Op 23-2-2011 10:12, Rzepa Henry schreef:
I appreciate a debate on this topic may or may not be suited for the
Jmol list, but if anyone wants to add their opinion, I would welcome
this, if only because my synthetic organic chemistry colleagues
need to know what the most realistic
Dear Rick, Eric,
What the simpler solution is I don't know, but I can tell what I do
(since a long time, before jmol.js emerged, so it could be a bit
outdated...):
Write your comments in javascript in a data array data[1], data[2] where
the index corresponds to the frame number it is related
A short question, concerning lines and planes in an animation (multiple
XYZ file).
When I call a script like
frame 1
draw line1 120 (atomno=1) (atomno=2)
draw plane1 200 PERP PLANE $line1
the line is shown in all frames of the animation, while the plane turns
out to be attached to frame1 only.
Hi Frieda
Solvent-accessible surfaces of macromolecules are what I am accustomed
to using vis Chime, hence what I am seeking to create. However I have
to admit that I am not aware of what the distinction is between
isosurface and solvent-accessible surface...
Isosurface became the name
Hi Frieda,
While Bob is crossing the ocean: As I understood it, JVXL files can be
generated from any surface displayed by Jmol.
The JVXL lines are written to the Java console (if your browser has
one..Mine at home hasn't, so I can't test what I'm writing here).
The source of the surface
Egon Willighagen wrote:
On Tuesday 01 August 2006 21:20, Eric Martz wrote:
1. I would be pleased to see a simple linear interpolation option built
into Jmol. The need for such morph animations is becoming more common as
more structures are solved in different conformations. Having it built
Jonathan Gutow wrote:
Bob,
I think I see where you are going, but am a little worried.
If it is a cartoon, it needs to be clear that it is.
..
I think a tool like Jmol should be used to provide as
accurate a representation of things as we can. Thus in relation to
Bob Hanson wrote:
What we can now do is depict isosurfaces for:
(a) CUBE files,
(b) essentially equivalent but 1/500 the size JVXL files,
(c) atomic orbitals centered at (0,0,0) and aligned with the molecular
xyz axis.
The fact that we can do (c) suggests that any reasonable built-in
Angel,
They are very clear, should be a great help.
Hens
Hi all.
Looking at several recent posts, it seems that new Jmol users tend to visit the
demo-
example pages on the Jmol web site, copy the source code of the page, then make
their changes and find that they don't work, usually because
Jonathan,
Very nice page indeed.
I once made a page with gaussian calculated AO's, and found that a 3p
orbital had some of the 2p mixed in, resulting in too many nodal planes.
A problem which you managed to avoid.
http://cheminf.cmbi.ru.nl/wetche/organic/srm1j/index.html
On top of Miguels
Bob Hanson wrote:
I just meant that's how I implemented it -- for crystals -- where runs
are not the issue. (or are they?)
Well, somebody already mentioned the relation with partial occupancy, a
phenomenon found in crystals.
A quick check showed that of the 1400 CSD structures with a
Hi Bob,
Nice initiative.
I don't have the definite file yet (think about ring detection
techniques during your sabbatical ;) ), just a few additions:
define ~nitroN nitrogen and connected(3) and connected(2,~sp2O)
define ~nitroO ~sp2O and connected(~nitroN)
define ~nitro ~nitroN or ~nitroO
Bob,
I think the point is that there is a role for a bond type that looks
like a single, thick, dotted line, not solid+dotted as in aromatic;
not thin and dotted like typical hbonds.
The fact that there is a file type that registers this suggests that
it is warranted.
Hens, for the life of
To follow up on this:
I realized that the suggestion to interpret partail01 as an hbond wasn't
such a good idea, as hbonds are drawn as thin lines.
However, when I checked Bob's 10.1 demo page I noticed something odd (to
me).
The last caffeine command CONNECT MODIFY HBOND turns all the existing
Bob,
Incredible what a nice, estetically pleasing pictures one can make this
way with a few commands.
The facet type of depiction I really like, as it doesn't hide the
central atom.
Not knowing what (or who? New sponsor?) maxFactor was I changed the
number to e.g, 1.9, and that froze the
Bob,
At the end of a difficult but ultimately satisfying day,
I offer the following page for comment:
http://www.stolaf.edu/people/hansonr/jmol/test/json/spin.htm
Worked great for me, except one thing:
Clicking an axis to rotate it didn't work with my MS IE6/WindowsXP;
it was in Mozilla
Bob Hanson wrote:
I'm guessing that your IE cached something; it makes no sense that
IE/Windows works differently from Firefox/Windows in this case. My
IE/Windows works fine.
You're right; working fine now. Sorry for the inconvenience.
Hens
Howard!
Hens Borkent
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Hi Bob,
AS A USER, WHAT DO YOU WANT?
a) Do you implement callbacks? If so, which ones?
AnimFrame to synchronize other Javascript functions with an animation
Pick to identify atoms, in particular in our molecule editor
Message to return measurements, now largely replaced by monitors though
a button that animates the structure, and the effect is that the bond is
switched on and off.
Send me a structure file if you want me to try it.
Regards,
Hens Borkent
CMBI, Nijmegen
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Hello Shravan,
Hi All,
We are trying to migrate an application from CHIME to JMol. We have a
setup which requires CHIME to read a *.pdb file and build an IR
spectra graph with the information provided. There is another frame
where CHIME creates an animated visual of the loaded PDB data.
Phillip Barak wrote:
I must weigh in here. I'll be surprised if the hundredths place has
reasonable significance in any protein crystal structure.
But Jmol is so adept at rendering non-proteins, too! :-)
And crystallography isn't the only source of coordinates.
But for the rest
Miguel wrote:
I like this but prefer one digit to the right for Angstroms.
If noone makes a strong argument to the contrary then we will change it to
one digit.
I support Rich in that one digit (in Angstroms) is too few for comparing
bond lengths in organic structures, two is the
Miguel wrote:
Currently, the pmesh code only supports triangles and quadrilaterals.
I did not see any reason to support polygons any bigger than that ... I
even hesitated before putting in quadrilateral support.
You are defining a plane ... Three non-colinear points are sufficient.
Q: Why
Hi Brandon,
Hello,
I was wondering if there is a way to color the bonds of
the structure instead of the atoms.
The answer is rather intuitive:
set bondmode and;select atomno1,atomno=2;color bonds blue
Hens
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Miguel wrote:
hi Miguel,
a suggestion: can you release the signed Jmol applet as a compiled
update? seems like it would address a lot of the recent (and ongoing)
issues about local use of the Jmol applet.
I know we can get the signed applet from CVS-HEAD, but I imagine the extra
steps involved
Hi,
To add to the confusion: we are talking about different things here.
As I understood it, Chris was talking about changing the units during
measurements, say from the default nm to angstroms, and then updating
the values already being displayed.
In one particular structure.
[a problem I never
Hervé,
Let your button call a javascript function, and in this function you
send any script to any applet you like
document.jmol1.script('script1...');
document.jmol2.script('script2...');
In this way one can construct toggle buttons as well, which I don't find
in the current jmol.js
Is this
Miguel,
The vanderWaals surface is useful to colour-code other information on it.
In Chime one can display the electrostatic potential (ESP) or the
lipophilicity on the vdw-surface.
Especially the ESP is useful, but in Chime it turned out to be rather
difficult to override the default charges
Miguel,
Q: Please confirm that if I put in support for partial charges in the
range (-1 partialCharge 1) inside the XyzReader then you will test and
use this capability.
Yes, I will.
Hens
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Colleagues,
To return to a familiar subject: visualization of vibrations.
In Chime I used multipleXYZ files, written out by MOLDEN for a
particular vibration and as calculated by Gaussian, MOPAC, etc.
In Jmol I can still animate these mXYZ file, however the animation
doesn't run smoothly.
After
)
document.formname.textareaname.value = data[framenr] ;
Something like that, try it.
Regards,
Hens Borkent
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Miguel,
You should also be able to select them as 'select elemno=0'
Note that I have not tried either of these things. If they do not work
then let me know.
It works, thanks.
The script command: restrict elemno=1
excludes the dummy atoms from the display.
Hens
.
Hens Borkent
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Miguel,
However if that can be controlled in JMol by a script command set
models nmr|anim ( set frames nmr|anim ?) it would be a good solution to
distinguish between the two applications.
Why is there a need to distinguish between the two?
You're right.
What I meant is that there
:tim wrote
AFAIK (again), xyz files are generally useful for small molecules but not for
larger macromolecules. but maybe that's not quite accurate?
Well, it is not so much the size that matters, as does the extra
information a pdb file carries for proteins:
e.g. secondary structure, amino
scripts have a provision for both: set picking distance etc.
(would require a mechanism to place the result somewhere) ,
and 'spacefill number'.
Greetings,
Hens Borkent
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