I'm about to make a surfaces examples page for a workshop I'm giving
-- I'll pass that on.
Phillip Barak wrote:
Yes indeed, LOBE works nicely! Hadn't noticed that among the two or three
dozen isosurface features and the many other new goodies!
;-)
- Original Message -
From: Bob
just select the models you want to write.
select 1.1
write coord XYZ model1.xyz
select 1.2
write coord XYZ model2.xyz
etc.
Sebastian Schwieger wrote:
Dear jmol team,
I was trying to write xyz coordinates of a specific frame from an
optimization done with gaussian.
Using write coords XYZ
a second buffer.
Bob
Raphael A. Bauer wrote:
Bob Hanson wrote:
2:1 you have a Mac. In any case, you need to find the control panel for
Java and increase the allowed memory. Others on the list can help you
...
unix like os was right - but i am running plain old linux here.
apart from
Aidan,
You CAN select bonds, but it's not advertised. To see how it's done, do
something with a few selected bonds (color them, for instance) and then do
show state
you will see how Jmol 11 allows selecting bonds and manipulating them as
entities. No labels, no pick.
If you want to label and
Liu hai, I've forwarded this reply to Jmol-users, because I think others
would be interested in it.
All:
Liu hai has a mol2 file with comments at the beginning. This tricked
Jmol into thinking it was a MOL file rather than a MOL2 file. If you are
ever in this situation where you know a file
Nick, have you put XML headers at the top of your page, or are you doing
something like
?xml version=1.0 encoding=iso-8859-1?
? That would be my guess, as there is no document object and no applet
object, either, based on this message:
jsoDocument returned null ... no DOM manipulations :-(
scale -- and then use that number. Might work.
Bob Hanson
Garnier Nicolas wrote:
hi,
I'm using Jmol with proteins that can be more than 800 residues. I
have some specific colorations where each residues can take a color.
So it's very long to color each residues by a select x; color y
no plans for that. I figured one could set that up with lobes. The
problem is defining the different directions. sp, sp2, sp3 are hard
enough to specify. sp3d2 I gave up. These should be able to be set
up with combinations of isosurface LOBE commands. Give that a try at least.
Phillip
Two replies -- one for hover, one for zoomto. This one is zoomto:
Eric Martz wrote:
Dear Bob,
2. zoomto with no parameters fails to zoom 2X as it did in earlier
versions. Similarly, zoomto out does not change the zoom in 11.3.0.
3. zoomto (center) results in an incorrect center when a range
part II hover. fixed for 11.2.2, 11.3.1
We saw problems with hover being interrupted in earlier prereleases of
Jmol. I thought I had fixed it at that time, but I guess not. I've now
set it to restart the thread if it gets interrupted whenever the mouse
is moved. Eric, when this is released,
2:1 you have a Mac. In any case, you need to find the control panel for
Java and increase the allowed memory. Others on the list can help you
figure out how to do that if you don't know how.
Raphael A. Bauer wrote:
Raphael A. Bauer wrote:
hi jmol list,
i am constantly getting out of
with the draw object.
If more complex, colored, or translucent text is desired, use ECHO instead:
set echo myecho {3 4 5}
echo some | more complex | text
color echo translucent white
Bob
Rolf Huehne wrote:
Rolf Huehne wrote:
Bob Hanson wrote:
Oops, that's a bug
Jmol 11.3.0 will have the capability to select specific vertexes from a
drawn object:
draw p plane perp (atomno=1) (atomno=2)
pointCenter = $p #average
point1 = $p[1]
point2 = $p[2]
point3 = $p[3]
point4 = $p[4]
Then you can do things like:
draw p1 @point1
rotate 10 $p[2] $p[4]
etc.
text1 off
Bob Hanson
Rolf Huehne wrote:
Dear all,
I try to label draw objects like planes. Currently the only way to do
this seems to be with a user-defined echo positioned at a
three-dimensionsonal coordinate.
First of all I noticed that the set echo syntax described
Please refer your question to the jmol-user list. Thank you.
Original Message
Subject:Jmol -Regarding Jmol.js file
Date: Mon, 18 Jun 2007 14:22:56 +0530
From: TK.Jiji [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Dear Sir,
When i was running JmolApplet.java file
Wow, no kidding? Jmol 7! That option is long gone -- considered unnecessary.
Frieda Reichsman wrote:
Hi,
I can across a web page,
http://www.chm.bris.ac.uk/motm/acetylcoa/acoajm.htm
and noticed a Jmol effect I had not seen before, wireframeRotation.
(Just rotate any structure on that
Jmol users:
Jmol 11.2 has been released. The following list summarizes the changes
since the most recent release, Jmol 11.0.
Please note that the default perspective model has been set to 11
instead of 10. This means that users who are installing this release in
web sites now using earlier
the
information to Jmol using Javascript, since that's how I created the line in
the first place.
Dean
On 6/15/07 12:58 AM, Bob Hanson [EMAIL PROTECTED] wrote:
This is better -- it uses improper angles to set the sign of the angle
correctly.
Bob Hanson wrote:
no simple way. HOWEVER
This is better -- it uses improper angles to set the sign of the angle
correctly.
Bob Hanson wrote:
no simple way. HOWEVER, you could do the calculation I think. Let's see
if it can be done with a Jmol script...
Let's say we want to align the axis between atom 1 and atom 2 along the
Z axis
Michael,
We are within days of releasing 11.2, and that is why the documentation
got a bit ahead of us.
Just go to the download page and select 11.1.48
Bob Hanson
[EMAIL PROTECTED] wrote:
Hello,
I tried to use the RotateSelected function, but it doesn't work. In the
documentation I found
might consider doing something like:
load files model1.sdf model2.sdf
frame 0
select 2.1
translateSelected {5 0 0}
zoomTo 0.0 (*) 80
Bob Hanson
Raphael A. Bauer wrote:
Angel Herraez wrote:
Can you think of anything inside jmol that helps me to visualize this
abstract superposition mapping
will get
there faster. You can load a file of coordinates and work with it to
draw just about anything you want, provided the objects are triangles or
quadrilaterals. Pmesh is another command that comes to mind.
Bob
Dean
On 6/9/07 12:51 AM, Bob Hanson [EMAIL PROTECTED] wrote:
Dean, sounds
Eric Martz wrote:
In
contrast, anim on restarts from the first frame.
and resets the frame range to all models
-
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express
good catch -- simple fix. 11.1.49
Frieda Reichsman wrote:
It seems that after issuing a script with a loop command:
move 0 -30 0 0 0 0 0 0 2.0
move 0 30 0 0 0 0 0 0 2.0
loop on
I cannot get the structure to spin using
quit; spin on
until I either
- click in the applet, or
- issue a
Sérgio Ceroni da Silva wrote:
Dear all
I've been doing some testing regarding the problem where Jmol
application freezes after a few changes in the default language.
Apparently it's a memory matter. Every time the language is changed
javaw uses more 6 to 15 MB. This happen with every language
Dean, please send me the script. I'd like to fix this.
Dean Johnston wrote:
I’m getting an odd (and hard to reproduce) crash with the Jmol applet
(Firefox or Safari on OS X, version 11.1.48_dev). I try and load an
inline model and sporadically get the error listed below. It seems to
I wholeheartedly support this discussion. Jmol 10 WAS strictly a
molecular viewer -- there is no question about that. It's intriguing
to think that Jmol 11 is more than a molecular viewer because of the
additional capabilities in the area of crystallography. Personally I
don't see the
, Bob Hanson [EMAIL PROTECTED] wrote:
Dean, please send me the script. I'd like to fix this.
Dean Johnston wrote:
I¹m getting an odd (and hard to reproduce) crash with the Jmol applet
(Firefox or Safari on OS X, version 11.1.48_dev). I try and load an
inline model and sporadically get
Dean, sounds like you might appreciate:
http://www.scienceu.com/geometry/facts/solids/coords/
Well, ah, let's just say it doesn't work the way you probably think it
does. The polyhedra code is a very complex algorithm that looks at
possible faces (combinations of three atoms around a central
Eric Martz wrote:
QUESTION 2: SKIPPING FRAMES.
When I run the Chime animation concurrently with the Jmol animation
(in the same or different browsers), Jmol's animation skips frames. I
interpret this to mean that when the CPU is heavily loaded, Jmol
skips frames. Perhaps frames would also be
own pages, and how much trouble it would be to add
set perspectiveModel 10 to them if you feel that would be necessary.
Then get back to us.
Thank you,
Bob Hanson
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does
David, you might also be interested in a site we developed here at St.
Olaf, as it has about 1000 small molecules;
http://www.stolaf.edu/depts/chemistry/mo/struc/
with associated model files in
http://www.stolaf.edu/depts/chemistry/mo/struc/data/
Bob Hanson
David Kim wrote:
Hello,
My
rspinney wrote:
I'm not sure we are on the same wavelength. As an example, frame 20 is a
key frame where echo and message are changed. If the animation is
playing (i.e. using animation direction +1; model resume;) the changes
(based on the frame number) are caught by animFrameCallback and passed
rspinney wrote:
I have a couple of questions for Bob. (I am using 11.1.44.)
1) I am not clear if frame (or model) next or previous make a call to
animFrameCallback. I have a jmolSetCallback linked to animFrameCallback, and
it works fine for model play, pause and resume (which will execute a
I have added inline help capability to the Jmol application for 11.1.46.
help
or
help commandName #targets that particular command
or just
help anything #does a search
Bob
Thank you, Nico!
Nicolas Vervelle wrote:
Bob Hanson a écrit :
This is about as close as we are going
rspinney wrote:
I have a couple of questions for Bob. (I am using 11.1.44.)
1) I am not clear if frame (or model) next or previous make a call to
animFrameCallback. I have a jmolSetCallback linked to animFrameCallback, and
it works fine for model play, pause and resume (which will execute a
applications.
Cheers,
.../Ola
On May 31, 2007, at 19:35 , Bob Hanson wrote:
Thanks, Angel. This is fixed for 11.1.45.
Nico, can you see if there is a simple way of having the export file
chooser retain the last-saved file type selected and not reset to JPG
each time? Thanks.
Bob
Angel
from the console, use
write STATE filename.here
But it must be a bug in the menu export business. I'll look into it.
Bob
Angel Herraez wrote:
(11.1.41)
I haven't tried extensively, but it seems that there is a problem
saving the state to a script file:
I prepared a model in the app, then
Thanks, Angel. This is fixed for 11.1.45.
Nico, can you see if there is a simple way of having the export file
chooser retain the last-saved file type selected and not reset to JPG
each time? Thanks.
Bob
Angel Herraez wrote:
(11.1.41)
I haven't tried extensively, but it seems that there
Pim,
The up-to-date full capability of Jmol is found in
http://www.stolaf.edu/academics/chemapps/jmol/docs/
This is kept rigorously up to date. So that is definitely the starting
point.
In addition, the applet has
help
or
help commandName
from the console, which delivers a segment of
And another question: does a link like:
http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#setbondstyles
always point to the latest version?
It always points to the default version, as defined near the top of
http://www.stolaf.edu/academics/chemapps/jmol/docs/code.js
This is
Alan,
It seems to me the most sensible thing to do is use Miller plane
notation hkl instead of plane for that WITHIN definition.
display within(-999,hkl,{0,40,0})
as long as you can use crystallographic coordinates instead of
Cartesian. Alternatively, you can define the plane using three
points rather than the
atoms. Perhaps a slab parameter in isosurface.
Bob
Alan Hewat wrote:
Bob Hanson said:
Actually, Alan, how ARE you getting that isosurface to slab that way?
On http://icsd.ill.fr/slabslider/slab3d.html I now have general 3D slabbing
with x,y,z sliders working
Aidan Heerdegen wrote:
Bob,
I can convert fractional coords to cartesian with a simple
a = {1/1 0 0}
is there (or could there be) a simple way to do the same in reverse?
I wish to obtain the fractional coordinates of my molecule (which I
currently do like so {molecule=1}.xyz). Can I get
What I meant by that was that Chime didn't have the wide-ranging
capability that Jmol has. So it's not as simple as sending the
user now moved the mouse HERE to the other applets. You would need to address
issues such as:
Do moveto, zoomto, navigate, translate, etc. all get synched, or is it
Tim, please open a feature request, copying into it this exchange we've
already had to start it off.
Thanks,
Bob
Timothy Driscoll wrote:
On May 24, 2007, at 9:30 AM, Bob Hanson wrote:
What I meant by that was that Chime didn't have the wide-ranging
capability that Jmol has. So it's
I think all of Jmol is synch on then isn't it? If you rotate any
structure, all structures rotate. To do otherwise you have to use Jmol
l1.1's rotateSelected command.
Do you know where a description of the Chime command is? I can't find it
at
can see if I can implement it. Maybe some interesting
issues there.
Bob
Timothy Driscoll wrote:
On May 23, 2007, at 10:44 AM, Bob Hanson wrote:
I think all of Jmol is synch on then isn't it? If you rotate any
structure, all structures rotate. To do otherwise you have to use Jmol
l1.1's
Frieda Reichsman wrote:
1. write history command -
the written history file includes the command to write history with
the same file name - this will lead to the file overwriting itself. If
you are editing the file and do not realize that, you'll be
overwriting the original file you
Nico has just released 11.1.43. This set of bug fixes covers:
version=11.1.43
# bug fix for labels mysteriously disappearing. Also probably taking up
HUGE amounts of hashtable space.
# bug fix for hydrogen bond calculation with incomplete nucleic acid
definitions.
# bug fix for set picking
Timothy Driscoll wrote:
On May 23, 2007, at 11:47 AM, Bob Hanson wrote:
Something like:
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/
compare.htm
but maybe better? I experimented with this a bit but didn't finish
the job.
not sure; that page hangs in Safari when
Timothy Driscoll wrote:
But if you can figure out a scheme that would be reasonable in
terms of
setting up this function wihtin Jmol -- I would want it to be possible
to designate what applets are to be synced, not just all applets
on the
page -- then I can see if I can implement it. Maybe
We are decidedly closer to 11.2. Nico has just released 11.1.42. All
testing appreciated.
version=11.1.42
# bug fix for lack of updating of certain variable predefined expressions
# bug fix for load append and structure commands
# bug fix for load files losing structure and cartoons
# bug fix
Ok, that's pretty clear. Jmol wasn't expecting incomplete nucleotides
when creating hydrogen bonds. In one of the residues N4 was not present,
and this caused the error. This is now fixed for 11.1.43, although it's
questionable whether Jmol's method of assigning hydrogen bonds between
nucleic
fixed for 11.1.43
rspinney wrote:
Message: 3
Date: Mon, 21 May 2007 08:22:46 -0500
From: Bob Hanson [EMAIL PROTECTED]
Subject: [Jmol-users] 11.1.42
To: Jmol Developers [EMAIL PROTECTED],
jmol-users@lists.sourceforge.net
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset
exactly how to remedy it.
Shouldn't be a major issue. Somehow the Java Virtual Machine gets messed
up and tries to read the wrong set of JAR files.
Bob
Frieda
On May 17, 2007, at May 17, 12:10 PM, Bob Hanson wrote:
I'll bet if you move them back it will work just fine as well. Really
Angel Herraez wrote:
I'm surprised at seing it working; it seems that only the isosurface
is being slabbed normally, the atom spheres are not sliced through,
but just show complete or nothing depending on their position with
respect to the plane. Have you done this on purpose, Alan, or is it a
:
FileManager.openStringInline()
file ERROR: string
unrecognized file format for file string
It doesn’t work with my site or with any of the examples in the Jmol doc.
Dean
On 5/18/07 10:06 AM, Sérgio Ceroni da Silva [EMAIL PROTECTED]
wrote:
Bob Hanson escreveu:
I think it's a level of change none
11.1.41 will have a fix; but yes, it is true, load append deletes all
secondary structure in the original file. It's possible that some day
someone will figure out a way around that, but for now that is the case.
Bob
Frieda Reichsman wrote:
Jmol 11.1.40 and I'm pretty sure 11.1.38_dev
this
change somewhere along the line?
Frieda
On May 16, 2007, at May 16, 11:05 PM, Bob Hanson wrote:
I think it's just a caching problem.
Frieda Reichsman wrote:
Hi, I have a tutorial that worked about 1 year ago with no problems. I
just re-uploaded it and get this error:
load: class
WOW! I like it! So you got the arbitrary internal slab going. Good job!
Bob
Alan Hewat wrote:
Alan wrote:
BTW, there is an example of nice javascript slider controls on br
http://www.blueshoes.org/_bsJavascript/components/slider/examples/example9.html/a
I now have an example double
this problem. This might be about as good
as we can do. I'd have to think more about it and test it more before I
would suggest that it be automatic for a load append, but that would be
another possibility.
Bob
Frieda Reichsman wrote:
On May 17, 2007, at May 17, 5:48 AM, Bob Hanson wrote
image below the applet. You should see it work. There are
browser limitations to this -- must be Firefox, not IE. But that should
be fine for development work. Let us know if that is not enough of a tip.
Bob Hanson
Thanks,
-Balram
I think it's just a caching problem.
Frieda Reichsman wrote:
Hi, I have a tutorial that worked about 1 year ago with no problems. I
just re-uploaded it and get this error:
load: class JmolApplet not found.
java.lang.ClassNotFoundException: JmolApplet
at
pim schravendijk wrote:
Hello there jmol fans!
I have a question. I can create planes, polyhedra, and isosurfaces in
jmol, but since I want a presentable picture of it as well, I want to
export this complete system to povray.
Just doing the menu-function 'export to povray' doesn't seem to do the
:56, Bob Hanson escribió:
load files =1crn =1blu =1hje
It means Go get these files from RCSB directly; I don't have them on my
computer
I'm starting to use this so that anyone can run the script and it should
work for them same as for me. No files required!
But only with the signed
Ah, that's why we need everyone involved to take a look. Thank you, Amy.
I will look back at the JmolViewer interface for 10.2 and make sure that
everything that was there is there in 11.
I do see that note also says unusable, so I definitely misunderstood
something there. Amy, can you tell me
Bob Hanson wrote:
Bug in Jmol 11.1.38 found and fixed: PDB files load but do not populate
popup menu select submenu with group lists.
[users who are not developers need not read further]
Actually, come to think of it, perhaps some users might be interested in
knowing that on a web page
Patrick J. Carroll wrote:
Bob,
I'm trying to work through your suggestions about using display,
but meanwhile, I've noticed some other strange behavior. On that same page,
http://macxray.chem.upenn.edu/gam/9129b.html
when I try to add a molecule by using symmetry
Ah, Frieda, you MUST use file.model notation with multiple files
anywhere you would like to say model n. Especially with PDB files,
set backgroundModel 1 would be too ambiguous.
For example:
load files =1crn.pdb =1blu.pdb =1hje.pdb
animation mode palindrome
animation fps 1
set backgroundmodel
hmm, a state save bug on that. Will fix
Bob
Frieda Reichsman wrote:
I'm looking for some scripting help. Using Jmol 11.1.38_dev,
I am attempting an animation with four files. Each has one model. FIle
1 has an isosurface. Bob just wrote a nice post the other day re:
frames and multiple
They are all already connected; that's not the problem. The problem is with:
cpk 0; wireframe 0; select none; select symop=+whichSymmetry()+; cpk 15%;
wireframe 0.10;
You are turning on and off atoms using cpk and wireframe instead of just
display. What you want is something like:
display
Say, David, I really like this feature:
Protein 1blu not found in the Protein Motif database.
This protein is catagorized as: ELECTRON TRANSPORT
Proteins in the database of type ‘ELECTRON TRANSPORT’ are listed below:
Very clever.
Glad to hear the new zooming capability was of use.
Bob
David
If you use animation in the context of multiple files, you may find that
Jmol does not behave quite as you would expect.
This message describes how frames need to be addressed in that context,
and what the animFrameCallback parameters mean.
frame numbering
---
In a multifile
Stephen Hillier wrote:
Hi,
could someone tell me what the all the different applet files are?
And why a signed and an unsigned set?
What a timely question! I was just drafting a message to users
Jmol users:
We were all a bit confused with the new file naming, so we've decided to
applied a zoom
That make sense?
Bob
Timothy Driscoll wrote:
On May 11, 2007, at 1:37 AM, Bob Hanson wrote:
See if by any chance going the other way works -- from the verified
coordinates to the original. If that's the case, then you need the
inverse of this matrix.
yeah, I've
Frieda Reichsman wrote:
On May 11, 2007, at May 11, 7:34 AM, Bob Hanson wrote:
JmolApplet.jar
---
A single jar file containing all Jmol applet components. Use this if
you want to keep your website simple or you just want to upload a single
JAR file whenever new versions
Frieda Reichsman wrote:
Hi Bob, is this in your bleeding edge release, right now?
Just uploading now.
Frieda
PS thanks for the info re: 0* series.
On May 11, 2007, at May 11, 1:33 AM, Bob Hanson wrote:
this is done. Will be part of 11.1.38. Be on the lookout for problems
like
rspinney wrote:
Hi Bob,
The script is loaded using a jmolbutton (there are two different
scripts/animations I want to be able to run which will have different
messages to send to the textbox). The animation is then controlled by a
series of additional jmolbuttons allowing the user to play, play
I'm interested in any observations on this. So far the idea is to wait
and see if there really is any issue. My guess is that a 50-60K download
generally won't be noticed, as it is about the size of a small image.
But it's possible that the delay would be noticeable and that we need to
allow
rspinney wrote:
jmolScript('set animframecallback testanim ')
and then have:
function testanim(app,frame,p3) {
jmolScript(if(_modelNumber = 5);message is5;else;message not5;endif) }
I do get the messages expected. So I think that is working properly.
Bob
I couldn't use this as is, but
Mauricio Carrillo Tripp wrote:
Hi, thanks Bob and Angel for your suggestions.
It turns out I had already solved the problem before I
read them though, the solution has to do with Angel's comment
about using jmolScript to load the molecule by a
'user action' (In general this will always be
I think you've got it now.
Timothy Driscoll wrote:
original
ATOM 1ATOM 2d(2-1)M*d
x 3.95 3.86 -0.08 -1.25
y 38.05 36.58 -1.48 0.59
z 17.44 17.32 -0.11 0.53
transformed
ATOM 1ATOM 2d(2-1)
x 52.94 51.69 -1.25
y 50.01
Mauricio Carrillo Tripp wrote:
BTW, for those web devs that don't know a way to easily debug their
pages/scripts, I recommend FireBug. Of course this means
you need to use FireFox, but I'd expect this is something you're
already using if you're smart, right? ;)
Can you tell us more about
It's a misprint/bug. You do have to specify the type of write you want:
write coord filename.xyz
or, if the filename is not explicit:
write XYZ filename
I see now that there is a typo in the documentation or a bug in Jmol in
that coord not coords is necessary. I think I will consider this a
Just a reminder that it can help to specify which version of Jmol you
are using anytime you are having problems with Jmol and ask about it on
this list. Not a problem using older version, of course; it's just that
then we can know what you are working with.
Bob
Rolf Huehne wrote:
Bob Hanson wrote:
Rolf, Ah! I know what it is. Alright, this is IMPORTANT. We need lots of
input on this.
Jmol 11.1 has two perspective models -- 10 and 11.
set perspectiveModel 10
is the default because of compatibility issues with Jmol 10. The problem
with this model
is downloaded 11.0.3, unzipped it and double clicked on
Jmol.jar to launch the application, is there more to it?
thanks
steve
Bob Hanson [EMAIL PROTECTED] 10-May-07 2:18 pm
Upgrade to latest version. If you look there, XYZ is not one of the
options. The current option list looks
I can see that this capability of loading multiple files is starting to
be a real hit. With that increased usage there are going to be issues
with features. I encourage anyone using
load files ... ... ...
to be alert to possible bugs or oddities in relation to this. For
example, I just
Rick, this Jmol script is being run when? When there is a frame change?
How are you setting it up to run these statements?
In the latest version of Jmol you can designate a Jmol script to be run
from an animation frame callback:
set animFrameCallback script:if(_modelNumber = 1);..
Mauricio,
the space after /jmol- concerns me.
Bob Hanson
Mauricio Carrillo Tripp wrote:
Hi,
I've been looking for an answer on other posts with no luck, is this
code supposed to work?
script type=text/javascript
jmolInitialize(../jmol- 11.0.1
This is always a royal pain to get right. Certainly looks like a
rotation matrix to me.
It's got the right form. My guess is you put the vector on the right and
multiply as:
x' = m11*x + m12*y + m13*z
across the top row of that matrix. Likewise for y' across the second.
Does that not work?
Right now Jmol does not support user-derived color schemes. It's on the
list of things to support, but it is not there yet. A color scheme is
simply a list of color values, which are integers, so in principle, this
is not too difficult -- we just need to have a data statement that can
load
this is done. Will be part of 11.1.38. Be on the lookout for problems
like this.
Frieda Reichsman wrote:
In Jmol 11.1.36, some label alignments are not saved. I will send a
script to Bob off-list.
Frieda
///
Frieda Reichsman
Molecules in
See if by any chance going the other way works -- from the verified
coordinates to the original. If that's the case, then you need the
inverse of this matrix.
Timothy Driscoll wrote:
On May 10, 2007, at 3:54 PM, Bob Hanson wrote:
This is always a royal pain to get right. Certainly looks
Rolf Huehne wrote:
Bob Hanson wrote:
checked in for Jmol 11.1.36:
zoom (atom expression) 0
zoomTo timeSec (atom expression) 0
zooms to the atom expression, filling the screen (roughly) with that set
of atoms.
I tried several examples and the zoom level wasn't as expected
10 or 11 as the
default? In either case, the alternative model can always be set (once
for any applet) using set perspectiveModel.
Bob
Rolf Huehne wrote:
Bob Hanson wrote:
checked in for Jmol 11.1.36:
zoom (atom expression) 0
zoomTo timeSec (atom expression) 0
zooms to the atom
nope
Frieda Reichsman wrote:
Do labels have superscript and subscript capabilities? I don't see any
documentation, just wondering if it might have been implemented
somewhere along the way without notice.
Frieda
///
Frieda Reichsman
Molecules
David Leader wrote:
Bob wrote:
checked in for Jmol 11.1.36:
zoom (atom expression) 0
zoomTo timeSec (atom expression) 0
zooms to the atom expression, filling the screen (roughly) with that set
of atoms.
Additional options include any of the following after the zero:
+ x
- x
* x
/ x
My tests indicate this is no problem any more. Records show this was
fixed for 11.1.26. Have you tried 11.1.36? Try that and get back to me,
please. If it still does not work, I need to know what the exact issue
is, since I can't reproduce it here.
Bob
Frieda Reichsman wrote:
On Mar 20
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