[Chimera-users] Labels of Metal atoms

[Tom Goddard]

Hi Mike,

   I see your test file contains Cu1 and Chimera shows that in a label 
as CU1 with all upper case.  That surprises me.  Our expert on that Eric 
Pettersen can explain it next week.  You may be right that Chimera knows 
the atomic elements and could selectively capitalize labels according to 
your preferences when the atom name matches the element symbol.  Again 
it is something Eric can advise on.

      Tom


> Tom,
>
> Thanks for the reply.
>
> The file is a PDB, a file with the first few lines is attached.
>
> I was hoping that since Chimera understood atom names well enough to 
> color them that there would be a file with atoms names used for labeling.
>
> If this is something I can change in my installation, great, if not, 
> no worries. I use a mac. I've already changes the python file to 
> understand the non-sttandard space group P21/N.
>
>
>
> Cheers,
> Mike
>
> <<< 
> ------------------------------------------------------------------------>>>
> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
> Mail Code 139-74
> Pasadena, CA 91125
>
> <>< <>< <>< <>< <>< <>< <>< <>< <>< <><
>
> Beckman Institute, Room 116
> Phone: (626) 395-2734
> Fax: (626) 449-4159
> e-mail: mikeday at caltech.edu <mailto:mikeday at caltech.edu>
> <<< 
> ------------------------------------------------------------------------>>>
>
> On Feb 11, 2011, at 2:27 PM, Tom Goddard wrote:
>
> Hi Mike,
>
>   Does the FE1 name come from a PDB or Mol2 file you opened?  If that 
> name appears in the file, one obvious approach is to change the file 
> replacing FE1 with Fe1.  I'm not sure if that will break code that 
> expects FE1.  I don't think there are any options in Chimera to 
> manipulate the case of names displayed in labels.  I believe Chimera 
> just uses the capitalization of names it obtains from the file it read in.
>
>   I guess Chimera could have some option to manipulate the case of 
> atom names in labels.  But it seems very specialized.  Someone looking 
> at a protein with a C-alpha atom named CA generally does not want Ca.  
> This also indicates that it isn't possible to know if an atom name 
> refers to an atomic element (e.g. Fe = iron, Ca = calcium) or 
> something else (like C-alpha).
>
>     Tom
>
>> How do I make the default label for metal atoms be upper and lower case?
>>
>> For instance in an iron compound, if I issue label ~H from the 
>> command line the result will be FE1 where I prefer Fe1, etc., etc.
>>
>> This is true for all two letter atom names.
>>
>> Thanks
>> Cheers,
>> Mike
>>
>> <<< 
>> ------------------------------------------------------------------------>>>
>> Dr. Michael W. Day
>> Director - X-ray Crystallography Lab & Molecular Observatory
>> California Institute of Technology
>> Mail Code 139-74
>> Pasadena, CA 91125
>>
>> <>< <>< <>< <>< <>< <>< <>< <>< <>< <><
>>
>> Beckman Institute, Room 116
>> Phone: (626) 395-2734
>> Fax: (626) 449-4159
>> e-mail: mikeday at caltech.edu <mailto:mikeday at caltech.edu>
>> <<< 
>> ------------------------------------------------------------------------>>>
>>
>>

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