> I have managed to convert 100+ files simultaneously into SVG and Jmol
> and display them in HTML. Works beautifully. [applet-4]. Thanks
Very good!
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Egon,
I have posted the current applet on the sourceforge site. You can get to
it at
http://jmol.sourceforge.net/applet6
This will give you a directory listing. There is only one html file
test1.html
To make it easy to look at this file I also put a copy as a text file
test1.html.txt
Miguel
> Yes, you can set it up on our SF website.
>
> With SF account and SSH you should be able to login on cdk.sf.net...
> make a subdir their for your test pages...
I can log in, but I do not know where the web content directories are.
Miguel
>> I see that cdk-render.jar is part of Jmol/src/manifest, but it is not
>> checked into jmol cvs. Would it be easier for you to just check the
>> file into jmol cvs?
>
> Yes, it would... I did not have time to do that yesterday, and should
> have told you that I planned to do it today... I've jus
> I am having an interesting problem with Jmol-applet4
> ...
> I disconnect. They unwhizz.
> ...
> Any ideas? Can it be replicated? Does the latest version solve this?
Peter,
I only joined the project recently and am not familiar with the state of
things as of release 4. Sorry I can't help.
The c
>> Sorry, I am unable to compile cdk in order to build cdk-render.jar Let
>> me know what you suggest.
> What error do you get? Have you tried "ant dist-render"?
I tried that.
The problem is that I have never compiled cdk before. So my system is not
configured properly. For example, I don't have j
> Egon,
>
> OK, I'm downloading cdk right now ...
>
> But I am skeptical. I don't think that cdk-render.jar is currently part
> of jmol cvs. And the application runs just fine without it. It is the
> app which is failing to work properly.
oops I meant to say:
It is the *applet* which is failing
Egon,
Sorry, I am unable to compile cdk in order to build cdk-render.jar
Let me know what you suggest.
Miguel
Original Message
Subject: Re: [Jmol-developers] extensive changes: interpreter + applet
From: "mth" <[EMAIL PROTECTED]>
Date: Tue, January 7, 2003 2
03 12:08, E.L. Willighagen wrote:
>> On Monday 06 January 2003 19:25, mth wrote:
>> > * The applet has problems which loading the CDK AtomColorer.
>> Therefore,
>> > all the atoms come up in grey. Egon, I will need your help to figure
>> out what is going wrong
>&g
> My analysis - which may be out of date - is:
> - A lot of people use Chime. I ran a virtual course an many of our
> students used it and loved it
That is what I have observed.
> - Chime is proprietary and, although free, its future availability and
> development is under proprietary control.
Ag
> My group at the
> National Cancer Institute is very interested in the JMol applet.
Very good!
> As soon as that work
> is done, we plan a number of things, including getting more involved
> with Jmol.
Great!
> We are also very interested in
> scripting and we would prob want to get involved in
I downloaded Beta 8 release of the Apple 1.4.1 JVM for Mac OS X 10.2.2 and
greater.
Received the message/exception listed below. Please let me know if I can
be of further assistance.
mth
===
---ATTENTION!--- JSX could not recognize your implementation of java,
which is
> Miguel, Fabian, shall we pick a release date for Jmol 6? Could we, for
> example, get a freeze in a few weeks, after we do a two week bug fixing
> on the new code?
Sounds OK to me. I do not have a fixed schedule.
What dates do you propose?
>> * The applet has problems which loading the CDK Atom
>> Sorry, what is SVG?
>
> Scalable Vector Graphics: http://www.w3.org/Graphics/SVG/Overview.htm8
Hmmm ... I think you told me this once before ;^)
>> Restated: If you tell me what you want I can probably put it in for
>> you and turn it around for you very quickly.
>
> Hens, you expressed intere
Fabian,
I had two small problems compiling the BandPlot code on Mac OS X.
Therefore I checked in a couple of changes to the code.
1. BandPlotPanel.java
Color.WHITE -> Color.white
for some reason it wouldn't compile with the all-caps version of
WHITE. I did not see anything in the java api
Jmol team,
I have good news and bad news.
The good news:
While I was on vacation the last week and a half I was able to do quite a
bit of work on scripting support and on the applet.
* The script interpreter is running quite well. It runs as a separate
thread and interacts properly with redispl
Peter,
I am very glad you got in touch with us regarding Jmol use as an applet.
>> > I have implemented an interpreter framework which supports all
>> rasmol and chime script commands.
While I was on vacation I did quite a bit more work on the script
interpreter.
>>
>>Ah! Chime scripts, that is
> I think it is OK. Just one little thing: the arrow head should end at
> the extremity of the vector (as when Arrow Head Size=0 ).
>
> Fabian
I noticed this and wondered if it was correct. I will fix it.
Separately, can you explain to me the relationship between the size of the
arrowheads?
-
Fabian and/or Egon,
Do you have any suggestions on how to make the vectors/lines look better?
Or is the current visual representation OK?
Miguel
Original Message
Subject: Vector & Line rendering style
From: "mth" <[EMAIL PROTECTED]>
Date: Fri, Decem
I recently checked in several changes which affect the interpretation of
rasmol scripts.
I have implemented an interpreter framework which supports all rasmol and
chime script commands.
script/Token.java
tokenizes *all* rasmol and chime commands
compiles atom expressions for constructing
Egon,
If I understand what you are trying to say here, it is that there is color
outside of the bond border.
I have worked on this issue a lot, but have not yet been able to correct it.
Is this what you were trying to say?
It looks like to me that the algorithm java uses for filling areas is
sli
> It looks good. I did not really identiy the difference...
Well, the honest answer is that the differences are hard to see unless you
are
1) zoomed in on a multiple bond
2) trying to look down the shaft of a bond
> Anyway, I just
> had a closer look, and saw that the inner bond color is also p
bugs.
!Adiós!
mth
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Guys,
I played around a little bit trying to make the vectors & boxes look
better. I tried making them transparent thinking that they would look like
they passed into the atom. But I wasn't very pleased with the results, so
I didn't check it in.
I changed the atom vibrational vectors so that they
Dan,
I have worked on the vibration code a bit and now understand why these
vibrational vectors only show up when you play the vibrations.
Miguel
> I figured out why I couldn't see some of your vectors on the screen.
>
> The vectors in the g??.out files only seem to show up when you do
> vibrati
I will be travelling for the next two weeks. Will be able to check email
occasionally, but no development.
Miguel
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I just checked in some code which makes the menu checkboxes and
radiobuttons work properly. In addition, they now are consistent with the
settings as set by the preferences dialog box.
- the menu checkbox state is updated to reflect the current settings
this did not work correctly in the past i
>
> Could you check if you have jmol/jars/cdk-io.jar
Yes
> and cdk-io.jar in the src/manifest file?
No
So I added cdk-io.jar to the src/manifest file. That helped, but now it
throws another exception.
java.lang.ClassCastException: java.lang.Integer
at org.openscience.cdk.io.cml.Convention.sto
Egon,
You probably already know this but ...
There seem to be some problems reading .cml files.
Previously I had problems reading several samples/*.cml files. But now I
cannot read samples/estron.cml ... one of my favorites :^(
The exception it throws is shown below.
Miguel
**
ReaderFactory:
> I am not sure how Jmol was behaving in the past... but I imagine this
> design handy:
>
> 1. the preferences are the boot settings... i.e. the values the
> several rendering options when Jmol is started...
> 2. we should define a list of options that the users is likely to
> change within one Jm
Many configuration settings show up on both the menus and in the
Preferences dialog. For example
atom style, bond style, label style
showAtoms, showBonds, showVectors, showHydrogens
I made a serious effort to make the checkbox behavior consistent between
the two ... but I failed.
With the menus
> Mmmm, no rather not ... ;) anyway, this color scheme is mostly used...
OK ... just checking
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> at this moment I am working on implementing the CDK way for determining
> the colors which are used to draw atoms and bonds...
Speaking of colors, I have a question about "Atom Charge Coloring"
One of the options in the underlying code is for atoms to be colored
according to their charge. Howev
>> Q: Are there molecules which have charges (and charge colors)
>> associated with them?
>
> For example: glycine-crystal.cml
when I loaded glycine-crystal.cml I got 269 messages saying
Not adding charge for atom ###
therefore, everything showed up white
I assume that this is a temporary situa
Dan,
I figured out why I couldn't see some of your vectors on the screen.
The vectors in the g??.out files only seem to show up when you do vibrations.
If you get a chance to answer some of my previous questions on this
subject I would appreciate it.
Gracias,
Miguel
---
I made some visible changes to the PreferencesDialog.
Users can now select some graphics display options
Use Graphics2D
- determines whether or not Java 2D operations are used
- controls antialiasing, pixel interpolation, dotted strokes for measures
Antialias
- option is greyed-out if prev
> Ah, yes... ofcourse... thought you mentioned a free version, like the
> jar that we distribute...
Actually, the jar that we distribute has a manifest that says Sun
Microsystems. So I assumed that it came from them.
I took a look at the implementation used for cdk. And clearly that version
is *su
In order to better fit with the cdk classes I converted all floats and
vecmath floats into doubles.
I went through and changed everything without looking at it too closely.
Afterwards, I loaded all sample files that I could to confirm that
everything still worked. The animations and vibrations see
The development version of Jmol has a problem on Mac OS X 10.2 jaguar.
There appears to be a bug in the jvm implementation which causes a severe
crash in the midst of Graphics2D operations. In Jmol, it only shows up
when displaying shaded atoms.
It crashes and put
Abort trap
on the console. All
> Is it actually maintained somewhere?
vecmath.jar is now included as a standard part of the Java3D API.
> I once had a private copy of the source somewhere to be used in CDK, or
> Jmol, or something else... but I cannot find it anymore...
I would love to take a look at the source. Let me know if
Egon,
Do you think it would be easy/possible to move to a newer version of the
javax.vecmath package?
I think it would be useful to use the Point3i class to represent screen
coordinates. It is not available in the older version of javax.vecmath
which we are using.
Miguel
---
>> I assume that moving to CDK is a good thing.
I intended that to be a statement, not a question.
But thanks for enumerating the advantages for me.
>
> Yes, it is ;)
> The advantages:
>
> 1. CDK has a larger developers community
> 2. CDK has a large repository of chemoinformatical libraries
>
> Mmm... that is precisely what I did... I'll look and see why it does not
> work...
> ...
> If I can't find the problem, I'll do a fresh co too...
>
I assume that you were able to compile from scratch?
Miguel
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>> Q: What was the reasoning behind using doubles instead of floats? Is
>> it the case that this level of precision (or range) is needed?
Is there any type of calculation in chemistry where it would ever make
sense to have that much range & precision?
> I did not report it yet, as I was wondering
As part of the conversion to the cdk Atom class I noticed that the
physical coordinate representation of atoms (in Angstroms) went from float
-> double ... Point3f -> Point3d.
It really doesn't matter to me. And remember that I am not a chemist ...
Q: What was the reasoning behind using doubles i
>> Great! No more flickering with double buffering!
> Very good. I'll commit the change shortly. I hope that it solves Egon's
> flickering too ...
I just checked in a version which uses double-buffering by default.
For the time being I left the setting under View -> Double Buffer
Miguel
-
>>NOTE: Please let me know if you do *not* like this transluscent
>> rendering and I will put a checkbox in the color options.
> I like it.
Good.
>>NOTE: Please let me know if you really want the "n atoms selected"
>> status message and I will reimplement it.
> Yes, I thi
> Great! No more flickering with double buffering!
Very good. I'll commit the change shortly. I hope that it solves Egon's
flickering too ...
> I did not notice any
> appreciable change in speed whatever Graphics2D or double buffering is
> on or off.
OK
> With Graphics2D, the quality is much bett
Egon,
In the course of testing before checking I observed that
samples/estron.cml is writing error messages to the jmol console.
I suspect that it is part of the conversion to the cdk base classes, so
you are probably already be aware of the issue.
The messages are:
Not adding charge for atom
It is now the case that the bond widths get smaller as you zoom away.
I have noticed an undesirable rather abrupt change in width as the bond
widths get small.
I'll take a look at it later and try to fix it.
Miguel
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I made changes to the selected (picked) atoms. Visible changes are:
- Halo is now transluscent on Graphics2D platforms, so you can see
the bonds and atoms through the halo. You can test it out by
toggling View -> Use Graphics2D
NOTE: Please let me know if you do *not* like this translusce
I just checked in a version of the code which adds two interesting items
to the View menu (temporarily).
- Double Buffering
This allows you to turn on/off double buffering under javax.swing.
!!NOTE!! Try this out and see if it eliminates your screen flickering
issues. Also, I would apprec
> By the way, I still have some display flickering while moving
> molecules. Do you see the same or is it JVM related?
>
> Fabian
I apologize. Egon also still gets flickering. But I don't see it on my
machine so I keep forgetting that it is an issue.
I will check something in soon to allow the two
> So in fact, don't waste any time on it now. I'll try it later and let
> you know if I have trouble.
Works fine now ... must have been a temporary glitch at sourceforge.
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Egon,
I tried to check out cdk with anonymous access ... unfortunately I was
unsuccessful.
I think I correctly followed the directons for anonymous access on the
sourceforge page:
cvs -d:pserver:[EMAIL PROTECTED]:/cvsroot/cdk login
When prompted for password I just press enter. But I get
...
> you last commit gives a compile problem:
I changed the parameter signatures on several existing methods.
I think you just need to do a full recompile
ant clean
ant
(I did a fresh checkout and everything compiled for me). Let me know if
you have more troubles.
Miguel
---
I have worked on the 3D rendering and perspective viewing in Jmol.
- 3D perspective scaling for z-depth now works on
* atom position/diameter
* bond length
* bond width
* vector position/length
Previously, atoms got smaller as you rotated. But bond length and bond
width did not cha
> In addition to those mentioned, I want to remove these obsolete methods
> from BaseAtomType:
fine with me
Miguel
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> On Thursday 28 November 2002 10:33, E.L. Willighagen wrote:
>> > I think that some of the code that is in the old Atom.java should be
>> moved out of there.
>> > For example, all the references to transform and screenPosition (and
>> screenX/Y/Z/Diameter) should be part of AtomShape, not part of
> Ok, had not really planned it this soon, but ok... if you're waiting for
> me to make the move... ;)
I didn't mean to be rushing you along.
I have plenty to do with scripting. So work at whatever pace you want.
Miguel
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>> Yes, I think it's usefull and quite easy to do. I will do it.
>> z-ordering is probably impossible to handle correclty with our pseudo
>> 3D.
> I am trying to learn more about 'real 3D' to improve our pseudo-3D.
>
> The main reason I went in to work on this section of the code was to fix
> a bug
> But a new button to recenter the molecule would be nice.
That button would be easy to add.
> Actually there is now an easy way to do it:
>
> void rotate(Point3f center, AxisAngle4f axisAngle) {
>
> oldcenter = center;
> setCenter(center);
> rotate(axisAngle);
> repaint();
> setCenter(o
>> - I could only find one example of an Atom Vector in samples ...
>> samples/cs2.xyz.
>
> Look at the normal mode calculations in the Gaussian log files to see
> more examples.
Dan,
I tried to take a look at some of the Gaussian files ... and ran into a
problem.
The vectors that are being read
>> I may send you some very small code snippets and ask you to comment on
>> them.
ChemFrameRenderer.java calculates the minMagnitude and maxMagnitude for
all the AtomVectors in molecules. Then magnitudeRange is calculated. These
values are passed as parameters to the constructor for AtomVectorSha
>> I may send you some very small code snippets and ask you to comment on
>> them.
>
> No problem.
Dan,
The following code is from the r5 relase of Jmol ... before I checked in
any changes to cvs.
==
In the transformation process, the vector is being scaled by a factor o
>> 3) In calculations involving models with point dipoles (as opposed
>> to point charges), the vectors can be used to store the
>> directional information for the dipoles.
>
> I should add that for point dipoles, it would be better to show the
> arrows *centered* on the atomic centers inst
Dan,
Thanks for such a detailed response.
In case it wasn't apparent, I am not a chemist ... nothing beyond Organic
... and that was many moons ago. ;^)
If you could answer this question I would appreciate it ...
Q: The molecule samples/cs2.xyz contains three atoms. Each of them has a
vector. T
I just checked in some code to include atom vectors in the calculations
for molecule diameter. It is now the case that atom vectors do not go off
the screen after a FitToScreen operation. For an example of this you can
see samples/cs2.xyz.
Q: What are these atom vectors used for? What do they repr
>> Do we need 'atom delete' functionality? Is it worth fixing?
>
> Yes, it was requested two times...
OK, not a problem.
Just wanted to know :-)
Miguel
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> Miguel asked about raising the required JVM version to 1.3.
...
> But, this should not mean that we can not use more advanced stuff...
>
> This is my proposal:
>
> For at least one year I want to keep the applet 1.1 only. If their are
> good reasons to have Java 1.2 stuff or higher, we should us
There are several bugs associated with delete. In particular, measure and
selections get messed up.
Do we need 'atom delete' functionality? Is it worth fixing?
Miguel
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> Miguel,
>
> I try to implement the rotational stuff we discussed previously but I
> get some problems.
> The purpose is to rotate around an axis defined by "axisAngle" and
> passing through the point "point" (see code below). The rotation angle
> is included in "axisAngle". The basic idea in the
>> I try to implement the rotational stuff we discussed previously but I
>> get some problems.
> I won't be able to take a look at this for a couple of hours.
Fabian,
I just checked in some code which takes a step in the right direction.
The code I checked in allows you to define a center of rota
> 1. I will turn on the double-buffering. We will test that and see what
> that does. I strongly suspect this will solve the problem.
> 2. I'll reintroduce some code to prevent multiple repaints from being
> scheduled. However, if *this* solves the problem then I will be very
> disappointed in Su
Fabian,
I won't be able to take a look at this for a couple of hours.
But I think I understand what you are trying to do.
I will get back to you.
Miguel
> Miguel,
>
> I try to implement the rotational stuff we discussed previously but I
> get some problems.
> The purpose is to rotate around an
> Sorry to keep bugging you... but I've got another thing...
Don't be foolish ... you are not bugging me.
> And now I've got flickering when rotation...
Well, we solved one problem, but encountered another. The good news is
that this one will be easier to fix.
I suspect that this is because I tur
>> Please try it again with samples/ch30h_ace.out and send me the new log
>> file.
>
> Attached. (gziped)
>
> BTW, the fact that it takes some time to happen, might suggest that the
> problem is caused by the exponential increase of some random error
> caused by machine accuracy... is that possibl
> Yes, I noticed that... but did not realize that i was important ;)
Well, I don't know if it was important or not. But I asked because I
wanted to make sure I was interpreting the log results correctly.
I just checked in a new version. It writes things to the log in a
different manner. Should not
>> Can you try to run the software with the the jmol vecmath package?
>> Perhaps rename the .jar file so that the Java3D version doesn't get
>> loaded first ...
>
> I've removeed them all... Same bug. jmolbug.log is attached...
It looks like to me that the behavior was different this time.
With thi
>> Q: Did you do any translations, or just rotation operations?
>
> Just rotation...
good
>> Q: Is it possible that you are running a different version of
>> javax.vecmath than the one that ships with Jmol?
>
> That might be... now that you ask me... the vecmath library comes from
> ...
> That jar
> Here it is. The bug is found on SunOS 5.8, sparc v9 with Sun JVM 1.4.0.
>
> Egon
Egon,
Well, the transformation matrices are pretty messed up.
Q: Did you do any translations, or just rotation operations?
Q: Is it possible that you are running a different version of
javax.vecmath than the one
> Sorry, but I can't mess anything. All is working pretty well both on my
> P4 Debian Unstable and my P3 Debian Stable/exported display.
>
Well that is good to hear.
I think that with extra debugging code Egon and I should be able to find
the problem.
Miguel
-
> there still is a display bug in HEAD...
>
> After a while the atoms move all over the screen... (if I knew how to
> make a animation of it, I could show you. I've asked about this on
> Slashdot...) Pressing HOME restores the molecule, but rotation now
> immediately corrupts the coordinates aga
I converted SortedTableModel.java to use the standard Arrays.sort method
and removed HeapSorter.java.
This is used in the table display of atom properties. If you click on the
column headers the table will be sorted on the selected column.
In the course of unit-testing this code I found two bugs
>> First another comment... the black lines around the atoms are very
>> small
>> now... Is the thickness configurable? I like the somewhat thicker
>> lines...
> Sorry, I should have explained this.
> I added an option to have the outline color be a darker version of the
> atom color. So, if the a
> On Thursday 21 November 2002 16:06, mth wrote:
>> > Are you only doing rotations? Or are you doing Zooms and
>> Translations also? To see if it is only related to rotations please
>> try the following:
>> > - rotate until it gets messed up
>> > - h
> Are you only doing rotations? Or are you doing Zooms and Translations
> also? To see if it is only related to rotations please try the
> following:
> - rotate until it gets messed up
> - hit home
> - click translation move the molecule. Does it mess up?
> - click zoom and shrink/enlarge the m
> On Thursday 21 November 2002 14:48, mth wrote:
>> Yes, they really are gone.
>>
>> Almost all the *Atom* code was cloned/duplicated. Same for all the
>> *Bond* code.
>>
>> Of course, the code still exists in cvs so we can go back and look at
>> it if
> Hi Miguel,
>
> there still is a display bug in HEAD...
>
> First another comment... the black lines around the atoms are very small
> now... Is the thickness configurable? I like the somewhat thicker
> lines...
Sorry, I should have explained this.
I added an option to have the outline color be a
I just checked in some pretty big changes to
DisplayPanel
PovrayDialog
io/PovraySaver
io/PovrayStyleWriter
This was a major overhaul of the transformation code that is used to
manage rotations, translations, and scaling to screen coordinates.
I now have a good understanding of most of thi
> i've you done anythine to CVS (like bug fix, new feature, performance
> enhencement), then please update the file doc/source/JmolHistory.xml
> file.
>
I haven't made any changes to this file yet.
I will do so in the near future.
Miguel
---
> Today I'll add a new package:
>
> org.openscience.jmol.io
>
> With the file IO classes.
Good.
> I would like to propose also a package:
>
> org.openscience.jmol.rendering
>
> But this would best be implemented by Miguel. He is working on
> the rendering part most right now... Miguel, do you
Egon,
Thanks for getting it fixed so quickly!
I see that some of the problems were mine (applet/DisplayPanel.java) ...
sorry.
Miguel
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> Not sure where that white square comes from... it is not drawn by the
> paint() method, because we would then see it on screen too, right?
>
> Egon
>
I still haven't looked at any of the printing code.
But I haven't seen any squares being drawin in any of the paint/rendering
code which I have l
I encountered an issue when building the latest b5. Something is hanging
in the jmolAppletGuide: step.
Haven't had time to investigate, but here is what happened.
On a Mac OSX 10.2 box I checked out the code to build it. I went on to
work on some other things. 20 minutes later I went back and the
>> Q:Is there a desire to export at a higher resolution, say for
>> printing? Q:Is there a desire to export a .png file as a vector
>> instead of
>> as a bitmap?
>
> Yes, I think so... The next release will have SVG support ... that is
> easy to add...
Adding higher resolution raster images
html pages to specify
the plug-in
> On Saturday 16 November 2002 02:17, mth wrote:
>> Which versions of Java do we officially support?
>>
>> There are some places in the display code which explicitly test for
>> version >= 1.2. In other places, calls are made whi
I forgot to say ...
I did not do anything about atom vectors. They still go off the screen
during rotations.
For example, samples/cs2.xyz contains atom vectors which still extend off
the screen. The atoms themselves now stay on the screen, whereas
previously they extended off the screen.
Miguel
I just checked in code which will automatically zoom to fit-to-screen when
the window is resized. The orientation of the molecule is not changed.
In addition, I changed CrystalFrame so that
- the center is defined to be the center of the box
- the radius is defined to be the greater of
1. th
I changed the povray code to use the changes I have made to screen scaling
calculations. It now uses the molecule center and radius to the outermost
atom to define the scaling.
There are a couple of scaling factors which are used in the povray code
that I don't understand. One looks legitimate (ma
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