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google-code-export / nmrrestrntsgrid

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A PDB MR file contains binary data #194

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Look at the entrie 1go0

How to work around?
1. Edit the original by cutting out the binary part.

Entries involved see problemEntryList.csv in this project.

*REVDAT   1   17-OCT-02 1GO0    0

dihedrals.tbl^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^
@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@0100644^
@0000764^@0000144^@00000037524^@07522456047^@012761^@ 
0^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^
@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^@^@^@^@^@^@ustar  
^@kbwong^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@users^
@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^
@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^
@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^
@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@!!Restraint file created by 
talos2xplor.pl
!!phi/psi angles predicted from TALOS using errfactor=1.5

Original issue reported on code.google.com by jurge...@gmail.com on 20 Mar 2009 at 1:28

GoogleCodeExporter commented 9 years ago 
Creating an inventory of these cases before forwarding the problem.

Original comment by jurge...@gmail.com on 24 Mar 2009 at 9:19

GoogleCodeExporter commented 9 years ago 
Only entry 1go0 has binary data as far as I can tell using the simple script 
attached.

There are a total of 35 entries listed below that have characters outside the 
127 character ASCII table range but 
my software has no problem dealing with those.

1djf 1dn3 1dng 1eub 1go0 1hz2 1kwj 1l3o 1lms 1luh 1mke 1pc0 1pxq 1pyj 1q48 1qq3 
1rg3 1rg4 1rij 1rik 1rim 
1rsf 1ry3 1t3o 1y2y 1zwu 1zy6 2a7y 2ajm 2ajo 2fbs 2fbu 2grw 2irn 2k1y

Original comment by jurge...@gmail.com on 24 Mar 2009 at 9:39

Attachments:

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 24 Mar 2009 at 9:39

GoogleCodeExporter commented 9 years ago 
This will be taken up by PDBe.

Original comment by jurge...@gmail.com on 24 Mar 2009 at 11:46

GoogleCodeExporter commented 9 years ago 
Done, and reprocessed by Chris.

Original comment by jurge...@gmail.com on 9 Apr 2009 at 2:51

GoogleCodeExporter commented 9 years ago 
Looks like entry 1go0 is the only one still having binary data.

jd:tadpole/~/ file 1go0.mr 
1go0.mr: data

My script doesn't pick it up but vi shows it too after line 282, 332.
Relaying to PDB.

Original comment by jurge...@gmail.com on 5 Aug 2009 at 12:57

GoogleCodeExporter commented 9 years ago 
relayed to pdbe who mentioned it was updated and we're awaiting rerelease

Original comment by jurge...@gmail.com on 5 Aug 2009 at 9:21

GoogleCodeExporter commented 9 years ago 
Looks like it went thru fine now.

Original comment by jurge...@gmail.com on 23 Sep 2009 at 8:56