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
bel_color match the residue color. I
vaguely remember something like this discussed x number of years ago, but do
not remember why not. Could label become property of the object and not just a
property of a session?
Thank you.
From: Jared Sampson
Sent: Tuesday, October 1, 2019
; 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:
>
>
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
Hi Nick,
I recently was playing with (aka learning) the crystallographic symmetry
information in PDB files and now took your feature request as an
exercise. See attached file, hope it does what you had in mind.
Cheers,
Thomas
On Mon, 2010-04-12 at 14:12 -0600, Nicolas Bock wrote:
> It would be
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
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
>
>
>
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
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