Re: [Jmol-users] lcaoCartoons

2012-07-02 Thread Robert Hanson
add the keyword MOLECULAR and you should have it: lcaocartoon CREATE pz MOLECULAR *Creates a new LCAO cartoon of the given type using the molecular axes system as reference. Applicable only for px, py, pz, -px, -py, and -pz. * On Sun, Jul 1, 2012 at 10:34 PM, Pshemak Maslak p...@chem.psu.edu

Re: [Jmol-users] Notify user if signed applet request is declined

2012-07-02 Thread Robert Hanson
Well, then you don't have the access you think you do. I thought your intent was to let the user know that the applet loaded would not load the file desired. What are you actually trying to do again? On Sun, Jul 1, 2012 at 12:03 PM, Martin Hediger ma@bluewin.ch wrote: ** problem is, using

Re: [Jmol-users] lcaoCartoons

2012-07-02 Thread Pshemak Maslak
On 7/2/2012 11:55 AM, Robert Hanson wrote: add the keyword MOLECULAR and you should have it: lcaocartoon CREATE pz MOLECULAR /Creates a new LCAO cartoon of the given type using the molecular axes system as reference. Applicable only for px, py, pz, -px, -py, and -pz. / I did not see it

Re: [Jmol-users] unused vertices in sasurface

2012-07-02 Thread Robert Hanson
I would check the bounds of map.dx to make sure it really spans the entire molecule. If a surface point is outside the range of mapped data, then this could happen because the value will be introduced as NaN Q: What does it look like at that vertex? You can use DRAW to show a dot at that point

Re: [Jmol-users] relationship beween isosurface of subset of atoms

2012-07-02 Thread Robert Hanson
On Sat, Jun 30, 2012 at 12:36 PM, Daniel Aioanei aioan...@gmail.com wrote: What is the relationship between the isosurface of a set of atoms and that of a subset of the atoms? I kind of expected that the latter be a subset of the former one, but that doesn't seem to be the case. Indeed, by

Re: [Jmol-users] contact command

2012-07-02 Thread Robert Hanson
You mean so that you see only non-clash contacts? You can do this: contact HBOND Those aren't clashes. On Fri, Jun 29, 2012 at 6:49 AM, Pascal Auffinger p.auffin...@ibmc-cnrs.unistra.fr wrote: Hi, Is there a way to set contact clash ON or OFF though set contact ON; set contact OFF ?

Re: [Jmol-users] Notify user if signed applet request is declined

2012-07-02 Thread Martin Hediger
Hi Robert, thanks for getting back, I'm not sure I understand your answer. I thought, as you wrote previously, if I see this message, it means my applet is not signed. But it is, because I grant it access. And from testing it, I know I can use my applet to write a state file to my local

Re: [Jmol-users] Notify user if signed applet request is declined

2012-07-02 Thread Robert Hanson
On Mon, Jul 2, 2012 at 2:42 PM, Martin Hediger ma@bluewin.ch wrote: ** Hi Robert, thanks for getting back, I'm not sure I understand your answer. I thought, as you wrote previously, if I see this message, it means my applet is not signed. right. But it is, because I grant it access.