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

[Jean Didier Pie Marechal]

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
> >
> 
>