Hi,
there is also
select groupindex=10
it starts at 0 and is unique for all residues, i.e. spanning multiple files or
models, but
using {modelindex=1}.min and .max you can get the range for each model. HTH.
Alex
Am 16.06.2014 um 19:25 schrieb Angel Herráez angel.herr...@uah.es:
Hi
Hi,
thx, loading seems to work now. I stumbled about this:
p = { 1 2 3 };
print p.X*p.X
script ERROR: invalid argument
print p . X*p . X
print (p.X)*p.X; // works
Alex
- Ursprüngliche Mail -
Von: Robert Hanson hans...@stolaf.edu
An:
Hi,
$ n = 2;
$ print n
2
$ print n* 2
script ERROR: invalid argument
print n* 2
$ print n*2
$ print n * 2
4
$ print n*2.0
script ERROR: invalid argument
print n*2 0.0
Alex
- Ursprüngliche Mail -
Von: Alexander Rose alexander.r...@weirdbyte.de
(){
return rot();
}
function no_rot2(){
var x = rot();
}
function rot_ok1(){
rot();
}
Alex
- Ursprüngliche Mail -
Von: Alexander Rose alexander.r...@weirdbyte.de
An: jmol-users@lists.sourceforge.net
Gesendet: Mittwoch, 16. April 2014 11:21:08
Betreff: Re
Hi,
jmol-14.1.14_2014.04.14 Application
$ load test.pdb
script ERROR: ERROR creating model: java.lang.NoSuchMethodError:
javajs.util.V3.cross(Ljavajs/util/V3;Ljavajs/util/V3;)V
load test.pdb
test.pdb
ATOM 1 N MET A 1 13.170 -71.138 -17.133 1.00 91.98
ATOM
Hi,
already fixed in jquery (http://bugs.jquery.com/ticket/14282) 1.11 or 2.1
Alex
Am 04.03.2014 um 23:38 schrieb Robert Hanson:
We're not really at liberty to modify the jQuery code (unless it's a critical
failure, of course). You could register a bug with jQuery about this, though.
Hi,
I get quite a few these in the Java console: isarray=false wasX=false
In the Jmol applet menu there is an entry 'JavaScript Console'
- Ursprüngliche Mail -
Von: Robert Hanson hans...@stolaf.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Mittwoch, 26. Februar 2014 21:43:11
,
blue, 50, true)[10][0] }
On Tue, Feb 25, 2014 at 2:04 PM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi Bob,
chaining should work or? haven't tried it.
color @{ hslChain=+color(red, white, 50, true) + +
color(white, blue, 50, true) };
That is quite flexible. A caveat
Hi,
print _version
1401011
load =1blu
color whiteRed=[xFF] [xFF]
color {*} property temperature whiteRed range 0 50
protein colored discretely in white and red
I would like to get an interpolated coloring from white to red.
Do I need to put the interpolation steps/colors myself in
a series from one color to another just based on a linear
gradient. Wonder what that would look like. Should we try it?
On Tue, Feb 25, 2014 at 10:59 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
print _version
1401011
load =1blu
color whiteRed=[xFF] [xFF
Hi Bob,
cool, I haven't tried it but it sounds great.
Can you name the color scheme created with color(...) to use them like this:
color property temperature myColorScheme
would this work?
color property temperature @color(...)
Best
Alexander
- Ursprüngliche Mail -
Von: Robert
Hi,
ok, but naming is still good to use it with color(myHSLcolorScheme, 1, 100,
20)
Alex
- Ursprüngliche Mail -
Von: Robert Hanson hans...@stolaf.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 25. Februar 2014 20:54:20
Betreff: Re: [Jmol-users] user defined color
Hi Bob,
chaining should work or? haven't tried it.
color @{ hslChain=+color(red, white, 50, true) + + color(white,
blue, 50, true) };
That is quite flexible. A caveat is white occurs twice. But for large n it is
probably negligible.
Alexander
- Ursprüngliche Mail -
Von: Robert
Hi,
there is an IONIC radius option for the isosurface comand, have you tried
that?
http://chemapps.stolaf.edu/jmol/docs/#isosurface
Alex
- Ursprüngliche Mail -
Von: Pshemak Maslak n...@psu.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 11. Februar 2014 16:19:44
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
Hi,
I am also quite interested in that.
Can I save my app’s private UI state (preferences, etc) as a variable
or static function in JSmol so that PNGJ will write it to the .png
file?
As far as I know user defined variables or functions (from jmolscript)
are not saved within the Jmol state.
Hi,
- the hash type is missing in the description of the type method under the
heading general .xxx functions
I do not know if this is intentional. Range selecting from lists returns a list
when there is more then one item in the list but only the item for single item
lists (and not a single
Hi,
The question is: how can I retrieve the label of the atom that was
clicked? I set such label in a Jmol script using the set
hoverLabel command and I would like to read it back in the
pickResidue function to decide what to do (visualize some
information or not).
If this is not
Hi,
in application there is this number in the lower right corner. ms/redraw or
something. Is there a way to get this in JSmol (and in the applet too)? Then we
could give you those numbers.
Alex
Am 16.08.2013 um 16:08 schrieb Robert Hanson:
I would very much appreciate feedback on a new
Hi,
what about a inverse full screen antialiasing, i.e. rendering at half the
screen resolution? That could help with full screen applications on all this
devices with high native resolutions.
Alex
Am 16.08.2013 um 16:08 schrieb Robert Hanson:
I would very much appreciate feedback on a new
Hi,
I found it. You can get the on/off aka visible status via 'isosurface list',
but not via shapeInfo (which is would be great)
Best
Alexander
- Ursprüngliche Mail -
Von: Alexander Rose alexander.r...@weirdbyte.de
An: jmol-users@lists.sourceforge.net
Gesendet: Montag, 5. August
Hi,
does anyone know how to programmatically get an isosurface's on/off status?
Best
Alexander
--
Get your SQL database under version control now!
Version control is standard for application code, but databases havent
Hi all,
here is an ad-hoc definition of a atom-vector format
function load_vector( url ){
if( !url ) return false;
var x = load( url );
var line1_end = x.find(\n);
var line1 = x[1][line1_end-1];
script INLINE @line1;
if(!colr) colr = red;
if(!diameter) diameter =
Hi,
try the pdb2pqr software (http://www.poissonboltzmann.org/pdb2pqr) to get the
partial charges. There is a server at http://nbcr-222.ucsd.edu/pdb2pqr_1.8/
Regards
Alexander
- Ursprüngliche Mail -
Von: Eric Martz ema...@microbio.umass.edu
An: jmol-users@lists.sourceforge.net
CC:
Hi,
use single quotes: '
jmolHtml('FONT face=Arial, Helvectica, sans-serif size=2aaa/font');
or escape the double quotes: \
jmolHtml(FONT face=\Arial, Helvectica, sans-seri\f size=\2\aaa/font);
Best
Alexander
Am 15.04.2013 um 21:07 schrieb grid bird:
how to deal with double quotes within
cool. Thanks!
Am 03.04.2013 um 19:50 schrieb Robert Hanson:
This is done. See http://chemapps.stolaf.edu/jmol/Jmol-13.zip
___JmolDate=$Date: 2013-04-03 12:40:49 -0500 (Wed, 03 Apr 2013) $
___JmolVersion=13.1.15_dev_2013.04.03
new feature: Jmol/JmolData application -I flag accepts input
, Alexander Rose wrote:
Hi,
A while ago I came up with this:
print {nhw}.groupindex.all.count().length
It is also very fast. Much faster then using a for loop in Jmolscript.
Best
Alex
Am 29.03.2013 um 18:39 schrieb Eric Martz:
I have been enjoying jmolEvaluate, e.g.
jmolEvaluate
Hi,
A while ago I came up with this:
print {nhw}.groupindex.all.count().length
It is also very fast. Much faster then using a for loop in Jmolscript.
Best
Alex
Am 29.03.2013 um 18:39 schrieb Eric Martz:
I have been enjoying jmolEvaluate, e.g.
jmolEvaluate({mse.ca}.count) to get the
Hi,
try:
center {visible}
Alex
- Ursprüngliche Mail -
Von: Andreas Truszkowski at_li...@gmx.de
An: jmol-users@lists.sourceforge.net
Gesendet: Freitag, 22. März 2013 10:53:29
Betreff: [Jmol-users] Center of mass of visible atoms
Hi,
I use Jmol to visualize PDB protein data.
Hi,
you could select just the C-alpha atom
select 79:C.CA; label Y79F
Best
Alexander
Am 20.03.2013 um 22:19 schrieb grid bird:
does anyone can give me suggestions about this label problem? thx.
On Wed, Mar 20, 2013 at 2:04 PM, grid bird gridb...@gmail.com wrote:
Thanks.
Currently, I
Hi Smith,
in Jmol script
# load files
load first.pdb;
load append second.pdb;
# initialization
set backgroundModel 1.1; # show the first.pdb as a background model during
animations, frame/model commands
frame 2.1; # show the first model of second.pdb
frame 2.1-2; # limit frame/model commands
with system
javax.vecmath.
Vecmath is included in some systems, I remember having troubles about this
because the vecmath package evolved between releases in some incompatible
ways.
Nico
On Sat, Oct 6, 2012 at 10:28 PM, Alexander Rose alexander.r...@weirdbyte.de
wrote:
Hi,
I'm
Hi,
I have it like this in use:
print load(/servlet/?POST?_PNGJBIN_your_own=parameters);
So you send a POST request to your server and within is the PNGJ enclosed (in
binary form). Th server reads this request and can do something with the
received POST parameters (i.e. save them somewhere)
://chemapps.stolaf.edu/jmol/Jmol-13.zip
On Thursday, August 16, 2012, Alexander Rose wrote:
Hi,
isosurface cavity is missing in state
test case (tested in 13.0.RC6):
load =1crn;
isosurface cavity;
this shows the isosurface but produces in the state
isosurface ID isosurface1 select ({0:326
Hi,
isosurface cavity is missing in state
test case (tested in 13.0.RC6):
load =1crn;
isosurface cavity;
this shows the isosurface but produces in the state
isosurface ID isosurface1 select ({0:326}) ; # here is cavity missing
isosurface ID isosurface1 fill noMesh noDots notFrontOnly
Hi Bob,
I would like to come back to the issue of internalizing an isosurface:
load =1crn;
isosurface ID isosurface1 select {*} molecular;
isosurface ID isosurface1
tmp = script(show isosurface);
isosurface ID isosurface1 INLINE @tmp;
to which you answered:
use
write xxx.jvxl
then
Hi Bob
using # Jmol state version 13.0.RC2 2012-07-21 19:52;
load =1u19;
OK, here you have three isosurfaces. set 1 is the outer set, but there
are two cavities, each of which is big enough to hold a molecule of
water.
there is something strange going on, I still get those fragments
was there in 11.1 at
least (back when I got started in Jmol.) This certainly will be a
challenge. Why do I feel like I've fixed this before?
Bob
On Tue, Jul 17, 2012 at 7:30 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
link to pngj https://www.dropbox.com/s/rcwwtns8rypi7qg
Hi Bob,
I disagree. One thing I changed is that we are also cataloging the
local-file names, and they have no CRC. So they have to be keyed to
their name. The simplest way I could think of was to catalog all files
by name and the remote files also by CRC. So Key is right.
oh, how could I
Hi,
just noticed that isosurface set is only in the state if it is part of the
initial isosurface command
load =1crn;
isosurface ID iso1 cavity set 1;
show state; # set 1 part of the state
isosurface ID iso1 set 2;
show state; # set 1 still part of the state but not set 2
isosurface ID iso1
Hi,
try frame All;display 1.3 OR 1.2.
The display command takes an atom expression, 1.3 OR 1.2, meaning take every
atom that is in model 1.3 or in model 1.2 - then displays these atoms.
Similarly, 1.3 AND 1.2, means take every atom that is part of model 1.3 and
part of model 1.2 - so here the
. Some character sequence such as # would make it more unlikely to
taint innocent file names.
Best
Alex
Bob
On Wed, Jul 18, 2012 at 8:40 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
attached is a small patch that changes zip file creation
- use just the file
)) {
Alex
- Ursprüngliche Mail -
Von: Alexander Rose alexander.r...@weirdbyte.de
An: jmol-users@lists.sourceforge.net
Gesendet: Donnerstag, 19. Juli 2012 17:37:42
Betreff: Re: [Jmol-users] repeated saving/loading of .jmol files
Hi Bob,
- Ursprüngliche Mail -
Von: Robert Hanson
with an identical
content has already been added and if so use that file instead
Best
Alex
- Ursprüngliche Mail -
Von: Alexander Rose alexander.r...@weirdbyte.de
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 17. Juli 2012 20:32:46
Betreff: [Jmol-users] repeated saving
Hi,
I think that was once solved but now there are artifacts inside protein
surfaces. See attached pngj, created on
http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm - Version
12.3.32_dev, I've seen it also in 12.3.33.
Best Alex
link to pngj https://www.dropbox.com/s/rcwwtns8rypi7qg/1crn.png
- Ursprüngliche Mail -
Von: Alexander Rose alexander.r...@weirdbyte.de
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 17. Juli 2012 13:36:26
Betreff: artifacts inside protein surfaces
Hi,
I think
Hi,
I have a problem with saving and loading PNGJ state files to and from a web
server. I load a pdb from the web server (http://host/path?getParams=pdb) and
save it via the ?POST?_PNGJBIN_ request feature. For the zip file collection
the pdb file name gets translated to
Hi,
I would like to sort an atom selection by some atom property. I can do 'var x =
{1}.vdw.all; x.sort; print x;' but then I loose the link to actual atoms. I
know what the 3rd smallest vdw radius is but not to which atom(s) it belongs.
I know that I could use a loop in Jmol-script but that
- Ursprüngliche Mail -
Von: Alexander Rose alexander.r...@weirdbyte.de
An: jmol-users@lists.sourceforge.net
Gesendet: Mittwoch, 20. Juni 2012 16:33:09
Betreff: label and pick isosurfaces/draw objects
Hi,
I try to get the ID of an isosurface/draw object upon clicking on it.
I
Hi,
I try to get the ID of an isosurface/draw object upon clicking on it. I tried
'bind LEFT _pickIsosurface' but I don't any message generated by it in the
Console or via the pick callback.
Is there a way to create a hover-label for isosurfaces other then the automatic
one when the
Hi,
Try testing for {cartoon=0}.length.
= select *; if ({cartoon0}.length) { wireframe -0.1;spacefill 23% } else {
cartoons only }
The .cartoon atom property is the size of the cartoon which in turn is a
mixture of sizes for the different parts - ribbons and traces - the cartoon is
made off.
Hi,
Am 24.05.2012 um 20:37 schrieb Oliver Stueker:
Still I think an option to let Jmol generate a legend for the applied
gradient would be a nice feature.
like 'set isosurfacekey on;' ?
Best
Alexander--
Live
Hi,
is there a way to get a list of all isosurface and contact objects? Like with
'getProperty modelInfo;', which gives you modelInfo.modelCount so you can loop
through modelInfo.models[i]. There is 'getProperty isosurfaceInfo' but this is
only for the currently selected isosurface, that is
Hi Bob,
thanks thats great.
Alex
Am 16.05.2012 um 16:21 schrieb Robert Hanson:
On Tue, May 15, 2012 at 8:31 AM, Alexander Rose alexander.r...@weirdbyte.de
wrote:
Hi Bob,
here is how I understand it now
compare {22-31} {7-16} SUBSET {*.CA} ATOMS {24-31} {9-16}
this moves {22-31
Hi,
I have problems with the compare command and 12.3.10 seems to be the first time
it occurs.
load =1crn;
compare {22-31} {7-16} rotate translate;
works in 12.3.9 but just says RMSD NaN -- NaN Angstroms in 12.3.10 and later.
Can someone confirm that.
Best
Alexander
to do it in this order:
load =1crn;compare SUBSET {*.CA} {22-31} {7-16}
That's a bug.
On Tue, May 15, 2012 at 3:47 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
I have problems with the compare command and 12.3.10 seems to be the
first time it occurs.
load
Hi,
what about:
isosurface ID @surfid ...
Alex
Am 17.03.2012 um 23:39 schrieb Eric Martz:
Bob, thanks for pointing me to resolution for mesh density, and
explaining why contour is not relevant to my unmapped spheres.
I have defined a function to generate one isosurface per
Hi Bob,
thank you so much, this is perfect! - and I see you're working on _OBJECT too,
which is even more great.
bind ALT-LEFT if(_MODE==2){ zoomTo 0.6 (_ATOM); };
Best
Alexnader
- Ursprüngliche Mail -
Von: Bob Hanson hans...@stolaf.edu
An: jmol-users@lists.sourceforge.net
CC:
Hi Bob,
Am 21.01.2012 um 13:28 schrieb Robert Hanson:
On Fri, Jan 20, 2012 at 1:27 PM, Alexander Rose alexander.r...@weirdbyte.de
wrote:
Hi Bob,
here is what I tried:
bind ALT-LEFT javascript jmol_center(_X, _Y, _picked);;
bind ALT-LEFT javascript jmol_center(_X, _Y, _atomPicked
Hi all,
when using Jmol I find myself using either 'set picking CENTER' or 'set picking
SELECT GROUP', so I would like to switch as fast and easy as possible between
the two modes via the mouse. My first idea was to use the 'bind' command to
bind centering to ALT-LEFT and selecting a group to
@lists.sourceforge.net
CC: jmol-users@lists.sourceforge.net
Gesendet: Freitag, 20. Januar 2012 18:20:38
Betreff: Re: [Jmol-users] bind command and picked atoms
_picked is a variable. I thought it was defined prior to the callback.
Sent from my stupid iphone
On Jan 20, 2012, at 10:35 AM, Alexander Rose
/test/test-fog-jmol.png
http://stolaf.edu/people/hansonr/jmol/test/test-fog-povray.png
On Tue, Nov 15, 2011 at 5:22 PM, Alexander Rose alexander.r...@weirdbyte.de
wrote:
Hi,
Am 15.11.2011 um 23:10 schrieb Robert Hanson:
Oh, you mean you were able to direct the fog from the back
Hi,
has anyone tried to get the fog/zShade effect from Jmol into POV-Ray? There is
a fog command in povray and the fog of type 2 looks the thing to use. I have
managed to get a fog in x or y direction that has full effect at half
width/height and decays fast before. However I am struggling
Hi Bob,
I agree to what you said regarding fog_type=1, but why do you think the ground
fog (fog_type=2) is not a solution? It's not just ground fog but fog along the
up vector.
So my idea was that with an up vector that points in the same direction as the
vector from the camera location to
{ pigment { color rgbft 0,0,0,1,0.7 } }
}
plane{ z, 5100
texture { pigment { color rgbft 0,0,0,1,0.6 } }
}
Though this fails for a white background...
I have the feeling I am missing something.
Best
Alex
On Tue, Nov 15, 2011 at 10:29 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi Bob
. No atoms are removed, just
connections. So I'll consider it a bug until someone tells me I have
to put it back in.
See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Wed, Oct 12, 2011 at 8:44 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
on http
Hi,
lol, I just found out about some nice atom properties while I was about to
suggest a feature...
{}.backbone
{}.cartoon
{}.cpk
{}.meshribbon
{}.radius
{}.ribbon
{}.rocket
{}.spacefill
{}.trace
You can use these in select statements as well as to set the style!
Afaik these are not
Hi,
on http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm with caffeine loaded
try 'measure {atomNo=2} {atomNo=7}; connect (atomNo=12) (atomNo=20) delete;'.
Annoyingly, the connect also deletes the measurement.
Best
Alexander
Hi,
afaik there is no 'onkeypress' event in Jmol, though I would like to have one.
However, there are the 'set allowKeystrokes true' setting
(http://chemapps.stolaf.edu/jmol/docs/?ver=12.2#setmisc) and the 'bind' command
(http://chemapps.stolaf.edu/jmol/docs/?ver=12.2#bind). The former can be
Hi all,
I have some problems with amino acids with non-standard sidechains. For the
cartoon/backbone/trace they are not recognized as amino acids though they
contain all the backbone atoms. This is with 12.2RC6. The workaround I have in
mind is to use glycines and have the sidechains as
Hi Bob, Angel,
sorry about the fuzz, I just didn't had the amino acids in the correct order in
the file. After I fixed that, the cartoons emerged in their full glory.
Alex
Am 04.10.2011 um 20:42 schrieb Robert Hanson:
right, this should not be any problem at all. Can you send me a file,
Hi,
In the Jmol application there is a button 'Select a set of atoms using
SHIFT-LEFT-DRAG.'. Can you activate this way of selecting atoms in the applet
somehow via a script command?
Best
Alexander
--
Doing More with
Hi,
I have looked at the diverse 'set picking' options and also the jmol-actions
for the bind command, but I haven't found something similar to the application
button were you can span a rectangle with your left mouse button pressed down
while holding the shift key to select all atoms inside
, 2011 at 12:52 PM, Robert Hanson hans...@stolaf.edu
wrote:
Argh. EnumPalette! OK. That's fixed; will get a copy out later today.
On Mon, Aug 8, 2011 at 7:35 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
when I do this on MAC OSX 10.6.8, Java 1.6.0_26, Jmol
Hi,
I looked at ways to customize the way to interact with Jmol. There is the
bind command, which is quite powerful to modify the mouse behavior. I also
found out about set allowKeystrokes and set showKeystrokes as a quick
alternative to the console. However, there seems to be no way to map
Hi,
when I do this on MAC OSX 10.6.8, Java 1.6.0_26, Jmol 12.2.RC2
load =1crn;
color hbonds blue;
or
load =1crn;
calculate hbonds;
color hbonds blue;
Jmol freezes/stops redrawing (works in 12.2.RC1 though)
Some more observations regarding hbonds
load =1crn; connect ({191}) ({219}) HBOND #
Hi,
all I know is that when you calculate surfaces and give them an ID
isosurface ID iso_molecular MOLECULAR;
isosurface ID iso_sasurface SASURFACE;
then you can hide them individually
hide $iso_molecular;
hide $iso_sasurface;
or show them
display $iso_molecular;
display $iso_sasurface;
Hi,
http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#setmisc
There is a command for rotation and translation each:
set allowRotateSelected FALSE
When set TRUE, this parameter allows user rotation of the molecule
containing the selected atom using the mouse (holding ALT down while
Hi,
thanks Bob for the new remapping feature and the bug fixing on isosurfaces -
very useful to me!
Alex
Am 28.04.2011 um 15:03 schrieb Robert Hanson:
Just a quick note -- Jmol 12.1.43 was released with a bug that broke MOs.
Thanks, Nico, for quickly releasing 12.1.44 to fix that. I'll do
Hi,
is there a way to start the Jmol application and then communicate with it via
the command line?
I have a series a simple calculations I want to do in Jmol (i.e extracting
certain atoms) and just starting the application takes about the same time as
doing the calculations. So I figure I
to this list, several users have used
Jmol that way.
-Paul
Le 12 mars 2011 à 13:09, Alexander Rose a écrit :
Hi,
is there a way to start the Jmol application and then communicate with it
via the command line?
I have a series a simple calculations I want to do in Jmol (i.e extracting
Hi Angel,
Am 12.03.2011 um 17:18 schrieb Angel Herráez:
Alex, I think I am not getting the whole picture. Can't you use the Jmol
script console for that?
Ah, yes, but I would like to do it programmatically, to automize some stuff.
Can I access the Jmol script console from the shell I used
Hi,
I think you can build on this:
jmolScriptWait('var foo = bar;');
var msg = jmolEvaluate( script('echo @foo'); );
Alex
Am 26.01.2011 um 01:05 schrieb Angel Herráez:
Hello all
This must be trivial, but I'm stuck
I need to extract the minimum and maximum residue nurmber from a
Hi Bob,
I tried it with the released 12.1.30 and to me it still looks like there are
points in $isosurfaceObject[] which are not on a surface or a cavity. The image
(http://dl.dropbox.com/u/3778149/3dqb_surface-points2.jpg) shows part of a cut
(via slab plane ...) through an molecular surface
Hi,
Am 21.12.2010 um 16:46 schrieb Robert Hanson:
The gridpoints are cleared from memory after use, and in many cases they are
streamed so as never to accumulate. But do you perhaps mean the vertices of
the triangles that make up the surface? You do have access to those points:
print
Hi,
(using 12.1.25)
I've been working with the 'isosurface cavity' command and got a couple of
questions regarding it.
load =3KDC
This produces a fragmented isosurface:
isosurface id foo select {protein} ignore {not protein} cavity 1.2 5;
Here I am interested in binding cavity
isosurface id
Hi,
I like the .jmol file which contain everything to display a model and added
data in a certain state. It is a quick and easy way to share some findings in a
model with colleagues. And it is obviously more powerful then an image because
it allows manipulation with all of Jmol's powers.
Hi,
I got this when trying to save .jmol file (Signed Applet, 12.1.25):
PDB::http:/127.0.0.1:7070/data/get/?id=1data_action=get_pdb (No such file or
directory)
When loading the file without the type indicator 'PDB::' saving to the .jmol
file works perfectly well.
Best
Alexander
is a water molecule. 113 is also
both a water molecule and a GLU. So the result is two regions,
roughly.
Bob
On Mon, Dec 6, 2010 at 10:12 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
I think there is some bug in the WITHIN(distance, withinAllModels,
atomExpression
the range:
color isosurface range 1 26 # whatever matches the number of colors
you have
Bob
On Fri, Nov 26, 2010 at 9:36 AM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
I'm trying to color the molecular surface by the color of the
underlying atoms/residues.
my naive
Hi,
I think there is some bug in the WITHIN(distance, withinAllModels,
atomExpression) function. It selects more then it is supposed to:
http://proteinformatics.charite.de/jmol-test/html/select_within.html
the page shows two examples where you can select for each first the
atomExpression
Hi,
- Ursprüngliche Mail -
Von: Nicolas Vervelle nverve...@gmail.com
An: List - JmolUsers jmol-users@lists.sourceforge.net
Gesendet: Samstag, 27. November 2010 16:07:56
Betreff: [Jmol-users] Simple popup window with Jmol in JavaScript
Hi,
I am working again on the Jmol MediaWiki
Hi,
I'm trying to color the molecular surface by the color of the underlying
atoms/residues.
my naive approach (not what I want, but colorful):
select protein;
color amino;
isosurface ignore {not protein} select {protein} molecular map property color
translucent;
if I understand it
Hi,
Bob recently showed me you can use script with evaluate, i.e.
jmolScriptWait('var foo = bar;');
var msg = jmolEvaluate( script('echo @foo'); );
console.log(msg);
this should print 'bar' to your browser console
Best
Alex
- Ursprüngliche Mail -
Von: Otis Rothenberger
- Ursprüngliche Mail -
Von: r...@ellerbach.com
An: jmol-users@lists.sourceforge.net
Gesendet: Mittwoch, 24. November 2010 16:26:39
Betreff: Re: [Jmol-users] obj surface files exported from pymol
On Wed, November 24, 2010 10:17 am, Alexander Rose wrote:
Manipulating the pdb file
send me the file; I'll fix it in short order.
Bob
On Tue, Nov 23, 2010 at 1:00 PM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
I tried to view obj files exported from pymol but could not get it to
work. The obj file from pymol looks reasonable, i.e.
# file
On Tue, Nov 9, 2010 at 6:23 AM, Robert Hanson hans...@stolaf.edu
wrote:
Alex,
That's what I needed. We will need a new parameter:
set rotateSelectedAtoms
It will be in Jmol 12.1.21, to be released later today.
Bob
On Tue, Nov 9, 2010 at 4:20 AM, Alexander Rose
Hi,
I tried to get the jvxl data for an isosurface as a string via Jmol.js. I used
'show isosurface' and at first jmolScriptWaitAsArray which does not quite work
and then jmolScriptWaitOutput which works fine.
jmolScriptWaitAsArray returns an array whih includes the jvxl data but all
double
Hi,
I tried to view obj files exported from pymol but could not get it to work. The
obj file from pymol looks reasonable, i.e.
# file: pymol.obj
v 9.775413 -10.004283 -3.190735
v 9.996734 -10.529106 -3.207321
v 9.653004 -10.796073 -2.960678
vn -0.552027 -0.351046 -0.756328
vn -0.541946
window axis, regardless of how
the model is oriented? Is that the problem? There might be a way of
doing that with quaternions.
On Mon, Nov 8, 2010 at 12:39 PM, Alexander Rose
alexander.r...@weirdbyte.de wrote:
Hi,
From the manual
set allowRotateSelected FALSE
When set TRUE
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