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jakesylvestre / cing

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Gly residues are handled incorrectly for D1D2 plots #232

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Run 1i1s and look at:
http://nmr.cmbi.ru.nl/tmp/proteinsDotDynDnsDotOrg/data/i1/1i1s/1i1s.cing/1i1s/HT
ML/Molecul
e/A/GLY45
It misses the plot.
Funny thing is that in 1brv this is not a problem. Must be entry specific then.

What is the expected output? What do you see instead?
All plots showing up like in:
http://nmr.cmbi.ru.nl/NRG-CING/data/br/1brv/1brv.cing/1brv/HTML/Dihedrals/D1D2.h
tml

Original issue reported on code.google.com by jurge...@gmail.com on 17 Mar 2010 at 9:02

GoogleCodeExporter commented 9 years ago 
this is due to input pdb file:
pdbParser.importCoordinates: Skipping duplicate coordinate within same record 
(ATOM   1131 2HA  GLY A  73     
100.459 111.908 -21.633  1.00  0.00           H  )

Original comment by jurge...@gmail.com on 17 Mar 2010 at 9:06

GoogleCodeExporter commented 9 years ago 
Same problem in entries 1ka3 & 1tgq.
Problem can be solved by updating the input pdb files by Yasara to a format 
that is easier to read by CING. Just 
have to find the right combination between Y & C. I tried a couple before that 
failed. 
Settled on Yasara's IUPAC format that is readible by CING's IUPAC. What a bless.

Original comment by jurge...@gmail.com on 17 Mar 2010 at 9:16

GoogleCodeExporter commented 9 years ago 
In r736 the modified PDB files were committed. Run seems to be going better 
now. Will check in morning.

Original comment by jurge...@gmail.com on 17 Mar 2010 at 10:01

GoogleCodeExporter commented 9 years ago 
Results look fine at: http://nmr.cmbi.ru.nl/ValidationExercises
Updating production version for iCing next.

Original comment by jurge...@gmail.com on 18 Mar 2010 at 9:41