Bob,
That's certainly more straight forward than addition. I was just envisioning
situations where an individual atom is deleted, and a user wants to add some
atom back in. Creating a quarternary nitrogen would also require addition of
a new atom.
At this point, via click, I can replace atoms, ch
I think you should always be able to know where the atom is to go. If it
were me, I would always do atom replacement, so when, say, I click on an H
atom, it becomes a CH3. Isn't that the way Spartan does it? I would just
follow their lead on that. No need to reinvent the wheel here.
Bob
On Fri, F
Exactly the problem. We have wildly different data sets -- from electron
diffraction to X-ray data. Where did we end up with that discussion about
sigma? I can certainly look at the Pymol code and see what Warren did there.
Bob
On Fri, Feb 19, 2010 at 11:37 AM, Thomas Stout wrote:
>
> But elect
The syntax is not correct:
measure RANGE 1.8 3.2 (within(molecule,_F)) (not within(molecule,_F))
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, a
Well, it depends upon the file size. Really the best way to do it is just
let the person use a file-type input tag (with the "browse" button) and let
them send the file to your server. No need to involve Jmol.
Bob
On Fri, Feb 19, 2010 at 1:02 PM, rob yang wrote:
> Hi List,
> I am using the sig
Thanks Angel --
I thought that might do the trick, but perhaps I am implementing it wrong.
I thought this might work:
measure RANGE 1.8 3.2 (within molecule) (not within molecule);
but that generates neither measurements nor errors. I think the symmetry
part here is a red-herring. Attached is
Or, molecules will be differentiable by
symop=1
symop=2
symop=3
symop=4
...
2010/2/19 Angel Herráez
> Tom,
>
> maybe "within molecule" ?
>
> http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#text10
>
>
>
>
> --
Rob, I'm quite sure this has been discussed before on the list. Try searching
the archives
Don't remember now, but the outset was not very encouraging I'm afraid.
--
Download Intel® Parallel Studio Eval
Try the new so
Tom,
maybe "within molecule" ?
http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#text10
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively
Otis Rothenberger schrieb:
> Rolf,
>
> Yup, that seems to work for getting the atomIndex. It just took a while
> for me to find the correct dot notation by playing with:
>
> var z={*}.atomIndex.max;echo @z;
>
> I'm new to the math component of Jmol, so I'm doing a lot of trial and
> error with
Rolf,
Yup, that seems to work for getting the atomIndex. It just took a while for
me to find the correct dot notation by playing with:
var z={*}.atomIndex.max;echo @z;
I'm new to the math component of Jmol, so I'm doing a lot of trial and error
with math notation right now.
I have not tried you
Otis Rothenberger schrieb:
> Subsequent methylamine to ethylamine adds the carbon atom, but it will
> not connect, nor will it add hydrogens. Checking all three atomInfo's
> shows the problem. There is atomIndex confusion with all the deleting
> and adding going on. The array lengths are correct
Bob and Rolf,
A fairly lengthy data list is appended to this email.
It looks like atomIndex assignment has problems with my approach. The
JavaScript function is now:
function appendC(x) {
var scpt = "select;var z={*}.length;set appendNew false;data
'append'|1|add|C 5 5 5|end 'append';show da
Hi List,
I am using the signed jmol applet to display client-side local files (this part
works great). I am wondering if there's a way to upload the file on display to
the server side? Thanks.
-Rob
__
Is there a convenient way of distinguishing molecules when there is more
than one in the asymmetric unit? In this case, I am not referring to
macromolecules or PDB files, which have the handy "chain ID", but rather
small organic molecules loaded from cif files. I'm looking to
(automatically) calc
But electron density maps can be on arbitrary scales, so the value "1.0" may
very well be meaningless (except in the particular case where normalization
has made 1.0=1e-/A**3), and will certainly produce wildly different results
from dataset to dataset depending on the provenance of each particular
Thanks Bob and Rolf.
{*}.length to get the atomIndex of the appended atom makes the embarrassing
astatine trick go away. It also has some general utility.
Bob, putting the appended atom anywhere in the reach of other atoms seems to
always get it mired in a web of strange bonds after "minimize add
On Thu, Feb 18, 2010 at 11:20 PM, Otis Rothenberger wrote:
> Hello-
>
> I'm working on an atom append script to click append a C atom (methyl group
> actually) to an existing atom in a Jmol model. The following JavaScript
> function works, but it is far from elegant. I'm fairly sure that there are
Eric, I think this is just that Pymol has a different definition -- 1.0
sigma is not 1.0 value. Jmol uses actual value 1.0, not "sigma" 1.0.
Bob
On Fri, Feb 19, 2010 at 7:26 AM, Eric Martz wrote:
> Dear Bob,
>
> I'm sorry to report that Jmol 11.9.29 is not displaying ccp4 electron
> density map
Dear Bob,
I'm sorry to report that Jmol 11.9.29 is not displaying ccp4 electron density
maps correctly as isomeshes. I have demonstrated a major problem here
(hopefully not major to fix):
http://www.umass.edu/molvis/tests/jmol_edm_test5/
-Eric
On 02/19/2010 06:20 AM, Otis Rothenberger wrote:
> 1) The ridiculous addition of astatine relates to my inability to use
> getProperty for the atomIndex of the newly appended atom, so I appended a
> very rare element, selected it, and changed it to carbon. Is there a way to
> get this atomIndex a b
On 02/19/2010 11:19 AM, Rolf Huehne wrote:
> I am not sure if I understand what the problem is here.
> Is it that you want to display everything except the appended atom at
> "50 50 50" filling the view?
> If this is the problem you could try "zoomto (atom expression)".
>
Sorry, I forgot the impor
On 02/19/2010 06:20 AM, Otis Rothenberger wrote:
> Hello-
>
> I'm working on an atom append script to click append a C atom (methyl group
> actually) to an existing atom in a Jmol model. The following JavaScript
> function works, but it is far from elegant. I'm fairly sure that there are
> Jmol ma
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