Hervé wrote:
> 1. read and display only the first molecular model
> [Hervé Azoulay] yes. I've sent you an SD file but basically I would like
> to
> display only one molecule at a time.
[snip]
> Q: Which of the 4 choices above best describes your desire?
> [Hervé Azoulay] The first one :-)! Don't w
> Take for example the structure of a dimeric protein with two chains.
> Jmol calculates at startup automatically the appropriate size for
> complete visibility and sets the center for rotation. Now you want to
> concentrate on a single chain of the structure.
>
> Q1: Would it be possible to have a
I fixed the bug relating to jumping when using
set windowCentered off
center
But there's still a little jump (and always will be, I think) with
set perspectiveMode on
because when you assign a new center that does not have the same
z-coordinate as the previous, the perspective changes. T
Quoting Miguel <[EMAIL PROTECTED]>:
Rolf Huehne wrote:
Q: Would it in principle be possible to have a command that would set
the zoom state (and rotation center) automatically according to the
current selection or an atom expression and would adjust the allowed
zoom range?
I don't understand.
great!
William Reusch wrote:
Bob Hanson wrote:
yeah, that explains that. There was a bug in the color business.
Somewhere in a script you use color [r,g,b]. That's fixed, but maybe
not in that particular version. I'll upload again tonight.
Bob,
I downloaded your new jar files, and they
>> One problem is ... I don't know how to do this. I do not know how
>> graphics
>> people decide to clip objects so that they do not obscure the camera.
>> How
>> do you deal with the fact that when you put the camera next to an atom
>> then the atom takes up the entire screen? How do you decide w
Bob Hanson wrote:
yeah, that explains that. There was a bug in the color business.
Somewhere in a script you use color [r,g,b]. That's fixed, but maybe
not in that particular version. I'll upload again tonight.
Bob,
I downloaded your new jar files, and they seem to work fine in all the
br
Frieda Reichsman wrote:
Is the implementation of 'set windowCentered on/off' the same as 'set
frieda on/off'?
set windowCentered OFF
is the old
set frieda ON
But "frieda" was never really tested fully, so it had some strange
behavior that windowCentered takes care of.
Using set w
Frieda Reichsman wrote:
When the movie finishes, imagine that the next thing you want to do as
an author is show interactions, hydrogen bonding for example, between
the protein and some part of ADP. Try to zoom in more on ADP and you'll
see that the limit of zoom "expires" before you ge
Miguel wrote:
* I believe that what we need is the ability to move the camera. This
would allow one to 'fly' through a molecule ... or position yourself
inside it and look around. Then one could put the camera near something
and we would not have to worry about the 'zoom' causing things to ex
> Is it feasible for Jmol to compute that moveTo?
> (This request may have a familiar ring to it, especially for Miguel...)
Yes ... familiar
Bob, let's move this discussion to jmol-developers.
I have some thoughts about the spin-rotate model. Since you are now
familiar with the transformations t
> When the movie finishes, imagine that the next thing you want to do
> as an author is show interactions, hydrogen bonding for example,
> between the protein and some part of ADP. Try to zoom in more on ADP
> and you'll see that the limit of zoom "expires" before you get close
> enough to show tho
> It seems to my naive eye that if things are getting distorted when you
zoom in too much then either
>
> a) objects that are too close to the camera are being shown but
> instead should not be shown, or
Not really ... see below
> b) there is a bug in the code for zoom
perhaps.
> When an object
On Mar 23, 2006, at 10:19 AM, Miguel wrote:Q: Why do people want to zoom in so much? I hope this is a decent example of when one might want to exceed the limit of zooming.Visithttp://moleculesinmotion.com/scitech/boyer_final/structure/kinesin/kinesin_intro.htmand click "continue" which is toward th
On Mar 23, 2006, at 12:41 AM, Bob Hanson wrote:You can also nowset windowCentered OFFExcellent]then when youcenter (atomno=3)the molecule rotates around atom 3, but there's no snap. Tested and agreed.-- Atom 3 isn't put at (150,150) on a 300x300 applet.An earlier implementation of this wasset fried
It seems to my naive eye that if things are getting distorted when you
zoom in too much then either
a) objects that are too close to the camera are being shown but
instead should not be shown, or
b) there is a bug in the code for zoom
When an object is very close to the camera, does Jmol ign
> Hi all,
>
> as far as I understood the initial zoom factor is selected by Jmol such
> that all atoms are visible (inside the applet display), taking the
> larger applet side (width or height) as a reference. Depending on this
> initial zoom also the limits are set for the interactive zoom
Hi all,
as far as I understood the initial zoom factor is selected by Jmol such
that all atoms are visible (inside the applet display), taking the
larger applet side (width or height) as a reference. Depending on this
initial zoom also the limits are set for the interactive zoom range.
This
100% agreed. Eventually, as a *nice to have* feature, we can imaging having
the capability of opening a SD file and have next and previous buttons to go
from a molecule in the SD file to another. Far from being mandatory now I
think
Hervé
-Original Message-
From: [EMAIL PROTECTED]
[mailto
Hello
Maybe I can give a hand here with some comments and Chime experience.
El 22 Mar 2006 a las 19:42, Miguel escribió:
> Q: When Chime reads a 2D file does it display it using the RasMol 3D
> engine? Or do they have a separate 2D renderer built into Chime?
Chime has a 2D renderer (formula draw
Answers below !
Hervé
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Miguel
Sent: jeudi 23 mars 2006 01:43
To: jmol-users@lists.sourceforge.net
Subject: RE: [Jmol-users] Support of V3000 Mol format
Herve wrote:
> But my users require support from infor
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