Hi Yeping,
You can also try
set cartoon_side_chain_helper, on
http://www.pymolwiki.org/index.php/Cartoon_side_chain_helper
Regards,
Folmer
2015-05-18 10:23 GMT+02:00 sunyeping :
>
> Dear all,
>
>
> I find that when I show the protein as cartoon representation in pymol,
> and select some residu
Hi Yeping Sun,
Try:
set cartoon_flat_sheets, 0
set cartoon_smooth_loops, 0
Cheers,
Tsjerk
On Mon, May 18, 2015 at 10:23 AM, sunyeping wrote:
>
> Dear all,
>
>
> I find that when I show the protein as cartoon representation in pymol,
> and select some residues to show as sticks, then the stic
Dear all,
I find that when I show the protein as cartoon representation in pymol, and
select some residues to show as sticks, then the sticks do not connect to the
backbone shown by the cartoon but looks as floating over the backbone. How to
make the sticks connect to the backbone?
With many tha
Hi Ahmet,
On 22 Dec 2013, at 12:17, Ahmet yıldırım wrote:
> Pymol show them as a sticks but they are very similar. How can I color each
> residue with different colors?
if you have incentive PyMOL 1.6, you can use the spectrum command to color by
residue type:
PyMOL> spectrum resn
With older
works ok for
you, then the problem is probably your pdb file.
Cheers,
Nick
From: Ahmet yıldırım [ahmedo...@gmail.com]
Sent: Sunday, December 22, 2013 12:39 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] sticks
Dear users,
I want to show the
Hi Ahmet,
could be a shader problem (missing support by your graphics driver). Try:
PyMOL> set cylinder_shader_ff_workaround
(see http://pymolwiki.org/index.php/Cylinder_shader_ff_workaround )
or:
PyMOL> set use_shaders, 0
Cheers,
Thomas
On 22 Dec 2013, at 00:39, Ahmet yıldırım wrote:
> D
Dear users,
I want to show the residue 15 as a stick in .pdb.
pymol-->file-->Open-->.pdb
PyMOL> hide everything, all
PyMOL> select active, resi 15
PyMOL> show sticks, resi 15
Unfortunately, pymol doesnt show it as a stick. Please see image
https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15
> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> Of Tsjerk Wassenaar
> Sent: Tuesday, June 26, 2007 9:26 PM
> To: Dr. Mark Mayer
> Cc: pymol-users@lists.sourceforge.net
> Subject
Hi Mark,
You could've found this one in the archives of this list. Settings
work on objects, not on selections. The solution is to make an object
for the solid sticks and one for the transparent sticks, using create.
Cheers,
Tsjerk
On 6/26/07, Dr. Mark Mayer wrote:
Dear All,
I'm trying t
Behalf Of Dr. Mark
Mayer
Sent: Tuesday, June 26, 2007 10:18 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Sticks and distances with individual transparencies -
repost
Apologies for prior post message font was nearly unreadable
Dear All,
I'm trying to write a Pymol script wi
Apologies for prior post message font was nearly unreadable
Dear All,
I'm trying to write a Pymol script with which produces a mixture of
both solid and transparent sticks
I'm using the current 1.0 incentive release of MacPymol. After
drawing all my sticks I issue following commands, but nothi
Dear All,
I'm trying to write a Pymol script with which produces a mixture of
both solid and transparent sticks
I'm using the current 1.0 incentive release of MacPymol. After
drawing all my sticks I issue following commands, but nothing changes
although the log output suggests the change is be
ers-boun...@lists.sourceforge.net
> > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> > Of James Knight
> > Sent: Sunday, June 04, 2006 6:28 PM
> > To: Robert Immormino
> > Cc: pymol-users@lists.sourceforge.net
> > Subject: Re: [PyMOL] sticks
:28 PM
> To: Robert Immormino
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] sticks don't touch backbone
>
> Thanks for the reply, but no luck. It seems the backbone can
> be refined using cartoon_refine, but there is a limit to how
> far. Unfortunately in som
Thanks for the reply, but no luck. It seems the backbone can be refined
using cartoon_refine, but there is a limit to how far. Unfortunately in
some cases the carbonyl (and the nitrogen as well) misses be a lot when
the area of interest is zoomed in on. I guess I just have to play with
the camera a
I'm trying to get a stick from the "C" carbon that is part of the
backbone to the "O" it is double bonded to. I use the command: "show
sticks, resi 100 and name c+o". I get a stick that doesn't touch the
backbone. If I turn off all smoothing (set cartoon_smooth_loops, 0; set
cartoon_flat_sheets, 0)
> You can't just do:
> set stick_radius, .5, name n+ca+c+o
> set stick_radius, .2, ! name n+ca+c+o
> because both selections belong to the same object and the whole object
> is affected by the setting change.
On the other hand, you CAN do this:
show lines
show sticks, name n+ca+c+o
set stick_radi
Hi Shohei,
* Shohei Koide [2005-04-12 15:39] wrote:
> Hi,
>
> I would like to use different stick radii for the backbone and side chains
> (e.g. thicker sticks for BB and thinner ones for SC). The command "set
> stick_radius=X" seems to set the global stick radius, so I cannot use this
> comman
Shohei,
Try this,
set stick_radius=0.5, (your BB selection)
set stick_radius=0.1, (your SC selection)
scott
On Apr 12, 2005, at 1:39 PM, Shohei Koide wrote:
Hi,
I would like to use different stick radii for the backbone and side
chains
(e.g. thicker sticks for BB and thinner ones for SC
Hi,
I would like to use different stick radii for the backbone and side chains
(e.g. thicker sticks for BB and thinner ones for SC). The command "set
stick_radius=X" seems to set the global stick radius, so I cannot use this
command to set different radii values for different selections. Does an
Hi,
I'm trying to get a cartoon model of a pdb file to display a few selected
sidechains as sticks, I can see them in OpenGL, but when raytraycing the
sticks disappear. Using Pymol 0.96 under Windows XP. Ta for any help or
pointers
Peter
--
Dr Peter Teriete
Laboratory of Molecular Biophysics
De
Hi,
I am trying to learn Pymol and have already run into a problem. When I try
displaying in "Sticks" mode, some of the bonds (about 50% of them) take on
the background color. The problem is also visible when displaying in "Dots"
mode, although in this case the amount of glitch is less than 5%.
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