[Chimera-users] many days after...another question Re: Select atom by serial number.

[Elaine Meng]

Hi JD,
Ranges aren't directly implemented, but you can do it with > >= < <=  
combinations.  For example,  you could select atoms with serial  
numbers 1-10 with:

sel @/serialNumber<=10
or
sel @/serialNumber<11

For a nonterminal range, for example, you could select atoms with  
serial numbers 11-20 with:

sel @/serialNumber>=11 and serialNumber<=20

I tested these on PDB entry 1zik.
Cheers,
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 Feb 26, 2007, at 11:03 AM, Jean Didier Pie Marechal wrote:

> Hi everybody,
>
> I'd like to select a series of atoms by their serial number  
> (again!!!) (e.g. from atom number 1 to atom number 10).
>
> the sel @/serialNumber=1-10 doesn't seem to be the right syntax.
>
> Is it possible to do this kind of selection? If yes, what is the  
> right syntax please.
>
> Cheers,
> JD
>
> Dr. Jean-Didier Maréchal
> Professor Lector
> Unitat de Química Física
> Departament de Química
> Universitat Autònoma de Barcelona
> Edifici C.n.
> 08193 Cerdonyola (Barcelona)
> Tel: +34.935814936
> e-mail: JeanDidier.Marechal at uab.es
>
> ----- Missatge original -----
> De: Elaine Meng <meng at cgl.ucsf.edu>
> Data: Dijous, Gener 11, 2007 8:59 pm
> Assumpte: Re: [Chimera-users] Select atom by serial number.
>
>>
>> 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
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>>
>
>