Hi Petro,
Try "Setting > Transparency > Multi-Layer" or "Multi-Layer (Real-time OIT)"
See also:
https://pymolwiki.org/index.php/transparency_mode
Cheers,
Thomas
On Wed, May 17, 2023 at 4:51 PM Petro wrote:
>
> HI., I have tried to use surface and cartoon transparency together but then I
>
Thanks.
I will try it.
Best regards.
Petro.
On Wed, 17 May 2023 at 19:49, Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:
> Hi Petro,
>
> You might have luck using Order Independent Transparency:
>
> `set transparency_mode, 3`
>
> Hope that helps,
> Jarrett J
>
> On Wed, May 17, 2023
Hi Petro,
You might have luck using Order Independent Transparency:
`set transparency_mode, 3`
Hope that helps,
Jarrett J
On Wed, May 17, 2023 at 10:50 AM Petro wrote:
> HI., I have tried to use surface and cartoon transparency together but
> then I can see only the surface. Cartoon
ral Biology: https://www.ou.edu/structuralbiology
>
> From: Ali Saad Kusay via PyMOL-users [pymol-users@lists.sourceforge.net]
> Sent: Monday, January 10, 2022 8:48 AM
> To: Enrico Martinez
> Cc: pymol-users
> Subject: [EXTERNAL] Re:
ymol-users@lists.sourceforge.net]
Sent: Monday, January 10, 2022 8:48 AM
To: Enrico Martinez
Cc: pymol-users
Subject: [EXTERNAL] Re: [PyMOL] surface representation of the protein-ligand
interactions
Hi Enrico,
This is beyond my understanding, try and run this bash script without making
the surface transparent (to
Hi Enrico,
This is beyond my understanding, try and run this bash script without making
the surface transparent (to figure out if the issue comes from the transparency)
Also try the rebuild command before saving the image:
https://pymolwiki.org/index.php/Rebuild
Cheers,
Ali
Ali Kusay |
Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
Hi Enrico,
You can carve the protein surface around the ligand, i.e. show only the surface
behind the ligand, see this guide:
https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces
You can also try and made the surface more transparent, but this doesn't always
give the best results,
Hi Pymolers
I have solved my problem. I am using surface cavity_mode, 3. I need to
change the ray_interior_color instead of the surface color. I guess this
is because pymol is visualizing the interior of the surface not the
exterior.
-Yarrow
On Thu, Jul 24, 2014 at 11:08 AM, Yarrow Madrona
Dear Spyros,
Do you know about the PyMOL wiki (http://pymolwiki.org/)?
Take a look here: http://pymolwiki.org/index.php/Color
for an explanation about colors.
In the default representation
Green: Carbon
Blue: Nitrogen
Red: Oxygen
Yellow: sulfur
For coloring eg.
color gray
will color everything
Hi Venki,
You need to first issue the following command:
set surface_mode, 1
Best, Luca
On Jun 8, 2011, at 17:05 , V. Ramakrishnan wrote:
On versions 1.3, 1.4, I cannot display a surface of anything that is not in
the standard dictionary. For example trying to draw a surface of
On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI r.and...@sns.it
wrote:
Hi!
Can somebody tell me why I can't create surfaces for the
oligosaccharide chains?
By default, the surface and mesh commands ignore all atoms in HETATM records
in a PDB file. You can change that with:
set
set surface_mode, 1
Cheers,
Warren
-Original Message-
From: chaix denis [mailto:ch...@cbs.cnrs.fr]
Sent: Tuesday, May 26, 2009 3:55 PM
To: pymol-users@lists.sourceforge.net
Cc: Chaix Denis; support; pymol-users@lists.sourceforge.net
Subject: [PyMOL] surface of ligand
Dear users
Dear Luisa,
2009/4/21 Maria Luisa Rodrigues mlrodrig...@igc.gulbenkian.pt:
Dear all,
Is there any PyMOL command to calculate surface areas?
Many thanks,
Did you try to search for information yourself first?
Anyways, the pymolwiki.org is always a good place to go and then you
would have
I would like to select surface residues via the surface calculation
algorithm of Pymol. Is this possible?
Not at present.
What is the surface calculation algorithm that Pymol use and is it
scattered among many source-code files or is it contained in just one
source-code file?
It
Use my hydrophobicity script... Please build this in as preset as I use
it all the time.
# Written by H. Adam Steinberg
# 08/22/2007
###set custom colors for each amino acid based on hydrophobicity scale
(scale derived by S. D. Black and D. R.
Mould):
set_color ala, [0.525490196, 0.792156863,
Mark,
PyMOL does not have such abilities at present.
Can such concepts even be defined in a precise, objective, and unambiguous
fashion?
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com
-Original Message-
From: Mark Collins
Hi Mark,
I remember that Kristian Rother's rTools could do hydrophobicity coloring:
http://www.rubor.de/pymol_extensions.html
it is some years ago, so maybe it needs some updateing..
Best,
Andreas
DeLano Scientific wrote:
Mark,
PyMOL does not have such abilities at present.
Can such
Jeff,
Extract the ligand into a new object, and then show the surface on that
object only:
extract lig, ligand-selection
show surface, lig
Cheers,
Warren
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
Hi Jim,
Hmmm. I think your best option is to color the surface according to
the atoms and write the surface in povray format. This will give you
all the vertices. Just another thought springing to mind, you could
cycle over the atoms using a script, writing away only the part of the
surface
Martin,
Just FYI, the gradient display in PyMOL you and I have been working on is
still too immature to be considered supportable or supported. Indeed, prior
to your post, you were one of the few PyMOL users even aware of it.
For everyone else, I suppose I should announce that one of the many
Paul,
I think the reason the surface coloring spills over is because
there are some surface triangles that are shared by the selection you
want (red) and the neighboring residues (grey)... So it should work
if you only use one selection, by saying something like:
load my_protein.pdb,
show
pymol-users-boun...@lists.sourceforge.net wrote on 09/20/2006 07:28:00 AM:
Paul,
I think the reason the surface coloring spills over is because
there are some surface triangles that are shared by the selection you
want (red) and the neighboring residues (grey)... So it should work
if you
I believe that you need to make these new objects to correct the problem,
at least this is a quick fix that I have done in the past. There may be a
more elegant solution:
load my.pdb, obj1
load my.pdb, obj2
[whatever to each obj]
When loaded separately you don't have this problem.
Cheers,
JTM
Hitz
Cc: pymol-users@lists.sourceforge.net
Subject: Re: : [PyMOL] Surface Vertex Coordinates
The Povray intermediate file generated when you do 'ray
renderer = 1'
contains all vertices, normals and colouring information
for cartoon
and surface object types. However you do need
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Laurence Pearl
Sent: Wednesday, March 15, 2006 9:35 AM
To: Benjamin Hitz
Cc: pymol-users@lists.sourceforge.net
Subject: Re: : [PyMOL] Surface Vertex Coordinates
The Povray intermediate file generated when you do 'ray
The Povray intermediate file generated when you do 'ray renderer = 1'
contains all vertices, normals and colouring information for cartoon
and surface object types. However you do need to produce a parsing
script to extract these in to a useful form for importing into other
programs. Have
On Wed, Mar 15, 2006 at 09:01:19AM -0800, Benjamin Hitz wrote:
I am interested in the coordinates of the vertices of the mesh
representation of the molecular surface. Is there any method to read
them out?
Thanks
Me too. With coloring and/or other property information as well.
Hi,
you may try to use caver:
http://viper.chemi.muni.cz/caver/concept.php
or castp
http://cast.engr.uic.edu/cast/oldindex.php
regards
andrea
2006/1/21, Paul Wilhelm Elsinghorst p...@uni-bonn.de:
Hi,
a little question regarding cavity surfaces :-)
I have a set of active atoms (GOLD
Hi Paul,
I have a set of active atoms (GOLD output) that surround a cavity. Now I
want to dipslay the surface only for the cavity wall, not on the
outside.
try this: show surface for the whole protein and then hide surface for
not the active residues - something like this:
from pymol
Paul,
PyMOL generally shows all sides of an exposed atom, but perhaps you
could load both the GOLD output and the original structure.
You could then only show the surface on the atoms in the original
structure with corresponding atoms in the gold output as follows:
load orig.pdb
load gold.pdb
Hi Sarma,
I can change the color of the surface to gray or a rainbow gradient
using the options but can't find a way to specify the residues that need
to be colored differently in a surface representation.
You most likely need to select the residues first. That will give you an
extra entry
Have you tried the select resi function? This allows you to specify the
identification numbers of the amino-acids you want to select (and color).
Have a look here for the complete description:
http://pymol.sourceforge.net/newman/user/S0220commands.html
Regards,
Grégori Gerebtzoff
Division of
Sarma,
I am trying to create a surface representation of a protein with
mutations that abolish activity in one color (say yellow) and the ones
that don't change activity in another (say green). The rest of the
residues colored gray.
I can change the color of the surface to gray or a rainbow
Dear Marcelo,
* castilho casti...@if.sc.usp.br [2004-08-23 17:02] wrote:
My name is Marcelo and I am a basic-level pymol user. I work with docking
programs and I am trying to make pymol our default program for analysing
docking results...this brings me to some questions:
Is it possible to
Nuno,
For a couple of reasons, I curently believe that electrostatic calculations
based on point charge models are not valid near or within the protein surface
-- you need to be at least one atom radius beyond the molecular envelope in
order to draw physically meaningful interpretations.
Joel,
Yes, PyMOL does have this capability, but it is immature and not
routinely validated.
The basic concepts are:
1) get_area selection command will return the effective surface area
of the dots that you would see from show dots, selection. This is a
discrete approximation -- not an exact
Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Kaushik
Raha
Sent: Wednesday, November 12, 2003 2:50 PM
To: Harp, Joel M
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] surface area calculation
To calculate surface
Molecular (a discrete approximation to the Connolly surface).
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
Camille,
This capability exists in the development version, but isn't ready for
prime-time yet. Look for it in the next release.
In the meantime, you might try using raster3d to render your grasp
surface, via its ungrasp tool.
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