[Chimera-users] Select atom by serial number.

[Elaine Meng]

Hi JD,
We also tested Chimera 1.2309 on Windows, and these specifications  
work correctly.  Example:
   Command: sel @/serialNumber=232
will select NZ of Lys 27 in chain A of the PDB entry 1zik. The only  
other thing I can think of (besides what was in the previous message)  
is to check if your PDB file is correctly formatted.  The ATOM/HETATM  
serial number is supposed to be in columns 7-11 and right-justified.
Best,
Elaine

On Jan 11, 2007, at 11:39 AM, Elaine Meng wrote:

> Hi JD,
> You are using the correct specifications - both of your examples  
> should work.  I tested both approaches in Chimera 1.2304 on Mac OSX  
> and they worked correctly.  We'll have to look into your specific  
> version/platform and get back to you.  If you want, you could send  
> me the PDB file you are using so I could test if there is some  
> issue specific to that structure.  To be clear: the serial number  
> is the number shown in the column after ATOM (or HETATM) in the PDB  
> file, regardless of what order the atoms are really in.  That is,  
> if the first ATOM has 2 in that column, its serial number is 2 and  
> not 1.
> Best,
> 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 Jan 11, 2007, at 10:47 AM, Jean-Didier Maréchal wrote:
>
>> Hi Everyone,
>>
>>
>>
>>
>>
>> I am desperately trying to select an atom of my pdb by its serial  
>> number.
>>
>> Looking at the archives, it seems that I should put something like  
>> @/serialNumber=525
>>
>> I tried “sel #0@/serialNumber=525” in the commandl ine and “@/ 
>> serialNumber=525” in the Atom Specifier. None of these selections  
>> worked. Can someone tell me the right way to do this, please ?
>>
>>
>>
>> Cheers
>>
>> JD
>>
>>
>>
>> Current running chimera: version 1 build 2309
>>
>> OS: windows
>>
>>
>>
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>