Re: [Jmol-users] [Jmol-developers] 11.1 _modelNumber suggestion
Jmol 11.1.12 implements
_currentFileNumber
_currentModelNumberInFile
for example:
set echo top left
echo File %{_currentFileNumber}|Model %{_currentModelNumber}|ID:
%{_modelNumber}
Note that:
1) if multiple models are displayed from a single file, then
_currentModelNumber goes to 0;
2) if multiple models are displayed from multiple files, then both
variables go to 0.
I've also added four new parameters to the animFrameCallback function:
animCallback(applet, frameNo, fileNo, modelNo, firstNo, lastNo)
the proper way to access the frame from JavaScript would be using
fileNo.modelNo.
As in:
jmolScript(frame + fileNo + . + modelNo)
When only one file is loaded, you can just use the modelNo (1,2,3,...),
as before, or you can use fileNo.modelNo, since in that case fileNo is
1, and 1.1, 1.2, 1.3 always work.
Note that to avoid floating point problems, firstNo and LastNo have the
file and model put together as:
fileNo * 100 + modelNo
This allows for up to 1000 files open at a time, each with up to 99
models. Should be plenty, I think. The 2001 1001 business still
works, but I don't recommend it.
Bob
Bob Hanson wrote:
[switch to Jmol-users list]
Dave, I did a little modification. Tell me if this suits you for
_modelNumber:
1) If only one file, one model is loaded, then you get 1 unless the
file is a PDB file with a MODEL record, in which case you get the
number on that record.
2) If only one file, multiple models are loaded, then you get 1.1,
1.2, 1.3, ... , etc. You can still use the standard 1 2 3 to
address these, but this seems to me a bit clearer in indicating to the
user that the models are all from the same file and that */1.1 may
be preferred to */1, though both work.
3) If several files are loaded, and each has only one model, then you
get 1 2 3 as usual.
4) If several files are loaded, and one or more has multiple models,
then FOR THOSE FILES, you will see 2.1 2.2 etc., but for files
that are loaded that don't have multiple models, you just see an
integer 2.
Note that the new file.model notation allows for a very handy way to
select all the models in a given file. You just specify the integer
file number:
select */2
selects all models of file 2 if more than one model exists. It's the
same as
select */2.0
This is so much better than 1001 1002 2001 that I'm taking those
out of the documentation.
I will look into _file and _model, but what do you want these to
say when there are multiple models displayed?
I have just checked in a set of modifications that makes frame much
more sensible. Now, for example, you can say:
frames 1.1-1.5
to see just these frames. This is the same as
frame range 1.1 1.5
frame 0
Also allowed now:
frames 1.5-
open ended.
Then, in addition, the _modelNumber variable is changed to a STRING
(which is necessary when displaying decimal numbers like 1.34), and so
it made sense to me to have it deliver the EXACT range of models being
displayed. So, for example, if you do:
frame range 1.5-
and the file has 13 models, then
message %{_modelNumber}
will return
1.5-1.13
which is far more useful, I think.
OK, so with that all set up, I'm ready to do the _file and _model
variables, but I need to know what you want for when multiple models
are displayed.
But I would like you to try the x.y--w.z type notation first and see
if it would work for you. If you are using a webpage you can always
dissect it out yourself from getProperty animationInfo as well or even
now a simple
var info = jmolScriptWait(message %{_modelNumber})
and then parse that.
Bob
[EMAIL PROTECTED] wrote:
Bob,
Thanks for the work you've done on the frame
command and the variable access. I've got
a nit-picky suggestion :
I've been using echo %{_modelNumber} with multiple
files loaded, and find that you get the numbers
in the format 1001, 1002.. 2001 etc, which is
a bit confusing to the end user. Would
it be possible to have separate variables _fileNumber
and _modelNumber (or whatever names you prefer), so you could echo
things like File 1, Frame 2 ?
Thanks,
Dave
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Re: [Jmol-users] [Jmol-developers] 11.1 _modelNumber suggestion
Bob,
Thank you for all your work on this, it's amazing
you can keep up with all these threads at once!
I've tested your bleeding-edge 11.1.12 zip file for these new
features, and the _currentFileNumber and _currentModelNumberInFile
are great for me, as is the 'frame m.x-n.y' syntax.
But, there does seem now to be a problem with 'frame next', 'frame prev'
and 'frame last' which wasn't there in 11.1.11 --- these commands
don't seem to work beyond the first file.
i.e. having done
load files file1.sdf file2.sdf
frame 2.1
all of 'frame next', 'frame prev' and 'frame last'
do nothing.
Thanks again,
Dave
On Wed, 14 Feb 2007 02:10:43 -0600, Bob Hanson [EMAIL PROTECTED]
said:
Jmol 11.1.12 implements
_currentFileNumber
_currentModelNumberInFile
for example:
set echo top left
echo File %{_currentFileNumber}|Model %{_currentModelNumber}|ID:
%{_modelNumber}
Note that:
1) if multiple models are displayed from a single file, then
_currentModelNumber goes to 0;
2) if multiple models are displayed from multiple files, then both
variables go to 0.
I've also added four new parameters to the animFrameCallback function:
animCallback(applet, frameNo, fileNo, modelNo, firstNo, lastNo)
the proper way to access the frame from JavaScript would be using
fileNo.modelNo.
As in:
jmolScript(frame + fileNo + . + modelNo)
When only one file is loaded, you can just use the modelNo (1,2,3,...),
as before, or you can use fileNo.modelNo, since in that case fileNo is
1, and 1.1, 1.2, 1.3 always work.
Note that to avoid floating point problems, firstNo and LastNo have the
file and model put together as:
fileNo * 100 + modelNo
This allows for up to 1000 files open at a time, each with up to 99
models. Should be plenty, I think. The 2001 1001 business still
works, but I don't recommend it.
Bob
Bob Hanson wrote:
[switch to Jmol-users list]
Dave, I did a little modification. Tell me if this suits you for
_modelNumber:
1) If only one file, one model is loaded, then you get 1 unless the
file is a PDB file with a MODEL record, in which case you get the
number on that record.
2) If only one file, multiple models are loaded, then you get 1.1,
1.2, 1.3, ... , etc. You can still use the standard 1 2 3 to
address these, but this seems to me a bit clearer in indicating to the
user that the models are all from the same file and that */1.1 may
be preferred to */1, though both work.
3) If several files are loaded, and each has only one model, then you
get 1 2 3 as usual.
4) If several files are loaded, and one or more has multiple models,
then FOR THOSE FILES, you will see 2.1 2.2 etc., but for files
that are loaded that don't have multiple models, you just see an
integer 2.
Note that the new file.model notation allows for a very handy way to
select all the models in a given file. You just specify the integer
file number:
select */2
selects all models of file 2 if more than one model exists. It's the
same as
select */2.0
This is so much better than 1001 1002 2001 that I'm taking those
out of the documentation.
I will look into _file and _model, but what do you want these to
say when there are multiple models displayed?
I have just checked in a set of modifications that makes frame much
more sensible. Now, for example, you can say:
frames 1.1-1.5
to see just these frames. This is the same as
frame range 1.1 1.5
frame 0
Also allowed now:
frames 1.5-
open ended.
Then, in addition, the _modelNumber variable is changed to a STRING
(which is necessary when displaying decimal numbers like 1.34), and so
it made sense to me to have it deliver the EXACT range of models being
displayed. So, for example, if you do:
frame range 1.5-
and the file has 13 models, then
message %{_modelNumber}
will return
1.5-1.13
which is far more useful, I think.
OK, so with that all set up, I'm ready to do the _file and _model
variables, but I need to know what you want for when multiple models
are displayed.
But I would like you to try the x.y--w.z type notation first and see
if it would work for you. If you are using a webpage you can always
dissect it out yourself from getProperty animationInfo as well or even
now a simple
var info = jmolScriptWait(message %{_modelNumber})
and then parse that.
Bob
[EMAIL PROTECTED] wrote:
Bob,
Thanks for the work you've done on the frame
command and the variable access. I've got
a nit-picky suggestion :
I've been using echo %{_modelNumber} with multiple
files loaded, and find that you get the numbers
in the format 1001, 1002.. 2001 etc, which is
a bit confusing to the end user. Would
it be possible to have separate variables _fileNumber
and _modelNumber (or whatever names you prefer), so you could echo
things
Re: [Jmol-users] Jmol and Moodle
Bob Hanson wrote: OK, you're on track. Check that file from the machine that is causing the problem. When you go to that exact URL with that browser, do you get a login message from the server? When I go there, I get a log in screen. Ah, so I'm betting only one of your browsers is passing on the secure password to the server when Jmol makes that call. Something like that. I'm going to change this error message to display the first 1000 characters of the file. That should be very helpful in general. Yes, ok, that's done. Jmol 11.1.12 will have this feature. When you look in the log file you will see the first three lines of the file. Also, this will display in the applet window. (a feature of 11.1) Bob When I do as you asked I get a window that asks me what I want to do with the file: open or save. No request for a password. I'm already logged in so probably it doesn't need my login while you weren't logged in when you tried it. * Jeff Hansen Department of Chemistry DePauw University Greencastle, IN 46135 [EMAIL PROTECTED] * - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 11.1.12 is ready for building
Jmol 11.1.12 is ready for Nico to release it. Two new items just in: 1) new file command file n like frame range n.1 - n.m where n is the file number and m is the number of models in the file. All models in this file are made displayable, and if we have display *, all atoms will be displayed. 2) select model= and select file= select file=2 # does the obvious, I think select model=2 # selects for the MODEL NUMBER irrespective of the number of files loaded So, for example, if file 1 had 3 models and file 2 has 5 models, then select file=1 # selects models 1.1, 1.2, and 1.3 select model=2 # selects models 1.2 and 2.2 PROVIDED they are not PDB files with MODEL records if any file has PDB MODEL records, then select model=n selects for THAT model designation. So, for example, if that first model has models 33, 22, and 11 in it, then select model=1 # only selects for 2.1, because there is no model 1 in file 1 select model=33 # selects for 1.1, because that model is listed as MODEL 33 I think its logical! Note also that you can use variables here: filename = 3 file @filename modelnum = 4 select [EMAIL PROTECTED] # or select model=modelnum # @ is unnecessary in this context Bob - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.1.12 is ready for building
Bob Hanson wrote: Jmol 11.1.12 is ready for Nico to release it. Done ! Bob, it's very useful your addition of the changes in JmolConstants :) I just copy / pasted it to get the change log of the release Nico - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 11.1.13 feature PROPOSAL
I have just checked in a version of Jmol that allows: inverting selected atoms about points and planes writing of selected coordinates and orientation reading those files back into Jmol Basically, there is a new command: invertSelection which by itself inverts all atoms through the center of rotation invertSelection POINT [some point description] which inverts selected atoms through a point invertSelection PLANE [some plane description] which inverts selected atoms across a plane Now, once this is done, of course, the atoms are not where they used to be. That would mess up the state, so I have added a new DATA type called coord: DATA coord set 24 ; Jmol Coordinate Data Format 1 -- Jmol 11.1.13 2007-02-14 15:54; 1 H H1_#1 2.9400268 2.3187106 -0.35901633 ; 2 N N2_#2 -1.4280989 2.2970076 0.9680812 ; 3 C C3_#3 -0.5195322 0.37288004 -0.24890617 ; ... 24 H H24_#24 0.7507625 -1.5374694 -1.5575587 ; end coord set; which allows setting of atom coordinates in bulk. This is necessary, of course, because if you move the atoms, we have to reproduce that in the script. So with that, it seemed simple enough (about 10 lines of code) to create: write coords which writes the same SPT script as write state except it also includes coordinate positions. SO, having done that, it seemed ridiculous if Jmol could write coordinates but not read what it had written, so I added a tiny JmolDataReader to read those files. I really don't know if that is of any particular use. But it was simple enough to do. But more useful, probably, would be the ability to write the coordinates in a more standard format, and if people feel strongly that we should NOT be able to read these script files this way, I would be happy to remove that capability. Comments? Suggestions for perhaps a SIMPLE general format for writing coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited, but with bonds), PDB? (unlimited, but rather involved). Alternatively, should Jmol have a new native format that includes the state? I don't want to make a big deal about this; just wondering. And, yes, I know -- the next thing needed is rotateSelected. I'm working on that. When that is in, we can start having quite some fun with loading two files, inverting one, moving it above the other, rotating it independently, etc. I think there might be some nice applications that would use this capability. Bob - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.1.13 feature PROPOSAL
I have just checked in a version of Jmol that allows: inverting selected atoms about points and planes I like it! I thought about asking to add something like this a while back, but never got around to submitting an official feature request. I can think of some really nice ways of using this capability. (I'm working on some pages that illustrate concepts of point-group symmetry - see http://www.otterbein.edu/home/fac/dnhjhns/xmltest/demo.html ) I still haven't had time to digest the cool new scripting capabilities... And, yes, I know -- the next thing needed is rotateSelected. I'm working on that. Any chance you can think about improper rotations as well? :-) Comments? Suggestions for perhaps a SIMPLE general format for writing coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited, but with bonds), PDB? (unlimited, but rather involved). Alternatively, should Jmol have a new native format that includes the state? If Jmol is creating it, what you have looks ok (except for connectivity). I don't know if bonds should be stored like MOL files or as Jmol commands (like the state). I like the idea (in principle) of using XML, though it certainly doesn't fit the simple criterion. Dean On 2/14/07 7:01 PM, Bob Hanson [EMAIL PROTECTED] wrote: I have just checked in a version of Jmol that allows: inverting selected atoms about points and planes writing of selected coordinates and orientation reading those files back into Jmol Basically, there is a new command: invertSelection which by itself inverts all atoms through the center of rotation invertSelection POINT [some point description] which inverts selected atoms through a point invertSelection PLANE [some plane description] which inverts selected atoms across a plane Now, once this is done, of course, the atoms are not where they used to be. That would mess up the state, so I have added a new DATA type called coord: DATA coord set 24 ; Jmol Coordinate Data Format 1 -- Jmol 11.1.13 2007-02-14 15:54; 1 H H1_#1 2.9400268 2.3187106 -0.35901633 ; 2 N N2_#2 -1.4280989 2.2970076 0.9680812 ; 3 C C3_#3 -0.5195322 0.37288004 -0.24890617 ; ... 24 H H24_#24 0.7507625 -1.5374694 -1.5575587 ; end coord set; which allows setting of atom coordinates in bulk. This is necessary, of course, because if you move the atoms, we have to reproduce that in the script. So with that, it seemed simple enough (about 10 lines of code) to create: write coords which writes the same SPT script as write state except it also includes coordinate positions. SO, having done that, it seemed ridiculous if Jmol could write coordinates but not read what it had written, so I added a tiny JmolDataReader to read those files. I really don't know if that is of any particular use. But it was simple enough to do. But more useful, probably, would be the ability to write the coordinates in a more standard format, and if people feel strongly that we should NOT be able to read these script files this way, I would be happy to remove that capability. Comments? Suggestions for perhaps a SIMPLE general format for writing coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited, but with bonds), PDB? (unlimited, but rather involved). Alternatively, should Jmol have a new native format that includes the state? I don't want to make a big deal about this; just wondering. And, yes, I know -- the next thing needed is rotateSelected. I'm working on that. When that is in, we can start having quite some fun with loading two files, inverting one, moving it above the other, rotating it independently, etc. I think there might be some nice applications that would use this capability. Bob - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.1.13 feature PROPOSAL
this now works. Aren't matrices great! I cannot believe how easy this
is. The new command is
rotateSelected
and then just like rotate or spin
Because I'm loathe to create still another command, I've added spin as
a keyword to rotate so now you can say, for example:
select file=1; rotateSelected spin internal 10 (C5/1) (C6/1)
or, in context:
load files cholesterol.mol cholesterol.mol
file 0;display *; show all models, all atoms
select file=1; invertselected # now I have two enantiomers
translateselected {0 5 5} # offset one
center visible
rotateselected x 180;rotateselected y 180
rotateSelected spin internal x 10
set picking select molecule
And, sure enough, only the top cholesterol spins. If you use the mouse,
both models rotate with the mouse -- unless you hold ALT down while
rotating, then only the spinning model rotates with you! And, if you
select the other model while this is happening, guess what? IT starts
spinning instead. Or, select all, and, yes, all start spinning. TOO much
fun!
Oh, and then do
set navigationmode
set navigationspeed 50
and use the arrow keys to enter the SPINNING molecule and look around.
Oh, oh. Oh, I think I'm going to get sick. I do NOT recommend doing
this. Seriously. I think some people might have to leave the room if you
do this for a crowd. Yeiks.
Bob
That's a slippery slope to molecule manipulation and other molecular
editing tasks. ;-)
Not interested.
Jmol should be able to load two models and rotate one so it can be
compared (visually) with another but I don't think it needs to *make*
the other model.
done
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Re: [Jmol-users] Jmol 11.1.13 feature PROPOSAL
Dean Johnston wrote:
I have just checked in a version of Jmol that allows:
inverting selected atoms about points and planes
I like it! I thought about asking to add something like this a while
back, but never got around to submitting an official feature request. I can
think of some really nice ways of using this capability. (I'm working on
some pages that illustrate concepts of point-group symmetry - see
http://www.otterbein.edu/home/fac/dnhjhns/xmltest/demo.html ) I still
haven't had time to digest the cool new scripting capabilities...
great -- you can use the Miller indices and select symmetry operation sets:
select symop=1555
invertselected HKL {1/2 1/2 0}
oooh.
And, yes, I know -- the next thing needed is rotateSelected. I'm
working on that.
done - that works, too.
Any chance you can think about improper rotations as well? :-)
Let's see.. What's an improper rotation again? Oh, sure, that's trivial --
angle = 60
rotate internal @angle {} {};
select *;invertSelected POINT {...};
Right?
Comments? Suggestions for perhaps a SIMPLE general format for writing
coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited,
but with bonds), PDB? (unlimited, but rather involved).
Alternatively, should Jmol have a new native format that includes the
state?
If Jmol is creating it, what you have looks ok (except for connectivity).
I don't know if bonds should be stored like MOL files or as Jmol commands
(like the state). I like the idea (in principle) of using XML, though it
certainly doesn't fit the simple criterion.
It's really not important. If you
write coord state.spt
and then
load state.spt
the nice thing is that it's all one file now. But you are pretty much
just back to what you get in an XYZ file.
But if you instead have that original file still in place and
script state.spt
then it loads the original file and moves the atoms to where they need
to be.
Bob
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[Jmol-users] advice needed
OK, I've got rotation, translation, and inversion of selected atoms
going now. It can all be scripted using
rotateSelected
translateSelected
invertSelected
The question is: How to specify this with the mouse? Right now I've set
it up (11.1.13) so that if you
set allowRotateSelected
and then hold down the ALT key, only the selected atoms rotate.
Here's a quiz for you. What does the following script do?
load files cholesterol.mol cholesterol.mol
file 0;display *;
select file=1; invertselected
translateselected {0 5 5}
center visible
rotateselected x 180
rotateselected y 180
thefile = 1
spinrate = 10
message _here
select file = thefile
rotateSelected spin internal x @spinrate
thefile = 3 - thefile
spinrate = - spinrate
delay 0.05
goto _here
Bob
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Re: [Jmol-users] advice needed
WOW! This is what I needed two months ago. You just made about half of my
Javascript code unnecessary, but it's so much easier and cleaner to do it
within Jmol.
OK, I've got rotation, translation, and inversion of selected atoms
going now. It can all be scripted using
rotateSelected
translateSelected
invertSelected
The question is: How to specify this with the mouse? Right now I've set
it up (11.1.13) so that if you
set allowRotateSelected
Should you do something like:
set altMouseMode ( rotateSelected | translateSelected | invertSelected )
???
It would be cool to be able to control inversion with the mouse.. (I really
like the rotateSelected with the mouse)
Another idea. Can you RESTRICT the rotateSelected to be only around an
arbitrary axis?
Here's a quiz for you. What does the following script do?
Ummm, synchronized spinners? Oddly enough, one molecule disappeared after
a minute or two.
great -- you can use the Miller indices and select symmetry operation sets:
select symop=1555
invertselected HKL {1/2 1/2 0}
Yeah, it's been a while since I've used Miller indices - ok, that will be
MUCH simpler.
Let's see.. What's an improper rotation again? Oh, sure, that's trivial --
Yes, just roto-reflection. Trivial.
Dean
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