many days after...another question Re: Select atom by serial number.
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@uab.es ----- Missatge original ----- De: Elaine Meng <meng@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@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@uab.es
----- Missatge original ----- De: Elaine Meng <meng@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@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Jean Didier Pie Marechal