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 :
> Hi Thomas,
>
> It is possibl
(){
return rot();
}
function no_rot2(){
var x = rot();
}
function rot_ok1(){
rot();
}
Alex
- Ursprüngliche Mail -
> Von: "Alexander Rose"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Mittwoch, 16. April 2014 11:21:08
> Betreff:
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: "A
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"
> An: jmol-users@lists.sourceforge.net
> Gese
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"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Mittwoch, 26. Februar 2014 21:43:11
> Betreff: [Jmol-
tag, 25. Februar 2014 21:28:59
> Betreff: Re: [Jmol-users] user defined color scheme
>
>
>
> absolutely! You could chop off the second white with:
>
> color @{ "hslChain="+color("red", "white", 50, true) + color("white",
> "bl
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 -
>
Hi,
ok, but naming is still good to use it with color("myHSLcolorScheme", 1, 100,
20)
Alex
- Ursprüngliche Mail -
> Von: "Robert Hanson"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Dienstag, 25. Februar 2014 20:54:20
> Betreff: Re: [Jmol-users] user defined color scheme
>
>
>
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
idea, though, to
> create 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]"
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
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"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Dienstag, 11. Februar 2014 16:19:44
> Betreff:
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:
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 singl
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 i
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 n
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 op
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"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Montag, 5. A
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"
> An: jmol-users@lists.sourceforge.net
> CC: "Joel Sussman" , "Vlad
Hi,
use single quotes: '
jmolHtml('aaa');
or escape the double quotes: \"
jmolHtml("aaa");
Best
Alexander
Am 15.04.2013 um 21:07 schrieb grid bird:
> how to deal with double quotes within jmolHtml(" ") ?
>
>
>
> On Mon, Apr 15, 2013 at 12:59 PM, Robert Hanson wrote:
> careful with those
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 accept
gt; ???
>
> Eric
>
> At 3/29/13, 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.
>>
&g
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 nu
Hi,
try:
center {visible}
Alex
- Ursprüngliche Mail -
> Von: "Andreas Truszkowski"
> 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. Thereb
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 wrote:
> Thanks.
>
> Currently, I am trying t
Hi,
it gets better and better, I wonder if there is a limit.
Alex
PS: While zooming I noticed that the leftmost line of pixels gets wrapped to
the right side.
- Ursprüngliche Mail -
> Von: "Robert Hanson"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Mittwoch, 24. Oktober 2012 07
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 com
l... package, so that there's no conflicts 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
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)
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 pr
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 f
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
>
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
osurface command:
>
> isosurface solvent set 1
>
> but it's definitely a bug. I will look into it. I can find
>
> Thanks. Checking in my archives, the problem was there in 11.1 at
> least (back when I got started in Jmol.) This certainly will be a
> challenge. Why do
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
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
Map.containsValue(newName)) {
Alex
- Ursprüngliche Mail -----
> Von: "Alexander Rose"
> 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,
>
> - Ursprün
so need to replace the "#" character
for all new file names as done in line 1270: newName =
TextFormat.replaceAllCharacters(newName, "#", "_"); Well, now we are back at
creating special names for all files (no "#" characters), with that I'm ok
though. Some char
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 her
test if a file with an identical
content has already been added and if so use that file instead
Best
Alex
- Ursprüngliche Mail -
> Von: "Alexander Rose"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Dienstag, 17. Juli 2012 20:32:46
> Betreff: [Jmol-users]
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 "http___host_path_getPa
link to pngj https://www.dropbox.com/s/rcwwtns8rypi7qg/1crn.png
- Ursprüngliche Mail -
> Von: "Alexander Rose"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Dienstag, 17. Juli 2012 13:36:26
> Betreff: artifacts inside protein surfaces
> Hi,
>
> I thi
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
-
- Ursprüngliche Mail -
> Von: "Alexander Rose"
> 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 clicki
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 ta
Hi,
Am 20.06.2012 um 17:26 schrieb Robert Hanson:
>
>
> On Wed, Jun 20, 2012 at 9:33 AM, Alexander Rose
> wrote:
> Hi,
>
> I try to get the ID of an isosurface/draw object upon clicking on it. I tried
> 'bind "LEFT" _pickIsosurface' but I don
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 isosurf
Hi,
Try testing for {cartoon=0}.length.
=> select *; if ({cartoon>0}.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,
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 the
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 Secur
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
> wrote:
> Hi Bob,
>
> here is how I understand it now
>
> compare {22-31} {7-16} SUBSET {*.CA} ATOMS {24-31} {9-16}
>
>
be:
>
> compare {22-31} {7-16} SUBSET {*.CA}
>
> ah, but I think there's a bug there. You have 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, Alexande
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
-
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"
> An: jmol-users@lists.sourceforge.net
> CC: jmol-users@l
Hi Bob,
Am 21.01.2012 um 13:28 schrieb Robert Hanson:
>
>
> On Fri, Jan 20, 2012 at 1:27 PM, Alexander Rose
> wrote:
> Hi Bob,
>
> here is what I tried:
>
> bind "ALT-LEFT" "javascript jmol_center(_X, _Y, _picked);";
> bind "ALT-LEFT&q
- Ursprüngliche Mail -
> Von: "Bob Hanson"
> An: jmol-users@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
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
gt;
> On Wed, Nov 16, 2011 at 11:22 AM, Robert Hanson wrote:
> I get it. That's what I needed. Please compare:
>
> http://stolaf.edu/people/hansonr/jmol/test/test-fog-jmol.png
> http://stolaf.edu/people/hansonr/jmol/test/test-fog-povray.png
>
>
>
> On Tue, Nov 1
pigment { color rgbft <0,0,0,1,0.8> } }
}
plane{ z, 5050
texture { 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
&g
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 the
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 with
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 documente
> connections were indicated differently. 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, 201
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 u
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 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 separat
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 th
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 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 m
chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip has the
> fix.
>
> Really appreciate your pointing that out.
>
>
>
> On Mon, Aug 8, 2011 at 12:52 PM, Robert Hanson < hans...@stolaf.edu >
> wrote:
>
>
> Argh. EnumPalette! OK. That's fixed; will get a cop
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 dragging).
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 d
h the Jmol
> application?
> there's a TimeOut command now.
>
>
> On Mon, Mar 14, 2011 at 4:44 AM, Rolf Huehne < rhue...@fli-leibniz.de
> > wrote:
>
>
>
> On 03/12/2011 05:07 PM, Alexander Rose wrote:
> > Hi,
> >
> > thanks Paul,
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 us
understand from the posts 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?
&g
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 cou
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
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:
>
> pri
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
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. Howeve
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=1&data_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
--
that. Yes, you could set up your own
> color scheme at the same time:
>
> isosurface sasurface map property groupid colorscheme
> "user=[xff],[x00ff00],[xff]"
>
> for example, but with 26+ colors. Then you also want to make sure you
> define the range:
>
&
s is to say within 5.0 angstroms of either group
> 0 or group 113. In your case, group 0 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, Alexande
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 aroun
Hi,
- Ursprüngliche Mail -
> Von: "Nicolas Vervelle"
> An: "List - JmolUsers"
> 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 extension , that is an
> extension to d
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 correctly
(resending was too big >40kb)
Hi,
- Ursprüngliche Mail -
Von: "Robert Hanson" < hans...@stolaf.edu >
An: jmol-users@lists.sourceforge.net
Gesendet: Mittwoch, 24. November 2010 19:02:53
Betreff: Re: [Jmol-users] obj surface files exported from pymol
> Alexander,
>
> Glad to hear
- 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:
> >
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"
> An:
1:47 PM, Robert Hanson < hans...@stolaf.edu >
> wrote:
>
>
> Jmol just hasn't been set up to read OBJ files written in quite that
> format (where the vertices and faces are intermixed that way). Please
> send me the file; I'll fix it in short order.
>
> Bo
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