[Chimera-users] Chimera does not always recognise atom name in PDB ATOM records

[Christian Schudoma]

Hello Chimera-Users and -Devs,

I encountered the following problem when trying to visualise the 
following purine molecule (Actually, I tried to do something more 
complex(*) but the same problem can be reproduced with this more simple 
example). For clarification, the first lines contain the column numbers.

         1         2         3         4         5         6         7
123456789012345678901234567890123456789012345678901234567890123456789012345678
HETATM    1   N1 CKN A   1      -0.003   1.586  -3.371  0.00  
0.00           N  
HETATM    2   C2 CKN A   1       1.016   1.511  -4.278  0.00  
0.00           C  
HETATM    3   N3 CKN A   1       2.313   1.566  -3.865  0.00  
0.00           N   
HETATM    4   C4 CKN A   1       2.576   1.683  -2.541  0.00  
0.00           C  
HETATM    5   C5 CKN A   1       1.559   1.758  -1.597  0.00  
0.00           C  
HETATM    6   C6 CKN A   1       0.224   1.717  -2.032  0.00  
0.00           C  
HETATM    7   N7 CKN A   1       2.100   1.858  -0.373  0.00  
0.00           N  
HETATM    8   C8 CKN A   1       3.434   1.842  -0.568  0.00  
0.00           C  
HETATM    9   N9 CKN A   1       3.731   1.742  -1.876  0.00  
0.00           N  

When I load a pdb file containing these coordinates into Chimera, I get 
9 non-connected dots (obviously representing the atoms) which can 
neither be coloured by hetero-atom, nor by element. Note that the atom 
names are located in the appropriate columns, i.e. between columns 13 
and 16, more specifically in columns 15 and 16.

I noticed that in other pdb structures 2-character atom names are 
located in columns 14 and 15 and when I put my atom names there, Chimera 
displays the purine ring system which then can be coloured by 
hetero-atom/element. Now it is nice that this workaround fixes my 
problem, however, according to the pdb file format specification 
(columns 13-16 are reserved for the atom name), atom names located in 
columns 15 and 16 are valid(*) and as such should be processible by 
visualisation tools etc.

The behaviour occurs with the latest daily build as well as some older 
versions I found on my hard disk...

(*) The purine is part of a larger cytokinin. I stumbled upon the 
described behaviour while using the AddHydrogen function on the whole 
molecule, which lead to the replacement of the purine with a hydrogen.
(**) Unless there are some additional rules regarding the placement of 
atom names shorter than 4 characters, in which case I apologise for 
bugging you with this.

Any comments on this?

Best regards,
Christian Schudoma



-- 
Christian Schudoma, M.Sc.

Bioinformatics Group 
System Integration Group

Max Planck Institute of Molecular Plant Physiology
Am Muehlenberg 1
14476 Potsdam-Golm
Germany

phone: +49 331 567-8624
email: schudoma at mpimp-golm.mpg.de
http://rloom.mpimp-golm.mpg.de