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
> c
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 a
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 disappear
HI., I have tried to use surface and cartoon transparency together but then
I can see only the surface. Cartoon disappears completely. Any trick to get
it working? Thanks,
Petro
___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-user
of-Biomolecular-Structure-and-Function
> COBRE in Structural 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 Mar
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: [PyMOL] surface representation of the protein-ligand
interactions
Hi Enrico,
This is beyond my understanding, try and run t
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 | BPha
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
the
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, s
Dear Pymol users!
Working on the vizualisation of the protein-ligand interactions I
would like to switch from cartoon to the surface representation of the
protein, while still being capable to see the ligand-binding cavity
(as well as non-covalent interactions)
Could you suggest me some combinatio
>
> Message: 4
> Date: Wed, 24 May 2017 16:45:23 +0800 (GMT+08:00)
> From: ???
> Subject: [PyMOL] show surface on pymol
> To: pymol-users@lists.sourceforge.net
> Message-ID:
> <1c6ade2.11d04.15c39a1cba6.coremail.liuyanc...@sibcb.ac.cn>
> Content-Type: text/plain; charset="gbk"
>
>
> Dear
Hi "Someone Else" -
The `rotate` command (http://pymolwiki.org/index.php/Rotate) actually
transforms the atomic coordinates of the object in model space, which I believe
are only stored to 3 decimal places (as in PDB files), so there will probably
be some slight changes in how the surface is re
Hi,
I made a movie with rotating protein structure:
https://vid.me/Y4Nb
The structure itself is static, so the surface should also stay the same.
But it clearly changes during the movie. Any round-off errors? Is there any
fix for this problem?
I rendered frames for the movie by generating a set
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 wr
I think the problem may have to do with the surface_cavity_mode being set
to 3. I try to change the surface_cavity_mode but I still detect cavities
instead of the surface. It seems like any option related to the surface is
locked.
-Yarrow
---
Hello Pymol users,
As anyone experienced an instance where the surface transparency remained
stuck in one color? I changed it to pink a while back. However, now issuing
the comand:
set surface_color, green, object1
does nothing. Object1 is the object I want to color. Even if I try to
change the
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
Hello PyMOLers,
A quick question on the surface model, is there anywhere where I can learn
how molecules are color-coded. The default scheme has green, red, and bits
of yellow (I know the accessible to solvents surface is what is shown, but
I'm not sure what red, green, and yellow bits mean)? Also
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 tR
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 tRNA shows gaps in
the modified bases. Drawing a surface of a ligand such as an antibiotic
similarly is just a blank. This was not true in the older versio
On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI
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 surface_mode,
Hi!
Can somebody tell me why I can't create surfaces for the
oligosaccharide chains?
Thank you,
Raluca
--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info P
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]
Dear users
How can I obtain the surface of a ligand in protein pdb file.
I just need the simple surface, i doesn't need in this case, the
electrostatic surface.
Thanks
--
CHAIX Denis
PHD student
Centre de Biochimie Structurale
INSERM U554/CNRS 5048
29 rue de Navacelles
F-34090
Dear Luisa,
2009/4/21 Maria Luisa Rodrigues :
> 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 found something like this
Dear all,
Is there any PyMOL command to calculate surface areas?
Many thanks,
Luisa Rodrigues
Hi folks,
Apologies for the relatively off topic question but I figured someone may be
able to help.
Does anyone know of a tool that will calculate the cross-sectional area of a
(small) molecule?
Cheers Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal C
ursday, January 29, 2009 8:57 PM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Surface Residues
Dear all,
Once again, I need some help from pymol experts. I would like to select
surface residues via the surface calculation algorithm of Pymol. Is
this possible? What is the surface calcu
Dear all,
Once again, I need some help from pymol experts. I would like to select
surface residues via the surface calculation algorithm of Pymol. Is this
possible? What is the surface calculation algorithm that Pymol use and is
it scattered among many source-code files or is it contained in ju
Sorry about the last post--I just figured out that removing alternate
conformers seems to solve the problem.
Pat
---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecu
-Original Message-
From: Mark Collins [mailto:mnc2...@columbia.edu]
Sent: Thursday, December 18, 2008 7:38 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] surface properties
Hi All
I have searched thru the archive and couldn't find an answer,
to this. I would like to make
M
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] surface properties
Hi All
I have searched thru the archive and couldn't find an answer,
to this. I would like to make pymol surface(s) colored by
(1) hydrophobicity and (2) concavity/convexity.
These are easily produced in gra
ollins [mailto:mnc2...@columbia.edu]
> Sent: Thursday, December 18, 2008 7:38 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] surface properties
>
> Hi All
> I have searched thru the archive and couldn't find an answer,
> to this. I would like to make p
Hi All
I have searched thru the archive and couldn't find an answer, to this. I
would like to make pymol surface(s) colored by (1) hydrophobicity and (2)
concavity/convexity.
These are easily produced in grasp, so one possibility maybe to import
some type of grasp file.
Thanks in advanc
Does anyone have any idea how to render the interior of a protein like
this example:
http://skuld.bmsc.washington.edu/raster3d/examples/slice.png
While I can do it for the entire scene, I'd like a solid slab of the
protein but be able to see sidechains in front of the solid slab.
Any ideas?
Che
12, 2007 11:04 AM
> To: 'Eric Larson'; pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] bug in pymol surface rendering?
>
> load some_smet_containing.pdb
>
> flag ignore, clear, resn mse
>
> show surface
> (or "rebuild" if surface is al
, June 11, 2007 1:41 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] bug in pymol surface rendering?
>
> Hello,
>
> I would like to report an apparent bug in Pymol's surface
> rendering. I am using version 0.99rc1.
>
> Pymol does not render a s
Hello,
I would like to report an apparent bug in Pymol's surface rendering. I am
using version 0.99rc1.
Pymol does not render a surface around SelenoMet residues. It leaves a large hole in the
surface surrounding them. The residue is fully visible in this surface hole when turning
on stick
e.net] On Behalf
> Of Jeff Taylor
> Sent: Wednesday, June 06, 2007 12:52 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Surface question
>
> Hello-
>
> I have a enzyme-ligand co-structure that I would like to
> display with a surface representation of t
Hello-
I have a enzyme-ligand co-structure that I would like to display with a
surface representation of the ligand and something different, sticks or
cartoon, for the protein. The problem comes when I try to surface the
ligand, only the actual solvent exposed portion is shown, when I'd like
to s
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 belon
Hello,
Is there a way to access the individual vertices of a surface abd there
association with atoms? I know it's done under the hood, but can I write
some code that say returns a list of surface vertices associated with a
particular atom?
In the end, I'd like to know if two atoms share a surfa
sers@lists.sourceforge.net
Subject: [PyMOL] surface coloring fails with gradient loaded
Hi there,
i am trying to render fieldlines and sf potential together in a movie.
The movie setup is like this:
import os
set gradient_spacing=5
load ProtOut.pdb,prot
load trajshort.xtc,prot
mset 1 -7
show sur
Hi there,
i am trying to render fieldlines and sf potential together in a movie.
The movie setup is like this:
import os
set gradient_spacing=5
load ProtOut.pdb,prot
load trajshort.xtc,prot
mset 1 -7
show surface
set surface_solvent=1
for a in range(1,7): cmd.mdo(a,"delete flines;delete dxmap;de
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
>
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
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 surf
Hi,
please have a look at this image: http://pwe.no-ip.org/other/1.png
I'm having trouble with the edge of a surface selection. It seems that
there is always some more surface shown than the selected part. What I
did is, that I selected the red part to show the surface in obj1 and to
hide the s
Dear all.
I need to select surface atoms. Friend of mine recommended me this way:
For solvent accessible surface one can try Molmol:
Load your molecule, say " SelectAtom '' " in command line, say "CalcSurface"
- select the solvent radius (1.4A for water by default), put "by atom" radio
button on
@lists.sourceforge.net
> Subject: RE: : [PyMOL] Surface Vertex Coordinates
>
> Does it do all drawing objects or just surfaces ?
>
> and will it be in MacPyMol ?
>
>
> Laurence
>
> --
> --
>
From: pymol-users-ad...@lists.sourceforge.net
> [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 Po
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
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 a
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.
--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database
Hello everybody,
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
Ewgenij
Hi,
is there a possibility to calculate and display surface charge distributions of
RNA molecules in pyMOL? At present I only see an option to do this for
proteins. Or is there some kind of plugin that provides such a function?
All the best,
Michael.
- - - - - - - - - -
Michael H.W. Weber
Chair
s-ad...@lists.sourceforge.net] On Behalf Of
> Paul Wilhelm Elsinghorst
> Sent: Friday, January 20, 2006 11:33 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Surface of cavity
>
> Hi,
>
>
> a little question regarding cavity surfaces :-)
>
>
> I have a
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
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 :
> Hi,
>
>
> a little question regarding cavity surfaces :-)
>
>
> I have a set of active atoms (GOLD output) t
Hi,
a little question regarding cavity surfaces :-)
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.
Any ideas?
Paul
signature.asc
Description: This is a digitally signed message part
sourceforge.net
> Subject: [PyMOL] Surface representations
>
> Hi Pymolers,
>
> I am looking at a protein molecule in surface representation.
> Is there a way to have the surface be "closer" to the
> atoms/sidechains, i.e. not as bulky? This is just
Hi Pymolers,
I am looking at a protein molecule in surface representation. Is there a
way to have the surface be "closer" to the atoms/sidechains, i.e. not as
bulky? This is just for illustration sake.
Thanks!
-Greg
lf Blankenfeldt
> Sent: Tuesday, December 13, 2005 8:11 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Surface scribing in pymol?
>
> Dear pymolers,
>
> is there any simple way to scribe/cut surfaces in pymol,
> similar to the scribing function in grasp? I'd
Dear pymolers,
is there any simple way to scribe/cut surfaces in pymol, similar to the
scribing function in grasp? I'd like to prepare a figure in which I only
show a small piece of surface in a certain area of my molecule.
Thanks for any help,
Wulf
--
Dr. Wulf Blankenfeldt
Max-Pl
ol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of co1
> Sent: Monday, June 06, 2005 3:26 AM
> To: pymol-users
> Subject: [PyMOL] surface with vdw > 6
>
>
> Hello,
> I would like to represent the surface of a model made of
&
Hello,
I would like to represent the surface of a model made of dummy C atoms, but
they should have a
van der Waals diameter bigger than 6 A. When I increase their vdw above 5.9
(for ex.: alter elem
c, vdw=6; rebuild), the surface just disappear.
Do I need to change some other parameters?
Is it
Hi all,
Thanks to Kristoffer, Gregori, Cameron, Torin and Kenneth for their
responses. Here's a representative of their suggestions:
> select mymut, (resi 23+32+45)
> select mywt, (resi 1+2+3+4+5)
> color grey, all
> color yellow, mymut
> color green, mywt
Cheers,
Sarma
e (on 04/03/2005 08:19
PM): ===
Today's Topics:
1. surface representation showing mutations (Ganapathy Sarma)
Subject:
[PyMOL] surface representation showing mutations
From:
Ganapathy Sarma
Date:
Sun, 03 Apr 2005 18:13:49 -0700
To:
pymol-users@lists.sourceforge.net
Hello PYMOLers,
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 B
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 entr
Hello PYMOLers,
I am a very new entry to the world of Pymol after seeing the program in
action at a recent conference.
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
Dear all,
is there an obvious way to get hold of surface/mesh coordinates in a
python object?
Thanks,
Andreas
--
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany
Phone: +49 351 463 40063
EMail: a...@biotec.tu-dresden.de
Hi all,
Is it possible to edit the color of the inner side of a surface?
I want to show some waters filling a cavity. To do this I have clipped
the image near the cavity and given some transparency to the surface.
This is fine, but the inner side of the surface is just black (or very
dark) I
Dear Marcelo,
* castilho [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 colour protein sur
Dear all,
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 colour protein surface according to Hydrogen
donor/acceptor properties
pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Nuno Micaelo
> Sent: Wednesday, February 04, 2004 1:49 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Surface triangulation of isopotential surfaces
>
>
> How do i improve the surface triangulation of isopotential
> surfaces?
How do i improve the surface triangulation of isopotential surfaces? The
isosurface triangulation near the protein is very poor and is independent
of the grid size chosen in MEAD.
Thanks for your attention.
--
º¤ø,¸,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,¸¸,ø¤º*`
,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,
N
Does surface coloring work with ChemPy bricks? I took the script in
examples/devel/brick01.py and changed it to make a ChemPy brick that goes
from [0,0,0]-->[5,5,5] like so
... ...
brik.setup_from_min_max(
[0.0,0.0,0.0],
[5.0,5.0,5.0],
[0.5,0.5,0.5])
... ...
and then loaded up a pdb f
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
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Harp, Joel
M
Sent: Wednesday, November 12, 2003 2:10 PM
To: pymol-users@lists.sourceforge.
To calculate surface area for a defined object from the PyMOL command
line type:
print cmd.get_area("obj")
where obj is the name of your object.
for arginines:
create ARG, resn ARG
print cmd.get_area("ARG")
Kaushik.
On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote:
Is it
Is it possible to get pymol to calculate surface area for a defined
object? For instance, can it calculate surface area occupied by arginines.
Thanks,
Joel
Joel M. Harp
Vanderbilt University
Hello PyMolers,
Before I go tinkering around with some of the PyMol settings for
surface I was wondering if anybody could tell me the effects of each
setting. I am interested in slightly increasing the number of triangles
in my molecules surface for that highly polished look in PovRay.
surfa
...@lists.sourceforge.net] On Behalf Of Dennis
Wolan
Sent: Tuesday, April 29, 2003 2:42 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] surface
Dear all,
This has probably been asked a thousand times, but is the default
surface representation a molecular surface or a solvent accessible
Dear all,
This has probably been asked a thousand times, but is the default
surface representation a molecular surface or a solvent accessible
surface?
Thanks in advance,
Dennis
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
cami...@mrc-lmb.cam.ac.uk
Sent: Wednesday, April 23, 2003 3:01 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] surface charge?
Hi Warren,
I'm using PyMol to ma
Hi Warren,
I'm using PyMol to make the figures in a paper I am currently writing.
I know that pymol can generate surfaces at the moment but not charge.
Is there any way to colour a surface by charge in pymol using charges
calculated in grasp? ...or can I import a grasp surface? I heard that
t
Dear all :
When I tried to make surface figure, I saw holes on the surface. It seems
that these holes were made by the water molecules on the protein surface. I
want to show only the surface of the protein, not water molecules. Did
anyone have same problem?
Cheom-Gil Cheong, Ph.D.
Research
09 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Surface on HETATM groups
>
>
> I would like to display a surface for a HETATM group in my
> structure, but
> PYMOL is not doing so. Has anyone ever done this and if so
> how? Thanks.
>
>
> David Chimento
I would like to display a surface for a HETATM group in my structure, but
PYMOL is not doing so. Has anyone ever done this and if so how? Thanks.
David Chimento University of Virginia
dp...@virginia.edu
W (804) 243-2730 or 924-9599
H (804) 984-0877
war...@sunesis.com (Warren L. DeLano) writes:
>If someone can find a better open-source surface calculation code, I'd be
>happy to include it in PyMOL as an option. The only catches: it must be
>written in C, and it must be available under a BSD-style open-source
>license (free for commercial use
Hi Dr. Warren!
I know about MSMS license. Indeed, I'm suggesting an approach
similar to what VMD did, i.e., it can link, run and catch results to plot,
all that as a option conditioned to one gets or not MSMS installed,
separately, in one's machine.
Sanner had done and released a
Alan,
Last I checked, MSMS was saddled with a number of constraints on its usage
and redistribution. Though source code can be obtained under certain
conditions, MSMS doesn't meet the minimal "open-source" software
requirements that would make it eligible for inclusion into PyMOL. I
talked with
Hi List!
Dear Dr. Warren, have you consider using MSMS to generate surface
in Pymol, as VMD already does?
Since MSMS can generate a list too, by using another programs, I
could calculate properties to each point in the mesh. So, I wonder,
applying a colour method linked to such p
Raha [mailto:kxr...@psu.edu]
> Sent: Friday, February 07, 2003 4:37 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Surface and SASA
>
>
> Maybe this has already been discussed but I was wondering if the
> surface that PyMOL generates is solvent accessible su
Maybe this has already been discussed but I was wondering if the
surface that PyMOL generates is solvent accessible surface area (SASA)
? If so what is the solvent probe radius? The reason I ask is some
atoms seem to have exposed surfaces when rendered with PyMOL whereas my
SASA program has it
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