Re: [Jmol-users] JMol API/Scripting

2012-07-19 Thread Andreas Truszkowski
I have used the solution from Angel with the "fake elements" and it works perfectly. Also thanks to Alex. The "AND" was the problem and with "OR" it performs well. Great support here at the Jmol-List. Kind regards, Andreas Am 19.07.2012 14:12, schrieb Robert Hanson: What you could do is jus

Re: [Jmol-users] JMol API/Scripting

2012-07-19 Thread Robert Hanson
What you could do is just give standard atoms labels like "Et" and "H2O" $ load $caffeine $ select _N 4 atoms selected $ label "OK" $ select label="OK" 4 atoms selected Bob On Wed, Jul 18, 2012 at 11:56 AM, Andreas Truszkowski wrote: > Hi Angel, > > Am 18.07.2012 18:41, schrieb Angel Herráez: >

Re: [Jmol-users] JMol API/Scripting

2012-07-18 Thread Andreas Truszkowski
Hi Angel, Am 18.07.2012 18:41, schrieb Angel Herráez: > I don't think you can define your own symbols. After all, they are > element symbols with precise chemical meaning. The XYZ reader expects > to see them. Ok. I was afraid of that :). So I have to define and write my own filter GUI. Fortunat

Re: [Jmol-users] JMol API/Scripting

2012-07-18 Thread Angel Herráez
Hi Andreas I don't think you can define your own symbols. After all, they are element symbols with precise chemical meaning. The XYZ reader expects to see them. What you can do is choose any element for each type of fragment and then assign custom colors and radii for each "fake element". For

Re: [Jmol-users] JMol API/Scripting

2012-07-18 Thread Andreas Truszkowski
Hi, @Robert: Thank you very much for your detailed answer. One problem is still open. I will display molecular fragement data consisting of fragments like methane, water, benze, and I only have the coordinates of this fragments. Hence I use the XYZ file format to describe my data. But ho

Re: [Jmol-users] JMol API/Scripting

2012-07-14 Thread Robert Hanson
On Sat, Jul 14, 2012 at 5:44 AM, Andreas Truszkowski wrote: > Hi together, > > I am new to JMol and I want to use it to visualize results from a > Molecular Fragment Dynamics simulation. The idea is to handle the fragments > as atoms thus I have to define my own elements. > > 1) Is it possible to

[Jmol-users] JMol API/Scripting

2012-07-14 Thread Andreas Truszkowski
Hi together, I am new to JMol and I want to use it to visualize results from a Molecular Fragment Dynamics simulation. The idea is to handle the fragments as atoms thus I have to define my own elements. 1) Is it possible to define your own elements with their own names, colors , size(radius/