coordinates from N-terminal H atoms and O-terminal O atoms not imported from Xplor pdb file

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When importing coordinates from re-annealed and re-refined entries (pdb files 
in PDBID.cing/Refine/PDBID_redo/Refined/PDBID_%03d.pdb), coordinates from 
N-terminal H atoms and O-terminal O atoms are not imported from the 
Xplor-formatted PDB-file.

==> Non-standard (residues and their) atoms to add:
GLU : OT1  OT2  [ 86]
LEU : HT1  HT2  HT3  [ 1]

WARNING: pdbParser.map2molecule: Strange! Warning mapping atom for:
GLU : OT1  OT2  [ 86]
LEU : HT1  HT2  HT3  [ 1]

I.e. the mapping goes wrong in 
http://code.google.com/p/cing/source/browse/trunk/cing/python/cing/Libs/pdb.py#2
91 

Applies to all entries.

Where do we fix this?

Original issue reported on code.google.com by WGTouw on 7 Jan 2013 at 3:43

[GoogleCodeExporter]

Fixed by r1202

Original comment by WGTouw on 8 Jan 2013 at 2:31

• Changed state: Fixed

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simply changing the def of xplor for the terminal atoms might work for one 
situation but not for another.
Make sure that all scenarios get checked. 
--testQ works?
nmr_redo works?

Cheers!

Original comment by jurge...@gmail.com on 8 Jan 2013 at 10:28

[GoogleCodeExporter]

This issue was closed by revision r1204.

Original comment by WGTouw on 9 Jan 2013 at 9:31