Hi,
I'm using a bash skript to generate movies from xyz files with multiple
frames. I'm using Jmol for rotation, deleting of bonds and coloring
atoms with a skript and generating a pov file. Is there a possibility of
using the Jmol comandline only, without the Jmol Window poping up?
Stephan
Stephan,
Yes, absolutely. Everything you can do with scripts you can do without any
graphical interface at all. The program to run is JmolData.jar. It is
completely headless and is designed for doing exactly what you describe.
(You can do the same with Jmol.jar or JmolData.jar, but JmolData.jar
On 02/07/2014 03:20 PM, Stephan Pfadenhauer wrote:
Thank you for the fast answer. The problem i encounter is, that using
the -x option the the skript works perfektly, but using the -n option
the skript halts.
Im executing following Jmol Skript called JWscript:
load auto file:./out0.xyz
Bob,
I'm missing something here. I've tried the following with both 2D and 3D
molfiles. The correct model and spectrum load, but there is no sync.
Jmol.script(jmol, load ../models.aspx?smi2sdf2d= +
smilesEscape(model, 1));
var s = Jmol.getPropertyAsString(jmol, extractModel);
Definitely works for me. JmolData does not require -n or -o or -x, as it
has no graphical interface and automatically includes those options.
Directory listing shows:
02/07/2014 08:47 AM15,143 out00.pov
02/07/2014 08:47 AM 413 out00.pov.ini
after:
jmoldata
On 02/07/2014 04:27 PM, Rolf Huehne wrote:
Hi all,
in Jmol 11.6.8 the following commands used to work (example: PDB entry
1DEH):
selection_expression = proteinogenic AND *: + A;
selected_atom_count = {@selection_expression}.size;
print selected_atom_count
I forgot to
Otis, I think the problem is that you expect to be able to use all the back
doors you are used to using. In this case you are constructing your own
simulation url and hoping that is all you need. If you do that, then you
would have to follow exactly what the JSME applet does when it delivers a
2D
OK, so there is something subtle going on here with the variables. I think
you are hitting a bug fix, actually. So how does this work?
*load =1crnx = cysprint xcysprint @xselect x0 atoms selectedselect @x36
atoms selected*
What is going on here?
a) *print x* does just that. It prints
Hi all,
in Jmol 11.6.8 the following commands used to work (example: PDB entry
1DEH):
selection_expression = proteinogenic AND *: + A;
selected_atom_count = {@selection_expression}.size;
print selected_atom_count
The output should be 2781.
In Jmol 14.0.5 and 14.1.8 it doesn't
Hi,
So the real question is this:
I have a variable that is the string form of an atom expression: cys
and :A, for instance. How do I get the atom expression itself in a
variable?
x = cys and :A
The answer may surprise you. The key is the old Jmol DEFINE command:
define x
Bob,
I was just testing 2d and 3d to make sure that was not the issue.
OK, I see that for Jmol.search(jmol, :smiles:CCOCC) also.
Does that mean that search is essential for the sync - i.e. you cannot load a
local server molfile into Jmol/JSpecView is a sync state?
The back door is not
On 02/07/2014 05:51 PM, Robert Hanson wrote:
OK, so there is something subtle going on here with the variables. I think
you are hitting a bug fix, actually. So how does this work?
*load =1crnx = cysprint xcysprint @xselect x0 atoms selectedselect @x36
atoms selected*
What is going on here?
Hi Robert,
Thanks for the suggestion. I do have a VPN set up, but no mapped drives, so
I looked into that a little but it did not seem to be involved.
One other observation: The load command works from the console. Is the
open button in the GUI doing something different than load? I guess it
is,
Thanks, I removed .zip and it started working.
Is there a way to speed up the load time? It takes ~20+ second to load it:
http://modbase.compbio.ucsf.edu/foxs/cgi/showRes2.pl?dirname=pdbfiles_38_22_11_7_1_114profileFileName=x140xlf.dat
On Wed, Feb 5, 2014 at 8:04 AM, Robert Hanson
Hi,
I'm clearly not reading the documentation correctly and I'm missing something.
I want to use the JSmol callback functionality. What am I doing wrong?
Thanks,
--Chuck
My javascript:
function init_jsmol(state) {
// … other initialization
Am 07.02.2014 20:38, schrieb Charles Harrison Shubert:
Hi,
I'm clearly not reading the documentation correctly and I'm missing
something. I want to use the JSmol callback functionality. What am I
doing wrong?
Thanks,
--Chuck
My javascript:
function init_jsmol(state) {
// … other
Thanks for the suggestion! I tried several versions of your suggestion.
Adding a readyFunction to Info worked (where Info.readyFunction points to
function rather than just the function name worked, but I couldn't make
messaagecallback work. I tried pointing Info.messagecallback to both the
Am 07.02.2014 22:54, schrieb Charles Harrison Shubert:
Thanks for the suggestion! I tried several versions of your suggestion.
Adding a readyFunction to Info worked (where Info.readyFunction points to
function rather than just the function name worked, but I couldn't make
messaagecallback
Bob,
I spent the day poking around, and I think I'm beginning to understand some of
this. I do see how to get a local file into the triumvirate of applets with
sync.
Two questions:
Where is this coming from:
Actelion Java MolfileCreator 1.0 FILE ???
NMRDB.ORG ???
I take it that this
I just started using 14.1.8 in a page and I have a strange error:
- when page is local (file:// ), JSmol loads fine the model + script
- when I load via local webserver (http://127.0.0.1/ ...), I get this error on
page
load:
Error: ReferenceError: href is not defined
Archivo de origen:
If load a file into Jmol, you have to send it a sync signal via
Jmol.updateView(jmolApplet0);
It won't do that automatically.
Bob
On Fri, Feb 7, 2014 at 11:37 AM, Otis Rothenberger osrot...@chemagic.comwrote:
Bob,
I was just testing 2d and 3d to make sure that was not the issue.
OK,
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