Margaret,
Could you try something like "select atomno=XXX and model=1" to get the specific atom in just one of the biological units? I think I remember being able to select just one of the models in an assembly using that "model=" command. I'm not by my CPU right now or I'd try it myself - but if I get a chance later, I will! -Mark MSOE Center for BioMolecular Modeling - http://cbm.msoe.edu 3D Molecular Designs - www.3dmoleculardesigns.com<http://www.3dmoleculardesigns.com> [email protected] office: 414-277-4554 cell: 414-640-8668 ________________________________ From: Franzen, Dr. Margaret <[email protected]> Sent: Friday, September 25, 2015 5:55 PM To: Angel Herráez; [email protected] Subject: Re: [Jmol-users] connecting atoms in two different models of a pdb file Since the goal is to show the interaction between atoms that are contained in two different models, the command to select two atoms in the same model doesn't work. I loaded the biological assembly; selected all models, and then tried to show interactions between models. Although we have a workaround for creating physical models of the proteins, I haven't found a way to display these types of interactions on the screen for educational purposes. Margaret From: Angel Herráez [mailto:[email protected]] Sent: Friday, September 25, 2015 5:19 PM To: Franzen, Dr. Margaret; [email protected] Subject: Re: [Jmol-users] connecting atoms in two different models of a pdb file On 25 Sep 2015 at 20:15, Franzen, Dr. Margaret wrote: > I am using Jmol Jmol 14.3.16_2015.08.11 (2015-08-11 16:13) Wow! It seems that "select" is not recognized, neither in my version 14.3.16_2015.09.15 $ select atomno=3 ERROR en guión: no se reconoce la instrucción ---- <<<<select << { atomno = 3 } Now THAT IS a bug, with 6 legs :-D But no freezing for me. Margaret, try with another version. e.g. with 14.2.13 it works: load =1hho.pdb select atomno=2193 or atomno=299; connect strut; strut 0.5; color strut green // 2 atoms selected select [LYS]40:A.NZ/1 or [HIS]146:B.OXT/2 // 1 atom selected - Where is the other? Wrong ID? // Ah! There's only one model: select [LYS]40:A.NZ/1 or [HIS]146:B.OXT/1 // works
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