On 2 Mar 2007 at 16:48, Bob Hanson wrote:
> > "Open" loads a molecule, so when I see "Close" beside "Exit", I
> >imagine that the first will remove the molecule, and the second will
> >exit the program = close the window.
> >
> >
> Sure --- that's a ZAP -- we couldn't "close the molecule" whe
Bob, I find this very attractive. Loading takes time when the server is not
close, and that could
help much. In fact, I always expected that the split of JmolApplet into 6 jar
files would do that,
but it seems not to be so.
Yes, I think that reduced functionality would be enough in many cases
Sorry I passed it wrong. In fact, I tested it with
atomno>5 and atomno<9(meaning atoms 6, 7 and 8, two bonds)
but changed the example for the post, so the AND stayed where it shouldn't.
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>
>
>>an option could be to "freeze" the perspective in the coordinates. This
>>would let you rotate a model around, hit copy, and have the data stored
>>with that orientation -- degrade the data a bit, but not too badly, I think.
>>
>>
>
>Will that be equivalent to saving to a script file
[I appreciate these answers -- I'm still not getting the originals for
some unknown reason.]
The command is
select atomno=8 or atomno=9; wireframe 0.1
"or" here because we need to include both atoms in the set.
In 11.1.16 you can select bonds directly:
select [{0}] selects the first bond, fo
Angel Herraez wrote:
>El 1 Mar 2007 a las 18:45, Egon Willighagen escribió:
>
>
>
>>Close is supposed to close one window but keep the application if there are
>>other windows, while Exit is supposed to close all windows and exit the
>>complete Jmol application.
>>
>>
>
>
>We should discus
In 11.1.x we are recommending going to a simpler method of naming models
in multiple file mode:
Files have each one model:
1.1, 2.1, 3.1,
Files have more than one model:
1.1, 1.2, 1.3, ... 2.1, 2.2, 2.3 etc.
Then, in analogy to
model 0
for displaying all models, now we have:
model
Glad it works. In general, 'and' signifies an additional requirement
for the selection set, as in,
select helix and carbon
which selects all the carbon atoms that are in the alpha helices (of
a protein), and no carbon atoms in other parts of the structure.
But it is easy to slip up.
Frieda
Thanks Frieda,
I can't say I'd have guessed the operator was "or".
It works fine.
I'd prefer something neater like "select atomno=8,9 and 10.11" but I can live
with this.
Thanks again
Nick
---
Message: 3
Date: Fri, 2 Mar 2007 15:19:30 -0500
From: Frieda Reichsman <[EMAIL
Dear Bob,
Interesting ideas! I guess I'm not convinced that the applet size is
enough of a problem to justify the complexity of what you propose.
However, Jmol is bound to keep growing, so eventually an AppletLite
may be more justifiable.a
-Eric
--
Jmol users,
I have an idea for slimming down the Jmol applet and need comments. The
idea is that few people will use ALL the capabilities of Jmol. Perhaps
there should be a set of Jar files that are optional add-ons to a basic
package. This package might have just a couple of file readers, no
Molecular Math in Jmol -- Part IV: Item Selectors [n][m] and @ substitution
A third capability now part of the Jmol query language is the ability to
select items from a set. This is done using one or two bracketed numbers
after the set. The sets include four types:
atom sets {oxygen}[2]
bo
Depending oinn how literally you took Angels' command syntax -
perhaps it's just that you need to use 'or' (in place of 'and'). So
for example,
select atomno=8 or atomno=9
color bonds cyan
works for me in Jmol11.1.12.
Frieda
On Mar 2, 2007, at 2:55 PM, Greeves, Nick wrote:
Hi Angel,
Hi Angel,
That was the sort of thing that I hoped would work but it doesn't (for me using
11.1.14).
Does it work for you?
Nick
-Original Message-
Message: 4
Date: Fri, 02 Mar 2007 12:17:24 +0100
From: "Angel Herraez" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Colouring/highlight
Some cool color effects could be obtained more easily if we could use
variable names in RGB or hex colors in Jmol.
For example, I tried using something like:
redness=0
message = _here1
color [EMAIL PROTECTED], 0, 0]
@redness= redness+5
refresh
if ... etc.
but Jmol did not like the redness var
I have been working on some animations and a couple of features would be
nice to have.
1) for the connect command a PARTIALTRIPLE bond similar to the
partialdouble bond
2) for the if statement the ability to test for which model is loaded,
i.e.
if (model = 12) . endif;
Hi Harris
Although others had posted more detailed solutions to your question,
I think the problem you had with
> jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;');
> It shows 1BZ8 structure. But if i do :
>
>
> jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select
On Mar 2, 2007, at 6:29 AM, Angel Herraez wrote:
> El 1 Mar 2007 a las 18:45, Egon Willighagen escribió:
>
>> Close is supposed to close one window but keep the application if
>> there are
>> other windows, while Exit is supposed to close all windows and
>> exit the
>> complete Jmol applicatio
El 1 Mar 2007 a las 18:45, Egon Willighagen escribió:
> Close is supposed to close one window but keep the application if there are
> other windows, while Exit is supposed to close all windows and exit the
> complete Jmol application.
We should discuss what is the most logical behaviour that u
Hi Nick
Have you tried selecting the atoms that form the bond?
select atomno=8 and atomno=9
color bonds cyan
wireframe .1
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> congratulations, Angel! You are the first to operate this menu since
> years ago!
I don't use the application frequently, but exploring the "logical" a
new user would follow, I perused the menu.
> Place a model file in the system clipboard from some other source, then
> use Edit..Paste.
I s
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