Hi all,
I always get a segmentation fault, when I click "help"->"about" to see the
version details of pymol. The respective entry in /var/log/messages is:
pymol.exe[4991]: segfault at 3e0019b ip f74857a0 sp f3bab9a8
error 4 in libtcl8.5.so[f741+ed0
00]
This happens on all mac
Hi Nicolas,
> can I selectively change coordinates of particular atoms in a state?
Yes, you just need to properly select that atom.
> It seems that "alter_state" is not able to do that, since the expression
> (at least according to the help text) seems to apply to the x-coordinate
> of all atoms
Hello,
can I selectively change coordinates of particular atoms in a state?
It seems that "alter_state" is not able to do that, since the expression
(at least according to the help text) seems to apply to the x-coordinate
of all atoms in the state for instance.
The result of cmd.get_model() migh
Hi Jason,
I have the incentive version, but how do I use rigimol? I can't find
documentation for it on the documentation webpage. The link from
http://pymol.org/dsc/dokuwiki/doku.php?id=ip&s=rigimol
seems to be dead.
Thanks, nick
On 05/18/11 15:20, Jason Vertrees wrote:
> Hi Nick,
>
> You ca
Hi Nick,
You can use the "smooth" command
(http://www.pymolwiki.org/index.php/Smooth) on the structure of
choice. Incentive PyMOL comes with a molecular morpher called
"rigimol" that morphs a starting structure into an ending structure.
I suggest trying the "smooth" command first if you already h
Hi Thomas,
Thanks for submitting the bug. I've modified and applied the patch
and pushed the code.
It's fixed.
Cheers,
-- Jason
On Wed, May 18, 2011 at 11:43 AM, Thomas Holder
wrote:
> On 05/18/2011 05:01 PM, Jason Vertrees wrote:
>>
>> This is a bug. Please file it on our open-source bug t
Hi,
can pymol interpolate between states in a movie? Suppose I have
coordinates of a docking process with several states, and I would like
to animate that process, but smoothly. I would
madd 1 x15
madd 2 x15
.
.
.
but would like pymol to interpolate in those 15 frames between state 1
and 2, then
Hi Jason,
thanks, that works!
nick
On 05/18/11 12:08, Jason Vertrees wrote:
> Hi Nick,
>
> Sticks are bonds. For that we use "set_bond" not set.
>
> Try:
>
> set_bond stick_transparency, 0.8, rest
> set_bond stick_transparency, 0.0, sel_01
>
> Cheers,
>
> -- Jason
>
> On Wed, May 18, 201
Hi Nick,
On Wed, 2011-05-18 11:39 EDT, Nicolas Bock wrote:
> Hello list,
>
> I would like to change the stick_transparency for a selection but it
> doesn't seem to work. I am using the xyz file from the wiki:
>
> http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_comment
Hi Nick,
Sticks are bonds. For that we use "set_bond" not set.
Try:
set_bond stick_transparency, 0.8, rest
set_bond stick_transparency, 0.0, sel_01
Cheers,
-- Jason
On Wed, May 18, 2011 at 1:39 PM, Nicolas Bock wrote:
> Hello list,
>
> I would like to change the stick_transparency for a sel
Hello list,
I would like to change the stick_transparency for a selection but it
doesn't seem to work. I am using the xyz file from the wiki:
http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example
and the attached script. What am I doing wrong?
Thanks already,
On 05/18/2011 06:50 PM, Sean Law wrote:
> Hi PyMOL Community,
>
> I have a trajectory file loaded into PyMOL but I would like to play the
> movie in reverse order. Is there a way to achieve this within PyMOL?
If you have 100 states, type:
mset 100-1
See also:
http://www.pymolwiki.org/index.php/M
Hi PyMOL Community,
I have a trajectory file loaded into PyMOL but I would like to play the movie
in reverse order. Is there a way to achieve this within PyMOL? I know that I
could do this by outputting the states as PNG files and then reversing them in
an external program but I would like to
On 05/18/2011 05:01 PM, Jason Vertrees wrote:
> This is a bug. Please file it on our open-source bug tracker
> http://sourceforge.net/tracker/?group_id=4546&atid=104546. I will fix
> it when I get the chance.
Bugs item #3304003
https://sourceforge.net/tracker/?func=detail&aid=3304003&group_id=4
Hi Pascal,
On 05/18/2011 04:46 PM, Pascal Auffinger wrote:
Thanks, could you do that and provide a binary ?
I can't provide a binary, sorry.
Or alternatively, could
you post precisely which line to change to what ? Or change it in the
source code so that we could download an updated version.
Hi,
On Wed, May 18, 2011 at 6:00 AM, Thomas Holder
wrote:
> that's true, residue names should be right-justified.
This is a bug. Please file it on our open-source bug tracker
http://sourceforge.net/tracker/?group_id=4546&atid=104546. I will fix
it when I get the chance.
Cheers,
-- Jason
>
>
On 05/18/2011 02:23 PM, Pascal Auffinger wrote:
> Thanks for confirmation.
>
> Any clues on how to fix this ???
it has to be fixed in the C-code. I guess it's CoordSetAtomToPDBStrVLA
in layer2/CoordSet.c
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
that's true, residue names should be right-justified.
http://www.wwpdb.org/documentation/format32/sect1.html
"Residue nameOne of the standard amino acid or nucleic
acids, as listed below, or the non-standard group designation as
defined in the HET dictionary. Field is right-justif
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