It should not load the structure if it is local, because it depends upon a
remote server to access the file first and transform it to base64, and the
remote server fails upon trying to access file://There obviously should
be a different message there: Sorry, your browser cannot open a local
Hi,
I think you's are ignoring me again. I asked if one could create
transparent PNG images using Jmol. Plus I would also like it if you could
give me a code I can copy and paste into Jmol's script editor that I could
use to create animated gif files without having to use a third party
software
Hi all,
I recall that there is some way in Jmol to “grab” and move an atom to a new
position. I don’t recall how to do this, can someone please remind me?
Also, if I move the atom and then write the pdb file, will the file include new
positions of atoms, rather than the original coordinates—or
A little more investigation paid off - I think this is it:
set allowMoveAtoms FALSE
Set this parameter TRUE to allow the moving of selected atoms (not just whole
molecules) using ALT-LEFT drag and ALT-SHIFT-LEFT drag.
On May 1, 2014, at 8:12 AM, Frieda Reichsman frieda...@mac.com wrote:
Hi
Why are you's ignoring me, again?
On Thu, May 1, 2014 at 8:15 PM, Brenton Horne brentonhorn...@gmail.comwrote:
Hi,
I think you's are ignoring me again. I asked if one could create
transparent PNG images using Jmol. Plus I would also like it if you could
give me a code I can copy and paste
Brenton,
Nobody ignores anyone here. This is a community of users who generously provide
support to one another. No one gets ppaid for doing this and everyone's time is
limited.
So you must be patient.
In addition, there is documentation that you can read and will provide at least
partial
Dear Frieda
Try some of the modes in set picking and also rotate selected, translate
selected
You can alos script movements by changing the XYZ values of an atom
De: Frieda Reichsman frieda...@mac.com
Enviado: jueves, 1 de mayo de 2014 14:26
Para: Jmol Users
Bob,
The problem is that I have a large number of these local pages on
various old computers for which nothing has changed except Java
updates. All these pages used to run and now don't. And nothing has
been changed in the javascript.
With one of my old computers, when I
Where's that reply directing me to the documentation? I didn't get it.
On Fri, May 2, 2014 at 12:00 AM, Herráez Sánchez Ángel angel.herr...@uah.es
wrote:
Brenton,
Nobody ignores anyone here. This is a community of users who generously
provide support to one another. No one gets
ppaid
For animated GIFs, check out these:
http://chemapps.stolaf.edu/jmol/docs/#capture
http://chemapps.stolaf.edu/jmol/docs/#writeimagesandframes
--
Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Hi Brenton,
I have to second what Angel said. This is a great community. With the
number of questions I asked when first getting started, if they didn't
ignore me, I'm pretty sure they don't ignore anyone ;)
I answered your animated gif question privately. The solution is only 2
lines of code.
it's in the list
[https://pod51047.outlook.com/owa/service.svc/s/GetPersonaPhoto?email=hansonr%40stolaf.eduUA=0size=HR96x96]
from Robert Hanson hans...@stolaf.edu
Tue 29/04/2014 15:02
http://sourceforge.net/p/jmol/mailman/message/32281689/
De: Brenton Horne
I had seen these two pages, but the first one gave me a non-looping GIF
file, the 2nd I've already used to create a functioning code
name = ./images/RTramadol.png;
nFrames = 40;
nDegrees =9 ;
thisFrame = 0;
width = 539;
height = 260;
message loop;
thisFrame = thisFrame + 1;
fileName =
Hi Pat
Java has indeed changes its security policy a lot.
Most of my old Jmol pages run from local disk were completely blocked with Java
updates
1. Are you using Jmol.js?
2. What version of Jmol and what version of Java?
You can partially overcome some problems just by updating to Jmol 14.
I am not aware that animated PNG files exist
De: Brenton Horne brentonhorn...@gmail.com
Enviado: jueves, 1 de mayo de 2014 16:11
Para: jmol-users@lists.sourceforge.net
Asunto: Re: [Jmol-users] Creating transparent PNG files
I had seen these two pages, but the
I just tested jmol-14.1.14_2014.04.29 downloaded from StOlaf
Jmol application
load $caffeine
ERROR en guión: java.io.FileNotFoundException: F:\descargas\
\chemical\structure\caffeine\file?format=sdfget3d=True (El sistema no puede
encontrar la ruta especificada)
load
Hi,
Does anybody know how I might overcome a problem with Jmol Wiki I'm
encountering? See I tried to create an account using this email account as
my email address and it's been over two hours since I created an account
and I'm yet to receive a confirmation email from Jmol wiki. I tried going
to
Brenton, I have some access to the wiki but not full admin access,
and right now I am not at my computer where I have the passwords.
Anyway, what was your username? I will try and see if I get any clues.
We have a lot of spammers at the wiki, so there are restrictions, but it should
allow you
I suspect that some of the confusion here is in the fact that the loop
command does not appear to be set when writing the GIF. Rather, if an
animation is set to loop in Jmol, then it generates a looping GIF by
default. In other words, you must set this:
animation MODE LOOP
before you export to a
Should be fixed in the 4/30 upload. I have a feeling the timestamp did not
change. But do try downloading the zip file from SourceForge again.
Ah -- this is not updated at chemapps yet
Bob
On Thu, May 1, 2014 at 10:27 AM, Herráez Sánchez Ángel angel.herr...@uah.es
wrote:
I just tested
when writing the file, use
write COORD ...
and make sure you have selected all the atoms you wish to save.
On Thu, May 1, 2014 at 9:01 AM, Herráez Sánchez Ángel
angel.herr...@uah.eswrote:
Dear Frieda
Try some of the modes in set picking and also rotate selected, translate
selected
Pat, from my limited experience, i woul d saggest you to take the chance now to
upload ur files on servers and moving to JSmol. Let it go Java that will still
be giving troubles all the way. The update to JSmol should not be taht bad as u
can imagine.
Pino
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