amber001 
and 2kh5_amber002 both become 2kh5_amber00. I don't know if that is what is 
used as the internal 
assembly id, but in both these cases, all restraints were mapped onto one chain 
_or_ the other.

Original issue reported on code.google.com by schulte....@gmail.com on 5 Mar 2010 at 4:03

GoogleCodeExporter commented 9 years ago 
This has come up again. 2kfy, 2kg0, and 2kg1 are all multi-chain amber files 
that assume everything belongs to xxx_amber00.

Original comment by schulte....@gmail.com on 8 Jun 2010 at 1:59

GoogleCodeExporter commented 9 years ago 
We talked about this while I was in Madison, and it turned out to be an issue 
on the Wattos side - is this sorted out now?

Original comment by wfvran...@gmail.com on 23 Jul 2010 at 10:05

GoogleCodeExporter commented 9 years ago 
Not yet, but I haven't forgotten about it.

Original comment by schulte....@gmail.com on 23 Jul 2010 at 1:30

GoogleCodeExporter commented 9 years ago 
Chris, please let me know if I should be fixing it.

Original comment by jurge...@gmail.com on 26 Jul 2010 at 6:43

GoogleCodeExporter commented 9 years ago 
The problem is that the _Dist_constraint.Auth_asym_ID's in multi-chain AMBER 
files are set to values like, 2kfy_amber001. However, the dictionary defines 
this as a short string with a max length of 12 characters, so 2kfy_amber001 
gets truncated to 2kfy_amber00, losing the chain information. I was trying to 
find where this was set in wattos with the idea of altering the string to 
2kfy_amber01, but haven't been able to yet.

If you could fix this Jurgen, that would be great. Otherwise, I'll keep poking 
at it when I get the chance.

Original comment by schulte....@gmail.com on 26 Jul 2010 at 1:55

GoogleCodeExporter commented 9 years ago 
In committed Wattos revvvvision 136:
Truncating file names so it will fit the 12 character limit set in NMR-STAR 
dictionary.

Original comment by jurge...@gmail.com on 27 Jul 2010 at 1:55

GoogleCodeExporter commented 9 years ago 
This looks like it is working. I've altered 8 of them and all but 2kwg 
processed. I beleive 2kwg has another issue,  though. I'm going to call this 
issue fixed.

There are 81 other amber files in the pdb_external folder. Do we go ahead and 
reprocess them?

Original comment by schulte....@gmail.com on 27 Jul 2010 at 6:54

GoogleCodeExporter commented 9 years ago 
Sounds great, go ahead.

Original comment by jurge...@gmail.com on 27 Jul 2010 at 6:56