So am I restricted to using Xe (or some other element) to indicate
pseudo-atoms? Or does Jmol support some form of pseudo atom
specifically (for SD format)?
Thanks,
- ---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint
n't miss this year's exciting event. There's still time to save
> $100.
> Use priority code J8TL2D2.
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://
> java.sun.com/javaone___
> Jmol-users mailing list
> Jmol-users@
rom smi23d (I think the licenses allow
that) - though I imagine it'd be quite a bit of work. alternatively
you could pull 3D structures via a web service.
Do you plan on generating minimum energy structures? Or just "a" 3D
structure?
- --
iasing? So that when the mouse is released the current view
would be drawn in an antialiased fashion, rather than during the
actual movements themselves
---
Rajarshi
Thanks for the pointer -solves my problem perfectly
On Aug 7, 2007, at 2:55 AM, [EMAIL PROTECTED] wrote:
> Quoting Rajarshi Guha <[EMAIL PROTECTED]>:
>
>> Hi, this is not really a Jmol question, but it is part of a Jmol
>> based app and the Jaavscript guru's ar
tp://some.where/something.cgi?smiles';
openWindow with the result of calling url;
}
Any pointers would be appreciated
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04
ew on the PDB website
-------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
plet:
jmolInitialize("./jmol");
jmolApplet(400, "console on");
jmolLoadInline([m3, m1]);
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerpri
s to
10.9.86)
Thanks a lot ,
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
Q: What do you get when you put a spinning flywheel in a caske
I could convert it to SDF but I figured that I'd
loose information (such as secondary structure etc) - is that correct?
If so, then it appears that converting the SDF to PDB and then
concatenating would be the way to go (?)
---
R
On Thu, 2006-10-26 at 19:38 +0200, Angel Herraez wrote:
> Timothy Driscoll answered to Rajarshi Guha:
>
> > > * Since Jmol cannot show multiple structures, I need to convert my SDF
> > > to PDB and concatenate it to the protein PDB. Is this correct?
> > >
>
ng directory :(
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
So the Zen master asked the hot-dog vendor,
"Can you make me one with everything?
jar files from the
10.9.85 tarball.
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
Q: Why did the mathematician name his dog "Cauchy
it's not clear as to how I attack this problem (at
least in an elegant/efficient manner)
Any pointers would be appreciated
Thanks,
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04
er it's brute force :(
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
Q: What is a dyslexic, agnostic, insomniac
On Mon, 2006-09-18 at 23:48 +0200, Nicolas Vervelle wrote:
> Hi,
>
> how are you including Jmol code in your own code :
> - using Jmol.jar ?
> - using Jmol source code ?
Jmol.jar
---
Rajarshi Guha <[EMA
since then?
Thanks,
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
The emacs religion: t
rwise available?
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
186,282 miles per second:
It isn't just
ngs up Jmol to view it (via CdkJmolAdapter)
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
Without love intelligence is dangerous;
without in
undError:
org/jmol/api/JmolAdapter
at org.guha.rcdk.view.ViewMolecule3D.show(ViewMolecule3D.java:37)
Also the above jar file is about 13Kb big - is that supposed to the case
(since compiling the sources gives me 2.2M jar file)?
-
d to the applet
jar file
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
Q: What do you get when you cross a mosquito with a mountain climber?
A: Nothing. You can&
3D.show(ViewMolecule3D.java:37)
NULL
Clearly, Jmol is starting up - but I cant see why I should get a
security exception when I'm running the application code (and not as an
applet).
My system is Fedora Core 5 64 bit, JDK 1.5.0_07, Jmol 10.3.1
--
totally wrong :(
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
How I wish I were what I was when I wis
hanks,
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
A committee is a group that keeps the minutes and loses hours.
-- M
? Or can I preprocess it and feed it to
JMol in some way?
Thanks,
---
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
-
DK 1.5, Fedora Core 4.
Is there something I need to install/setup? - I haven't kept up with the
browser/jdk requirements for the applet :(
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CC
and send me the resulting output ?
The output of running ant -v is attached.
Thanks,
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2
ssing something from my build environment? xgettext is present.
Thanks,
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1B
On Tue, 2005-08-30 at 12:06 +0200, Egon Willighagen wrote:
> On Tuesday 30 August 2005 11:48 am, Rajarshi Guha wrote:
> > If the former then along with the text, if structures could be converted
> > to SMILES that would be useful. Similarly, reactions could be converted
> >
with the text, if structures could be converted
to SMILES that would be useful. Similarly, reactions could be converted
to a similar format.
Is this what you were planning to do?
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jij
You specify a source and one or more targets in a CONECT record.
>
> If you specify a target more than once then Jmol will recognize it as a
> double/triple bond.
Aah, thanks for the pointer
---
Raja
em to
work.
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
If you don't get a good night kiss, you
fine
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
A red sign on the door of a physics pro
from the plugin menu. So
> > how do I get a plugin to show up in Jmol?
>
> On the page http://www.woc.science.ru.nl/cdk/, it is said that the plugins
> must be copied to ${HOME}/.jmol/plugins to be recognized by Jmol
Aah, yes. Thanks for the pointer
arting Jmol did'nt show my plugin from the plugin menu. So
how do I get a plugin to show up in Jmol?
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint:
thm. Once the
transformation matrix is obtained, the coordinates of all the atoms can
then be converted.
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2
r would it have to be written
from scratch (license issues)?
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2
ics research. I was wondering if there are any
faculty members on this list (as well as the CDK lists) that might have
seen this. Clearly, coding of a visualization tool or cheminformatics
framework cannot the sole goal of such a funding opportunity - but they
could be useful components.
--
/ MOE etc). In that case its understandable that
they would not introduce a new tool. However a I mentioned above, if you look
at Jmol as a component then I think that is an important and useful peice of
software.
But I'd be interested in hea
is not visible) and a corresponding option to unhide it
Right now these are things I'd think would be useful. Are there other
aspects you'd like more input about?
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.
rst 3
residues. That might explain why theres no overlap
> Q: Do the behaviors in PyMOL or MOE make sense to you?
Both seem to make sense to me - I prefer the way MOE is setup )I think MOE is a
little better in terms of interface)
Rajarshi Guha
<[EMAIL
a point somewhere near the first molecule that
was loaded - which makes sense since the first molecule was 'centered'
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7
apart and hence only one is
'visible' at a time - unless I translate them
I have'nt been able to load them into MOE yet (it does'nt like the babel
converted PDB files). I'll let you knwo what happens
---
Rajarsh
ule - it seems to be
in the same position (not further off or closer in) - basically no
change in view
Am I meant to see this? Or should I be seeing something else?
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net&
ery* cool!
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
Q: What's yellow, linear, normed and com
ule, Alt+drag middle button
rotates the selected molecule
(Personally, I like the idea of extending selections - makes working
with large proteins very handy - does Jmol have this capability?)
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8E
be considered (rather than a specific one). In that case
would it be reasonable to consider either
a) the centroid of all the points (of all the molecules) or
b) the center of the coordinate system that constitutes the current
viewport
---
ure how this would translate in terms of coordinate systems for
the individual molecules (each molecule having its own world
coordinate?) or whether this doable :-/
But it would be very nice :)
---
Rajarshi Guha <[EMAIL PROTECTED]>
the values from the B factor column to color the region corresponding to
the atom - though I don't know how feasible this would in terms of code
(This is the way I color surfaces by hydrophobicity in Pymol.)
---
Rajarshi Guha
t to render solid surfaces of
The Connolloy surface rendered pretty fast for a protein (PDB entry 1A22). It
appears that the Williams surface takes longer (at least from the command
line). That might be due to unoptimized code or maybe its just slower than the
Connolly algorithm.
If you want to take a
hy I have it written.
> Q: Do you just have a set of points? Or do you have edges+points in order
> to define triangles?
Just a set of points
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.ne
somehow to overlay these points on the structure in Jmol?
I recall somebody mentioning that there was a trick to do something
similar but I can't find the original post.
Any pointers would be appreciated
Thanks,
---
Rajarshi Guha &l
ch to the Renderer2D class and it works like a
charm
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
s and associated data to see if anything obvious pops
up.
A slighlty, unrelated question - would it be more feasible to do this
with the CDK 2D renderer?
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerpri
ociated data to see if anything obvious pops up.
A slighlty, unrelated question - would it be more feasible to do this
with the CDK 2D renderer?
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0
run out of
memory. Is this a problem I should be concerned about?
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7
you sent me.
> Please let me know if people encounter problems with other output files,
> or with output from other versions of gamess.
Thanks a lot. I'll check it out with some more molecules.
---
Rajarshi Guha <[EMA
ase let me know if people encounter problems with other output files,
> or with output from other versions of gamess.
Thanks a lot. I'll test it out on some molecules.
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.
decimal point.
I'm not really sure about that - I'd have to do some digging, though I
think Egons interpretation is correct.
As for the coordinates a geometry optimization was'nt specified so I
think those are the input coordinates.
mistakes.
If this could be bundled in a webpage which takes the 3D coordinates,
writes a job script, takes the output and displays it Jmol that would be
great.
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
is because my version of gamess is old? Or am I supposed to post
process the output file? Has anybody used gamess output for this
purpose?
Thanks,
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprin
I thought
that Jmol was capable of using CDK's I/O capabilities and since CDK
supports HIN, is there a way to get Jmol to use the CDK facilities?
Thanks,
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
d line that you are using to try to retrieve the Jmol
> source from CVS?
I was missing the Jmol-HEAD - its working now.
---
Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net>
GPG Fingerprint:
Hi,
I'm trying to get the Jmol source code via CVS but it seems to be
hanging on the login stage. Is there a problem with the Jmol CVS or can
I get the source from elsewhere?
Thanks,
---
Rajarshi Guha <[EMAIL PROTECTED
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