Hi Jared and Vaheh -
We've implemented two modes and pushed the change to the github repository.
set internal_gui_name_color_mode,
set internal_gui_name_color_mode, 2
Mode 1 is color by first carbon color. We think this is the most relevant use
case and what the user typically would expect. Th
Hi Thomas -
When I said it's easy to implement, I was only thinking of object color. Among
the various cases you describe, the "dominant color" is probably the most
important one, as it might not be obvious to the user that object color can be
different from atom colors.
Indeed, I was among th
>
> From: Jared Sampson
> Sent: Tuesday, October 1, 2019 2:45 PM
> To: Oganesyan, Vaheh ; Thomas Holder
>
> Cc: pymol-users
> Subject: Re: [PyMOL] feature request
>
> Hi Thomas and Vaheh -
>
> This is indeed an interesting idea. I was thinking about this
2:45 PM
To: Oganesyan, Vaheh ; Thomas Holder
Cc: pymol-users
Subject: Re: [PyMOL] feature request
Hi Thomas and Vaheh -
This is indeed an interesting idea. I was thinking about this in terms of
implementation, and what the edge cases might be. I wonder what would be the
mechanism for a
; Thomas Holder
Cc: pymol-users
Subject: Re: [PyMOL] feature request
Hi Thomas and Vaheh -
This is indeed an interesting idea. I was thinking about this in terms of
implementation, and what the edge cases might be. I wonder what would be the
mechanism for assigning the color if the object is
Hi Thomas and Vaheh -
This is indeed an interesting idea. I was thinking about this in terms of
implementation, and what the edge cases might be. I wonder what would be the
mechanism for assigning the color if the object is not just a single color.
Would it be the color that is the dominant
Hi Vaheh,
I see that this can be useful, and it's fairly easy to implement. We can add a
new setting to turn this on and off, like "internal_gui_name_color_mode" (or do
you have a suggestion for a better name?).
Cheers,
Thomas
> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh
> wrote:
>
>
Thomas and other PyMOL developers,
It looks as if we color the object name similar to the object color it will be
easier to distinguish which structure am I manipulating now. While models can
be colored, the names of the models can't.
Anybody else think it might be helpful?
Thank you.
Regards,
Hi Nick,
> I noticed a few things:
>
> - when I run "supercell 2, 1, 1" I get another cell outline along the
> a axis, but no atoms are shown in the second cell. Do I have to run
> another command for them to show up?
the script does not create symmetry mates. The "symexp" command can
create sym
Hi Thomas,
thanks!
I noticed a few things:
- when I run "supercell 2, 1, 1" I get another cell outline along the a
axis, but no atoms are shown in the second cell. Do I have to run another
command for them to show up?
- when I run the command again with other values for a, b, or c, nothing
chang
def supercell(a=1, b=1, c=1, object=None, color='blue'):
'''
DESCRIPTION
Draw a supercell, as requested by Nicolas Bock on the pymol-users
mailing list (Subject: [PyMOL] feature request: supercell construction
Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12
It would be great if pymol had support for constructing and displaying a
supercell:
For data files that support crystallographic information, e.g. pdb, pymol
can already display the unit cell (show cell). It would be great if one
could easily display multiple copies of the unit cell, along the lin
Could the connect_mode setting be better documented? The current
documentation doesn't say much about what that setting does.
nick
On Fri, Mar 12, 2010 at 12:08, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Nicolas,
>
> Try:
>
> set connect_mode, 2
> load yourXYZ.xyz, discrete=1
>
Great, that works!
On Fri, Mar 12, 2010 at 12:08, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Nicolas,
>
> Try:
>
> set connect_mode, 2
> load yourXYZ.xyz, discrete=1
>
> -- Jason
>
> On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock
> wrote:
> > Please find attached an example xyz fil
Nicolas,
Try:
set connect_mode, 2
load yourXYZ.xyz, discrete=1
-- Jason
On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock wrote:
> Please find attached an example xyz file.
>
> nick
>
>
> On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote:
>>
>> When I load an xyz file with several frames (for exa
I should mention that the first 3 columns are the cartesian coordinates in
Angstroms, and the last 3 columes the forces in eV/A.
On Fri, Mar 12, 2010 at 11:50, Nicolas Bock wrote:
> Please find attached an example xyz file.
>
> nick
>
>
>
> On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote:
>
>
Please find attached an example xyz file.
nick
On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote:
> When I load an xyz file with several frames (for example the result of an
> MD simulation) I find that pymol calculates and sets the bonds only using
> the initial frame. For frames > 1 the bond
After editing a molecule it can happen that the bonds that used to be there
don't all make sense anymore, for example, because I moved an atom pretty
far away from its original place. It would be nice if one could call a
function to force pymol at some point to recalculate the bonds in the
molecule
When I load an xyz file with several frames (for example the result of an MD
simulation) I find that pymol calculates and sets the bonds only using the
initial frame. For frames > 1 the bonds are not recalculated. The only "work
around" I found is to load(..., multiplex=1) which loads the frames in
Nick,
Please email bug reports and feature suggestions to
h...@schrodinger.com. CC the list if you like.
Cheers,
-- Jason
On Fri, Mar 12, 2010 at 11:17 AM, Nicolas Bock wrote:
> Hello list,
>
> what's the mechanism for submitting feature requests or bug reports? To this
> list?
>
> nick
>
>
>
Hello list,
what's the mechanism for submitting feature requests or bug reports? To this
list?
nick
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively,
Hi,
I would definitely not like to see a default representation to be any
more than lines (as it is now). Opening one of my 100,000 atom MD
trajectory frames would take far longer than it's worth.
Regarding png output, I think this is in there already (but don't
remember) - I'd like to be able to
let everyone know when it make sense for more people to try it!
-Original Message-
From: H. Adam Steinberg [mailto:a...@steinbergs.us]
Sent: Fri 1/16/2009 6:41 PM
To: Sarina Bromberg
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] feature request
It is especially difficult to reme
It is especially difficult to remember which scene is which when you
open a pse file that you haven't looked at for a few months. Would it be
simple or easy to just let us name the scenes like we name the objects
and selections in the pane on the right?
Sarina Bromberg wrote:
I find it difficu
I find it difficult to keep track of all the scenes I create in a
PyMOL session and where they are in the stack. Would it be possible,
at some point, to add a feature that displays numbered thumbnails of
scenes in another window on the desktop?
Thanks,
Sarina
Sarina Bromberg
(650) 879-1492
Hello Michelle,
You can also edit the SetEditor.py file. The file is in the
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the
feature. It can be done by adding to small portion of add-on code to the
file. If you do so:
Keep a copy of the original file in a safe place !
Hello Michelle,
You can also edit the SetEditor.py file. The file is in the
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the
feature. It can be done by adding to small portion of add-on code to the
file. If you do so:
Keep a copy of the original file in a safe place !
Hey Michelle,
Ezequiel Panepucci wrote grepset, a little script that allows you to do
exactly what you want and even more. No need even to open the edit
settings menu, just type 'grepset ray', and you're cruising.
Get grepset from http://www.pymolwiki.org/index.php/Grepset and put it
into y
While we're discussing ways to make our favorite program a little
better, I had an idea I thought I'd throw out there...
While making some figures the other day, I found myself scrolling
endlessly through the edit settings menu (under Setting --> Edit All) a
number of times, mostly to locate a
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