Re: [PyMOL] Surface and cartoon transparency together?

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 >

Re: [PyMOL] Surface and cartoon transparency together?

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

Re: [PyMOL] Surface and cartoon transparency together?

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

[PyMOL] Surface and cartoon transparency together?

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:

Re: [PyMOL] surface representation of the protein-ligand interactions

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:

Re: [PyMOL] surface representation of the protein-ligand interactions

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

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 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 |

Re: [PyMOL] surface representation of the protein-ligand interactions

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

Re: [PyMOL] surface representation of the protein-ligand interactions

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,

[PyMOL] surface representation of the protein-ligand interactions

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

[PyMOL] Surface not including methyl-lysine

> > 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;

[PyMOL] surface transparency not chaning

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

[PyMOL] surface stuck on one color

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

Re: [PyMOL] surface stuck on one color

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

Re: [PyMOL] SURFACE MODEL

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

[PyMOL] surface display in new pymol

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

Re: [PyMOL] surface display in new pymol

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

[PyMOL] surface for oligosaccharide chains

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

Re: [PyMOL] surface for oligosaccharide chains

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

[PyMOL] surface of ligand

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

Re: [PyMOL] surface of ligand

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

[PyMOL] surface area calculation

Dear all, Is there any PyMOL command to calculate surface areas? Many thanks, Luisa Rodrigues

Re: [PyMOL] surface area calculation

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

Re: [PyMOL] Surface Residues

, 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 calculation

[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 calculation algorithm that Pymol use and is it scattered among many source-code files or is it contained in

[PyMOL] surface appearance

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

Re: [PyMOL] surface properties

-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 pymol

Re: [PyMOL] surface properties

[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 pymol surface(s) colored by (1) hydrophobicity

Re: [PyMOL] surface properties

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 grasp, so one

[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 grasp, so one possibility maybe to import some type of grasp file. Thanks in advance

[PyMOL] surface rendering question

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?

Re: [PyMOL] bug in pymol surface rendering?

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 already shown) -- DeLano Scientific LLC Subscriber Support Services mailto:del

Re: [PyMOL] bug in pymol surface rendering?

@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 surface around SelenoMet residues. It leaves a large hole in the surface surrounding them

Re: [PyMOL] Surface question

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 the ligand and something different, sticks or cartoon

Re: [PyMOL] Surface vertex list

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

[PyMOL] Surface vertex list

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

[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 surface set surface_solvent=1 for a in range(1,7): cmd.mdo(a,delete flines;delete

Re: [PyMOL] surface coloring fails with gradient loaded

: [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 surface set surface_solvent=1

[PyMOL] Surface Edge

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

Re: [PyMOL] Surface Edge

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

Re: [PyMOL] Surface Edge

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

Re: [PyMOL] Surface Edge

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

[PyMOL] Surface atoms again

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 and

RE: : [PyMOL] Surface Vertex Coordinates

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

RE: : [PyMOL] Surface Vertex Coordinates

[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

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 to produce a parsing script to extract these in to a useful form for importing into other programs. Have

Re: : [PyMOL] Surface Vertex Coordinates

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.

[PyMOL] Surface Vertex Coordinates

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

[PyMOL] surface display of electrostatic potential of nucleic acids possible in pyMOL?

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

Re: [PyMOL] Surface of cavity

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

Re: [PyMOL] Surface of cavity

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

RE: [PyMOL] Surface of cavity

: 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 set of active atoms (GOLD output) that surround a cavity. Now I want to dipslay the surface only for the cavity

[PyMOL] Surface of cavity

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

[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 for illustration sake. Thanks! -Greg

[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 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

Re: [PyMOL] surface representation showing mutations

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

RE: [PyMOL] surface representation showing mutations

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

Re: [PyMOL] surface representation showing mutations

mutations (Ganapathy Sarma) Subject: [PyMOL] surface representation showing mutations From: Ganapathy Sarma gnsa...@gmail.com Date: Sun, 03 Apr 2005 18:13:49 -0700 To: pymol-users@lists.sourceforge.net Hello PYMOLers, I am a very new entry to the world of Pymol after seeing the program in action

[PyMOL] Surface/mesh coordinates

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

[PyMOL] surface inner color

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

Re: [PyMOL] surface/grid questions

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

[PyMOL] surface/grid questions

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

[PyMOL] 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,

RE: [PyMOL] Surface triangulation of isopotential surfaces

] 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? The isosurface triangulation near the protein

[PyMOL] Surface coloring with ChemPy bricks?

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 ... examples/devel/brick01.py ... brik.setup_from_min_max( [0.0,0.0,0.0], [5.0,5.0,5.0], [0.5,0.5,0.5]) ...

RE: [PyMOL] surface area calculation

: 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.net Subject: [PyMOL] surface area calculation Is it possible to get pymol to calculate surface area

RE: [PyMOL] surface area calculation

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

[PyMOL] surface settings?

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.

RE: [PyMOL] surface

...@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

[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 surface? Thanks in advance, Dennis

[PyMOL] surface charge?

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

RE: [PyMOL] surface charge?

...@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 make the figures in a paper I am

[PyMOL] surface of protein

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.