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

[Elaine Meng]

Hi Christian,
Here are the rules for atom names in correct PDB format, as I  
understand them:

Atom names start with element symbols right-justified in columns 13-14  
as permitted by the length of the name. For example, the symbol FE for  
iron appears in columns 13-14, whereas the symbol C for carbon appears  
in column 14. If an atom name has four characters, however, it must  
start in column 13 even if the element symbol is a single character  
(for example, some hydrogens).

So while it is true that columns 13-16 are for atom names, just  
putting the names anywhere in that area does not mean the format is  
correct.

The Chimera User's Guide includes some information on PDB format:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html 
 >

I hope this helps,
ELaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Mar 17, 2009, at 6:57 AM, Christian Schudoma wrote:

> 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