[Jmol-users] Display only a single protein chain

2012-09-25 Thread Andreas Truszkowski
Hi, I can't find any script snippets on how to display only a single chain of an entire protein. E.g. Insulin (PDB: 4INS) has two compounds with each having 2 chains. How can I hide/display the chains independently. Kind regards, Andreas

Re: [Jmol-users] Display only a single protein chain

2012-09-25 Thread Angel Herráez
Hi Andreas You need to find out the chain IDs (usually A, B ... but not always) Then display *:A; // will also hide all the others display add *:A; // makes A visible without hiding others etc. Check the DISPLAY and HIDE commands in the documentation

Re: [Jmol-users] Display only a single protein chain

2012-09-25 Thread Andreas Truszkowski
Thank you very much. But hiding/displaying of protein chains is not documented. Kind regards, Andreas Am 25.09.2012 15:18, schrieb Angel Herráez: Hi Andreas You need to find out the chain IDs (usually A, B ... but not always) Then display *:A; // will also hide all the others display

Re: [Jmol-users] Display only a single protein chain

2012-09-25 Thread Angel Herráez
Sorry, hiding and displaying of ANYTHING is documented. You just combine display command with atom expressions, which are described in the doc (and used by most commands). Good luck! -- Live Security Virtual

Re: [Jmol-users] write command to server

2012-09-25 Thread Tamas Horvath
Yes. It's possible that my servlet that should accept the file isn't configured quite right, but I don't understand where the FileNotFoundException is coming from. And I don't see a POST attempt either on firebug. I can get the state with 'show STATE' and I can ajax that back to the server, which

[Jmol-users] ion sizes

2012-09-25 Thread Pshemak Maslak
Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of Cl-. I am assuming that atomic radii are use. Is there ionic radii info in Jmol? If so, how can one display it? PM -- Live Security Virtual

Re: [Jmol-users] ion sizes

2012-09-25 Thread Phillip Barak
spacefill ionic --pb On 09/25/12, Pshemak Maslak wrote: Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of Cl-. I am assuming that atomic radii are use. Is there ionic radii info in Jmol? If so, how can one display it? PM

Re: [Jmol-users] write command to server

2012-09-25 Thread Robert Hanson
it might be as simple as the final / after servlet You tried http://./?POST? on the URL line of your browser, and it worked? -- I mean, it found a page? (not that it would actually post anything) Bob On Tue, Sep 25, 2012 at 8:37 AM, Tamas Horvath hota...@gmail.com wrote: Yes. It's

Re: [Jmol-users] ion sizes

2012-09-25 Thread Otis Rothenberger
I'm playing with CIF files for the first time myself. The radii are VdW, and the following script components may be useful to you: connect delete;spacefill IONIC 30%;label Edit features in or out per your needs. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Sep 25,