Yes, that's before the fix.
Jmol.___JmolVersion="14.4.0_2015.12.05"
bug fix: JmolData.jar does not update atom screen positions upon REFRESH or
select {visible}
bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not
execute model
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should all be working with the latest at SourceForge (14.4) now.
On Sat, Dec 5, 2015 at 1:27 PM, Rolf Huehne wrote:
> Am 05.12.15 um 19:49 schrieb Robert Hanson:
> > I find that JmolData does not work as expected and requires a bug fix to
> > get this work. Not sure why/how it is working for you
Am 05.12.15 um 19:49 schrieb Robert Hanson:
> I find that JmolData does not work as expected and requires a bug fix to
> get this work. Not sure why/how it is working for you both. I have had
> to fix JmolData.jar to make the following work:
>
> // script t3.spt
>
> function getScreenBoundary(atomS
Just a few comments here:
Be aware that I just recently fixed a bug in point(,true) as well as
atom.sxyz. So use the latest SourceForge version of Jmol 14.4 if you
utilize those functions.
function getScreenBoundary could be simply the following, which executes
far faster:
function getScreen
Just tried your example with my modified script - using
http://publcif.iucr.org/cifmoldb/gui/cifjmol.php?jsmol=y&pdbid=1DEH
and the console.
Works except for the final translation - i.e. for mmcifs I will have
to remove the last bit:
rm=_width-sxInfo[2];
lm=sxInfo[1];
t=(rm-lm)/2;tp=t/_width*100;
It wasn't that your script didn't work, it was my modified script that
didn't work (i.e. using the atom sites that correspond to the initial
min max positions in subsequent calls):
rotate best; # moved here
startZoom = 100;
zoom {visible} @startZoom;
# rotate best; # if done here the initial c
Am 05.12.15 um 13:49 schrieb si...@publcif.co.uk:
> Curiously this showed that the 'rotate best' needed to be done first
> (before the initial zoom) otherwise the coordinates did not reflect
> the rotated model.
> Perhaps the subsequent zoom forces a refresh...
>
It seemed to work at least for my e
Thanks - this works.
I modified your script to also return the atoms at the max min
positions so that these could be selected and subsequent calls to
getScreenBoundary only had to examine the {selected} atoms (because
there's no rotation between calls).
Curiously this showed that the 'rota
Am 04.12.15 um 18:47 schrieb si...@publcif.co.uk:
>
> Thanks for this Angel
>
> My task was to effectively "crop" the model so that a static image
> could be created that was as large as possible with respect to the
> model, but also exactly reflected what would be seen in the applet -
> i.e. the s
Thanks for this Angel
My task was to effectively "crop" the model so that a static image
could be created that was as large as possible with respect to the
model, but also exactly reflected what would be seen in the applet -
i.e. the static image could be used in e.g. a PDF but scaled to a
Simon,
although you seem to have the solution, I'd like to give my view
As I understand it, "zoom 100" will fit the model in spacefill into the window,
at any rotation angle; maybe yor perception is due to your having a single
"best" orientation, for which there may be empty margin left.
I do n
The existence of .sx, .sy... doesn't actually seem to be documented -
though a long-way round might've been suggested by 'x = point({x,y,z},
true)' in http://chemapps.stolaf.edu/jmol/docs/#jmolmath
In any case, knowing the screen coordinates is exactly what I wanted
so am glad for the info a
Initial zoom depends, if your Jmol is rectangular, on set zoomlarge and
set zoomheight. Just in case you didn't remember those. With zoomlarge
true I often set zoom to 110% to pretty much fill Jmol to the edges.
-Eric
On 12/3/15 7:05 AM, si...@publcif.co.uk wrote:
> Dear all
>
> If I do "rotate
On 12/03/2015 03:52 PM, si...@publcif.co.uk wrote:
> Thanks Bob - just what I needed
>
> (Note to self - read the documentation thoroughly! :-)
>
Is this really documented?
I couldn't find it in the scripting documentation.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute on Aging - Fri
Thanks Bob - just what I needed
(Note to self - read the documentation thoroughly! :-)
Cheers
Simon
Quoting Robert Hanson :
> You can get max and min for screen coordinates like this:
>
> minx = {visible}.sx.all.min
> maxx = {visible}.sx.all.max
>
> etc.
>
> You can compare those with _width
You can get max and min for screen coordinates like this:
minx = {visible}.sx.all.min
maxx = {visible}.sx.all.max
etc.
You can compare those with _width (_height for y)
Bob
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Thanks for this Otis
Problem with the boundboxInfo (and atomInfo...) is that the
coordinates etc do not seem to reflect the current orientation, so I
guess I would have to do something clever to translate the data
according to the current rotation/translation/zoom factors and
normalize the
Simon,
This will get you the dimensions of the bound box:
Jmol.getPropertyAsString(jmolApplet0, "boundboxInfo.vector")
I'm not sure what to do next in your case, but it's the only relevant data that
I'm aware of.
I use this data in a slightly different way to make model translation changes
b
Dear all
If I do "rotate best;center visible;zoom 0;" I get a nice view of a
model, but in most cases it wont entirely fill the applet because the
zoom is optimized with respect to the 3d bounding box (I think).
Does anyone know how to automatically zoom a model so that it is as
large as po
Thanks a lot, Rolf.
shihai
On 11/5/15, 7:49 PM, "Rolf Huehne" wrote:
>Am 06.11.15 um 00:43 schrieb Feng, Shihai:
>> Hi all,
>>
>> Is there way to zoom in to certain residues (say 112-123 in protein
>>2B4C)
>> in jsmol?
>Yes, the 'zoom' and 'zoomto' command have options for this. 'zoom' jumps
>d
Am 06.11.15 um 00:43 schrieb Feng, Shihai:
> Hi all,
>
> Is there way to zoom in to certain residues (say 112-123 in protein 2B4C)
> in jsmol?
Yes, the 'zoom' and 'zoomto' command have options for this. 'zoom' jumps
directly to the new position and zoom factor. 'zoomto' transforms the
current vie
Hi all,
Is there way to zoom in to certain residues (say 112-123 in protein 2B4C)
in jsmol?
Thanks
shihai
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I tried to set the focus manually (via Chrome console) but it hat no
effect. I don't think it's a focus issue because if I focus an input (after
I clicked the JSmol canvas), zooming JSmol just works.
2014-06-14 19:55 GMT+02:00 Angel Herráez :
> Herman, that's probably because the browser must ha
Herman, that's probably because the browser must have focus set to the
JSmol object before this is responsive to mouse actions.
I am seeing the same with Firefox/Win
I don't think this is a problem in JSmol.
Maybe you can try to set focus when your page loads and see it that helps
getting what
Scroll zoom in JSmol only works after you have clicked or moved the 3D
molecule. Same for this one:
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (try
scroll zooming the molecule immediately after loading)
Regards,
Herman Bergwerf
-
very true. It's incorrect documentation.
set zoomLarge FALSE
needs to be set for that to be the case.
A recent addition is
set zoomHeight TRUE
This is a PyMOL-like zoom setting that only changes the zoom if the height,
not the width, is changed.
On Fri, Oct 25, 2013 at 10:53 AM, Dave Howor
And here's another one:
The documentation http://chemapps.stolaf.edu/jmol/docs/#zoom says:
"A percentage value specifies the zoom relative to 100, the default
value, which in Jmol is calculated so that all atoms are completely
visible on the screen through all rotations using the default
vanderWa
Yingjie,
You need to close your browser -- all windows -- and restart it to be sure
that it is not caching files. It used to be that script files were not
cached by Java, but now they are, and that is still another issue. Closing
and re-opening the browser should work for that as well, though.
Bo
Hi Jmol,
I noticed that if Jmol applet loads from cache if the specified path+filename
exists in cache.
In my case, I would like Jmol Applet to always load from the web server because
sometimes the content of the files could change.
So, is there a way to avoid loading from cache?
Thanks!
Hi R
x = getProperty("orientationInfo.zoom")
On Tue, Jul 19, 2011 at 8:53 AM, Yingjie Lin wrote:
> Hi Robert and Angel,
>
> Thanks for the help.
>
> This is what I was looking for.
>
> > zoom {whateverAtoms} 0
>
> As to "show zoom", could the number be assigned to a variable?
>
> > Open the script co
Hi Robert and Angel,
Thanks for the help.
This is what I was looking for.
> zoom {whateverAtoms} 0
As to "show zoom", could the number be assigned to a variable?
> Open the script console and type
> show zoom
Thank you.
- Yingjie
--
zoom {whateverAtoms} 0
On Mon, Jul 18, 2011 at 10:17 AM, Yingjie Lin wrote:
> Dear Jmol,
>
> Is there a relative way to zoom which automatically makes sure that
> selected atoms are neither too small nor too large?
> I would like to zoom in to seleted atoms as close as possible but not so
> clos
Dear Jmol,
Is there a relative way to zoom which automatically makes sure that selected
atoms are neither too small nor too large?
I would like to zoom in to seleted atoms as close as possible but not so close
that some atoms are out of view.
zoom 100 doesn't always do what I want especially wh
in the math itself you just use variables names. $xx would be an identifier
for a drawn object or isosurface and would not be appropriate in that
context.
for (var j=1; j<20; j=j+1)
var scale=5*j;
zoom scale;
write image 800 600 @{"movie" + (""+j)[-3][0] + ".jpg"};
end for
On Thu, D
Hi,
I've been trying to make this work but the program doesn't seem to
do anything when I run it. What I'm trying to do is write a series of
images that zoom into a structure. Suggestions?
---
for (var j=1; j<20; j=j+1)
scale=5*$j;
zoom $scale;
write i
Eric,
print getProperty("orientationInfo.zoom")
See also
print getProperty("orientationInfo")
So, for example, you could divide the zoom in half and not change anything
else by:
var x = getProperty("orientationInfo.moveto").split(" ")
x[8] = x[8]/2
script inline @{x.join(" ")}
// get an array
Hi again Eric
Don't know if there is such variable, but this can get it for you:
z = script("show zoom")
then e.g.
echo @z
gives
zoom 54.343338
so you still need to remove the "zoom" text, don't know if it's possible
Is there a Jmol math variable (I would have expected _zoom) that has
the current zoom percentage value in a form that can be used directly
in math and zoom commands? For example
if (_zoom != 350)
...
or
zoomDelta = 350 - _zoom
...
For Molecular Playground, I cannot use zoomTo because we want
t; From: Robert Hanson [mailto:hans...@stolaf.edu]
> Sent: Friday, September 25, 2009 2:37 PM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] zoom callback
>
> what version of Jmol are you using?
>
>
>
> ---
MyCallbackListener());
Joe
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Friday, September 25, 2009 2:37 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] zoom callback
what version of Jmol are you using
jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] zoom callback
>
> [this should be on Jmol-Developers list]
>
> It all looks right to me. But a System.out.println(type) in notifyEnabled
> to
> see if it is checking for
,
Joe
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Friday, September 25, 2009 12:51 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] zoom callback
[this should be on Jmol-Developers list]
It all looks right to me. But a System.out.println
From: Robert Hanson [mailto:hans...@stolaf.edu]
> Sent: Friday, September 25, 2009 11:08 AM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] zoom callback
>
> When I do that, I get callback messages coming into notifyCallback.
>
> Are you should you issu
mol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] zoom callback
When I do that, I get callback messages coming into notifyCallback.
Are you should you issued
sync *
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Come build with us! The BlackBerry® De
_
> From: Robert Hanson [mailto:hans...@stolaf.edu]
> Sent: Friday, September 25, 2009 10:24 AM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] zoom callback
>
> not specifically. To do that, set up a callback for sync and then sync the
> applet
applicable to
applications?
Thanks,
Joe
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Friday, September 25, 2009 10:24 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] zoom callback
not specifically. To do that, set up a callback for
not specifically. To do that, set up a callback for sync and then sync the
applet:
sync *;set syncMouse;set syncScript
set synccallback "yourCallbackFunctionName"
Then you will start getting messages when the user has zoomed either using
commands or using the mouse. You will have to parse those,
I am using 11.8.4 on Linux with java 1.6.0_13
I have the callback listener working great for atom picking. I also need to
capture when a zoom operation has completed. I am currently using a
combination of key and mouse handlers to pickup the end of zoom. Is there a
callback associated with zoom
say more. Be specific. Can you attach model files or point to a page?
Judy Edwards wrote:
>Hi
>
>I am trying to display some large polymers, enlarged, in rectangular
>boxes say 550 x 150.
>
>No matter what zoom I put in the script they come up as tiny
>molecules in the middle of the big box.
>
Hi
I am trying to display some large polymers, enlarged, in rectangular
boxes say 550 x 150.
No matter what zoom I put in the script they come up as tiny
molecules in the middle of the big box.
Is this able to be worked round?
Judy
-
On Oct 26, 2006, at 10:18 AM, [EMAIL PROTECTED] wrote:Q: What is the highest zoom setting you use IN YOUR SCRIPTS?In my scripts the highest zoom has probably been well under 5000, perhaps around 2000 or 3000. If there are occurences that are higher, I would gladly re-write them in order to be able
I was playing with 1d66.pdb and realizing again that in such cases the
zoom maxes out too soon. Way back I had tried allowing for a larger
maximum zoom setting, but that fails to do the job. Just now I implemented
locally what I think is an ideal solution.
The problem is not that zoom can't go ver
I'll look at it now that it's starting to look like something official
and not just my tinkering.
[EMAIL PROTECTED] wrote:
Although I see plenty of blank space at the bottom of the page, the
divs (table cells?) are short (each with a scroll bar) such that I
cannot view the whole applet and
>Although I see plenty of blank space at the bottom of the page, the
>divs (table cells?) are short (each with a scroll bar) such that I
>cannot view the whole applet and the messaging beneath it at the same
>time. I can take a screen shot and post it if this is not clear. The
>bottom lin
I hadn't taken the time to look at that on a Mac. But I agree -- it's
looking like this is a good way to get the ideas out there and being
tested. No need for a screen shot; there are plenty of Macs around
here I could test it on. I'll see what I can do.
Frieda Reichsman wrote:
On Apr 6, 20
On Apr 6, 2006, at 11:18 AM, Bob Hanson wrote:http://www.stolaf.edu/people/hansonr/jmol/test/10.1/new.htmBob, this is a great new feature, having a page that specifically is used to access new features/bug fixes for a specific release. It seems so useful that it prompts me to ask about the layout o
I have zipped up the entire test/10.1 directory (minus the mol/*
files)into
http://www.stolaf.edu/people/hansonr/jmol/test/jmol-new-proto.zip
The jars are there, and the html and js files are, too, so you should
be able to test it a bit.
Bob
Frieda Reichsman wrote:
On Apr 6, 2006, at 11
On Apr 6, 2006, at 11:18 AM, Bob Hanson wrote:In fixing some bugs that were on my short list, a benefit became that zoom is essentially limitless.I would appreciate people checking this out (especially Frieda) in the next few days. The demo is athttp://www.stolaf.edu/people/hansonr/jmol/test/10.1/n
In fixing some bugs that were on my short list, a benefit became that
zoom is essentially limitless.
I would appreciate people checking this out (especially Frieda) in the
next few days. The demo is at
http://www.stolaf.edu/people/hansonr/jmol/test/10.1/new.htm
Zoom maximum is now 50%. The
> Hi,
>
> The zoom setting in jmol.jar seems to have changed between 10.00 and
> 10.00.43 - so my scripts written in 10.00 are wrongly zoomed in 10.00.43.
> Is there a reason?
I believe that the only difference in zoom level occurs when the applet is
not square.
In 10.00 the applet was scaled s
Hello, John
This may be the cause (former post by me and Miguel's reply):
> I am using a rectangular applet (I know Miguel does not recommend this,
> but it works nicely, I have long narrow molecules and need space for
> text).
> I am finding a difference in the default zoom according to which ve
Hi,
The zoom setting in jmol.jar seems to have
changed between 10.00 and 10.00.43 - so my scripts written in 10.00 are
wrongly zoomed in 10.00.43. Is there a reason?
Thanks
John
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