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

[Eric Pettersen]

To supplement what Elaine said, without the column-positioning of the  
atom name it would be impossible to distinguish a carbon alpha (CA)  
from a calcium (CA).  Though if you provide the element symbol in  
columns 77-78 then the atom name will be ignored for determining the  
element.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Mar 17, 2009, at 8:41 AM, Elaine Meng wrote:

> 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
>
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