Re: [PyMOL] Ray tracing transparent sticks

Hello, Which version are you using? We had this regression in 2.3.0 but was fixed in the 2.3.2 patch update. On Thu, Jan 30, 2020 at 9:34 AM Ioannis Riziotis wrote: > Hello! > > I have been trying to ray trace stick representations with transparency > (i.e. stick_transparency = 0.5). Although s

[PyMOL] Ray tracing transparent sticks

Hello! I have been trying to ray trace stick representations with transparency (i.e. stick_transparency = 0.5). Although surface transparency is visible in ray tracing, transparent sticks always appear opaque in the rendered image. Is there a way to resolve this? Note that in OpenGL, stick tra

Re: [PyMOL] Re. Pymol Ray problem

Hi Changdev -  Try the following command, which will save a ray-traced PNG image with transparent background (which is what is represented by the checkerboard pattern):     png myfigure.png, ray=1 Alternatively, you can adjust the ray background setting:     set ray_opaque_background, 1 Hope

[PyMOL] Re. Pymol Ray problem

Hello there, When I do ray, it shows brown and white square in the background. I want to capture image directly from screen but squares also get copied. Is there any way to remove these squares and capture image directly from the screen. Regards, Changdev _

Re: [PyMOL] Ray tracing after morphing

t; > Today's Topics: > > 1. Ray tracing after morphing (Pascal Egea) > > > -- > > Message: 1 > Date: Sun, 21 Apr 2019 08:58:52 -0700 > From: Pascal Egea > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Ray tracing after morp

[PyMOL] Ray tracing after morphing

Dear All, I have been making a morph in pymol and saved the different states using the mpng command in the active window. However, I cannot figure out how to get ray-traced images to make a high quality movie in quicktime, right now it is quite pixelated. Is there a way to ray0trace each state of

Re: [PyMOL] ray 2400 (NOT ray_trace) each frame of a movie

Hi AC, In PyMOL 1.8.6 we added width and height arguments to the mpng command. So this is now possible: set ray_trace_frames mpng imageprefix, width=2400 With older PyMOL versions, you have two options: 1) Run PyMOL headless (pymol -c script.pml) so that the display doesn't limit the view

[PyMOL] ray 2400 (NOT ray_trace) each frame of a movie

So far there is only info about how to "ray_trace" each frame of a movie while exporting to .png images. My question: How can I "ray 2400" each image (regardless of my computer screen size - because I have a small computer) so i can get very high resolution images that i can combine together

Re: [PyMOL] ray command

Hi Mohsen, So raytracing is indeed not available in the educational version. I find this a bit strange, as I regarded the educational version the least-changed-with-respect-to-the-original (say 0.99), which did have raytracing available. Also, I like students to give me reports with pretty picture

Re: [PyMOL] ray command

Hi Mohsen, What happens? What error do you get? Best, Tsjerk On Jul 12, 2016 10:46 AM, "Mohsen Chitsaz" wrote: Hi Pymol users, The “ray command” is not working in my Educational version of Pymol. It seems that educational version does not allow to use this command. Does anyone have a sol

[PyMOL] ray command

Hi Pymol users, The "ray command" is not working in my Educational version of Pymol. It seems that educational version does not allow to use this command. Does anyone have a solution for this please? Your reply is very much appreciated. Cheers Mohsen ---

Re: [PyMOL] Ray tracing max_threads

Karlsen wrote: > Hi, > > I am doing some heavy duty ray tracing in PyMOL. > > I realize spreading the job over multiple nodes in a PBS requires MPI > integration in PyMOL, but this is run on a single machine with 36 > physical CPU cores and 72 logical threads. > Al

[PyMOL] Ray tracing max_threads

Hi, I am doing some heavy duty ray tracing in PyMOL. I realize spreading the job over multiple nodes in a PBS requires MPI integration in PyMOL, but this is run on a single machine with 36 physical CPU cores and 72 logical threads. Although, during PyMOL ray tracing CPU usage maxes-out at 32

Re: [PyMOL] Ray tracing on PBS queue with multiple cores?

over multiple CPUs when these are located on different boxes. HTH Carsten From: Dan Lin [mailto:dh...@caltech.edu] Sent: Monday, August 31, 2015 8:29 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ray tracing on PBS queue with multiple cores? Hello all: I'm tryi

[PyMOL] Ray tracing on PBS queue with multiple cores?

Hello all: I'm trying to ray trace some large movies and I have access to a cluster that uses PBS queues. However, I am having difficulty getting pymol to render with more than 1 CPU. Has anybody encountered this problem and found a solution? Thanks in advance! -Dan -

[PyMOL] Ray Trace Modes - selectively trace mesh objects

Hi Pymol-Users list, I'm trying to ray-trace images using ray_trace_mode = 1 (solid surfaces, with black lines at the borders of elements). I would like to have this tracing on elements of the image except for meshes, which get really ugly because they shouldn't have a border. Is there any way t

Re: [PyMOL] PyMOL ray tracing errors

Hi Brenton, regarding "SVN download doesn't color by secondary structure": If you want to use the SVN version, then please always have a look at the top of the ChangeLog, or follow SVN commit messages. In the latest commit I changed the default of the "ignore_case" setting to "off". This mean t

Re: [PyMOL] PyMOL ray tracing errors

Hi Brenton The script seems to work for me A couple of questions: - Why aren’t you installing PyMOL from the repository? sudo apt-get install pymol - Are you sure that the name of the pdb file is correct? (remember that names are case sensitive) Cheers, Osvaldo On Fri, Jun

[PyMOL] PyMOL ray tracing errors

Hi, I installed PyMOL on 32 bit Ubuntu 15.04 by following the Linux install guide on PyMOL Wiki. Although I ended up redoing it using the tarball available at Source Forge instead of the directory downloaded via Subversion (SVN) as SVN downloads an unstable release 1.7.7.1 which I found was u

Re: [PyMOL] Ray Trace of Icosahedral Viral Capsids using NVIDIA GE Force

Hi, Did you try with this recipe ? Did you try doing the ray-traicing from a script (and not using the GUI)? Cheers, Osvaldo. On Tue, Apr 28, 2015 at 11:46 AM, Rallapalli, Pavithra < pavithra.rallapalli...@ucl.ac.uk> wrote: Hi all > > > > I am

[PyMOL] Ray Trace of Icosahedral Viral Capsids using NVIDIA GE Force

Hi all I am trying to ray trace my icosahedram viral capsid, a 75 MB .pse file. I am running this on a 16 GB windows 64 bit machine with 2 GB NVIDEA GEFORCE graphics. But the memory still seems to be low as for some reason PyMOL's virtual memory is still low. I have tried set hash_max but does

[PyMOL] ray trace mode

Hi pymol users How can I trace my model (like when using set ray_trace_mode, 1), without tracing the mesh around it? Thanks! Donna -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Int

Re: [PyMOL] ray trace mode 1 playing up pymol 1.7.4?

Hi, This may also be related to the setting: ray_trace_mode Try: set ray_trace_mode, 0 This will deactivate outlines (ray_trace_color) during ray tracing. The wiki page has some examples. Cheers, Andreas On Dec 16, 2014 6:05 PM, "H. Adam Steinberg" wrote: > The thickness, or weight of the bl

Re: [PyMOL] ray trace mode 1 playing up pymol 1.7.4?

The thickness, or weight of the black outline is related to the size of the viewport or the ray command. If you ray the image larger, the thickness of the black outline will be greatly reduced. This will improve the clarity of colored sphere surface by reducing the amount of black in those area

Re: [PyMOL] Ray trace mode 1 outline thickness

Hi Martin - Try increasing the `ray_trace_gain` setting. Default value is 0.12, so maybe try 1 or 2. If you go much higher, you’ll start to see additional lines or spots. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 14, 20

[PyMOL] Ray trace mode 1 outline thickness

Hi guys I wonder if you could help, I'm rendering this image: http://qmviews.blogspot.ch/2014/05/illustrating-protein-structures.html and I wonder if and how I could increase the thickness of the black outlines? Thanks for help Martin --

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

Thomas Holder" > Para: "Ricardo O. S. Soares" > Cc: "pymol-users" > Enviadas: Quarta-feira, 15 de Janeiro de 2014 17:32:00 > Assunto: Re: [PyMOL] Ray tracing with no GUI yields segmentation > fault > Hi Ricardo, > you didn't mention that you laun

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

ne gives segmentation fault > pymol.cmd.png("image.png", 640, 640, 300,1) -> this wont work without > loaded GUI > > pymol.cmd.quit() > > Cheers, > > Ricardo. > > --- > Biological Chemistry and Physics > Faculty of Pharmaceutical Sciences at Ribeir

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

istry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil - Mensagem original - > De: "Thomas Holder" > Para: "Ricardo O. S. Soares" > Cc: "pymol-users" > Enviadas: Terça-feira, 14 de Janeiro de 20

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

Hi Ricardo, you probably want to do this, without calling the ray command: cmd.png("image.png", 640, 640, dpi=300, ray=1) Also, your ray command sets antialias=300 and angle=-1, which I guess was not your intention. I'm not getting a segmentation fault with the latest SVN code using your comma

[PyMOL] Ray tracing with no GUI yields segmentation fault

Hello everyone, I wrote a python script where pymol performs some color changes, ray tracing and image export. The script works perfectly if I enable the GUI, however if I load pymol without the GUI (-c flag) I receive a segmentation fault error. I found out that this issue is resolved by com

Re: [PyMOL] ray-tracing cones

Hi Robert, this looks like a bug, none of the closed CGOs is rendered on the inside, even with two_sided_lighting=on. I filed a bug report: https://sourceforge.net/p/pymol/bugs/134/ Cheers, Thomas Bryn Fenwick wrote, On 08/20/13 00:42: > > Hi All, > > I am trying to ray trace an empty cone.

[PyMOL] ray-tracing cones

Hi All, I am trying to ray trace an empty cone. I can find no way to get an image of the inside of the cone. Does anyone have a work around. Example attached. run test.py cone ray when the ray command is issued the cone disappears from view. robert # # test.py # from pymol import cmd from

Re: [PyMOL] Ray-trace of volume visualization

Hi Jason Great, it works, but as you say there is not much difference really. And thanks - we're talking about right now how to include this in an upcoming publication. When and if it is published, I can send you an image. Cheers /Per 2 nov 2012 kl. 22:50 skrev Jason Vertrees: > Hi Per, > >

Re: [PyMOL] Ray-trace of volume visualization

Hi Per, set ray_volume, 1 We disabled this feature because it wasn't of high enough quality to be used. Once we fix this, we'll change PyMOL to automatically ray trace the volumes. Until then, you can try the trick I noted above. If you feel like sharing I'd love to see what you came up with. C

[PyMOL] Ray-trace of volume visualization

Hi! Following up on my earlier post http://sourceforge.net/mailarchive/message.php?msg_id=30017929, I have managed to make some very nice volume visualizations in Pymol. I now wonder about the possibilities of ray-tracing the volume? I should add that I'm not a graphics guru, so maybe this doe

Re: [PyMOL] Ray tracing transparent Isopotential surfaces

Hi Warren, What commands did you use? I just tested the following on PyMOL v1.5.0.4 and everything worked as advertised: fetch 1rx1, async=0 fetch 1rx1, type=2fofc, async=0 isosurface mySurf, 1rx1_2fofc, 1.0, (organic) orient organic set transparency, 0.5 ray Can you try the above code and let m

[PyMOL] Ray tracing transparent Isopotential surfaces

Hi, I have generated isopotential surfaces for a protein that completely enclose the basic structure using the APBS plugin. I can increase the transparency so I can visualize an underlying cartoon representation of the structure. However, when I do a ray tracing to get

Re: [PyMOL] ray - volume

Hi David, > Since I happen to be playing with volumes right now, I tried that and > it causes my sticks to pop out of the volumes (see attached).  This is > on a build of the latest open source code in SVN. You have found the reason why this isn't turned on by default. There are still some proble

Re: [PyMOL] ray - volume

On Wed, Nov 30, 2011 at 12:25 AM, Jason Vertrees wrote: > Hi David, > > Are your data and color ramp points correct? If you send me the data, > I can double-check what we've done. I am also confusing how to put the quasi-center of volume on some certain atom. Even I only chose one atom, but the

Re: [PyMOL] ray - volume

Hi David, Are your data and color ramp points correct? If you send me the data, I can double-check what we've done. Cheers, -- Jason On Tue, Nov 29, 2011 at 10:56 AM, David Hall wrote: > Since I happen to be playing with volumes right now, I tried that and > it causes my sticks to pop out of t

Re: [PyMOL] ray - volume

On Tue, Nov 29, 2011 at 11:56 PM, David Hall wrote: > Since I happen to be playing with volumes right now, I tried that and > it causes my sticks to pop out of the volumes (see attached).  This is > on a build of the latest open source code in SVN. Thanks for confirmation. There are some unmet d

Re: [PyMOL] ray - volume

On Tue, Nov 29, 2011 at 11:34 PM, Jason Vertrees wrote: > Hi Lina, > > set ray_volume, on Thanks, is the ray_volume some new feature in latest version? seems Version 1.4. no ray_volume feature. Best regards, > > Cheers, > > -- Jason > > On Tue, Nov 29, 2011 at 10:27 AM, lina wrote: >> Hi, >> >

Re: [PyMOL] ray - volume

Hi Lina, set ray_volume, on Cheers, -- Jason On Tue, Nov 29, 2011 at 10:27 AM, lina wrote: > Hi, > > a quick question, how to keep the volume during ray. > > the volume is here, > > but after ray, > > it's gone, > > what's kinda of special settings I need to take care? > > Thanks with best reg

[PyMOL] ray - volume

Hi, a quick question, how to keep the volume during ray. the volume is here, but after ray, it's gone, what's kinda of special settings I need to take care? Thanks with best regards, -- All the data continuously gene

Re: [PyMOL] Ray Trace Mode 1 and Labels

Hi Jack, you could render the labels to a separate image and assemble both images using Photoshop, Gimp, etc. set ray_trace_mode, 1 hide labels png image1.png, ray=1 set ray_trace_mode, 0 as labels set label_font_id, 7 set label_size, 20 set label_color, black set label_outline_color, white png

Re: [PyMOL] Ray Trace Mode 1 and Labels

Hi Jack, Unfortunately, that is not possible. The ray-trace mode affects the behaviour/display of edges during raytracing, It's basically doing edge detection, similar to what can be done in image processing afterwards. So, it's similar to having an image and wanting to enhance edges on some, but

[PyMOL] Ray Trace Mode 1 and Labels

Is there a way to stop ray_trace_mode 1 putting an outline on labels? Although the outline looks quite good for the graphics, especially once they are printed, it makes the text look like blocky typewriter font. Any advice appreciated. Thanks --

Re: [PyMOL] Ray tracing - distinction between inside and outside of binding pocket

On 23/8/2011, at 11:02 a.m., Jason Vertrees wrote: > Hi Ben, > > This isn't yet available. PyMOL only support inside and outside color > on surface objects (surfaces from maps), not surface representations > (what we typically consider a surface). > > I'll let you know if this changes. Thanks

Re: [PyMOL] Ray tracing - distinction between inside and outside of binding pocket

Hi Ben, This isn't yet available. PyMOL only support inside and outside color on surface objects (surfaces from maps), not surface representations (what we typically consider a surface). I'll let you know if this changes. Cheers, -- Jason On Mon, Aug 22, 2011 at 5:57 PM, Ben Roberts wrote: >

[PyMOL] Ray tracing - distinction between inside and outside of binding pocket

Hi, Having prepared and superimposed the binding pockets that I spoke of in my earlier email, I'm now trying to come up with a way of producing high resolution images of them. The problem I'm now facing is that I can't seem to come up with a high-res rendering that clearly distinguishes betwee

[PyMOL] Ray tracing problems

When I ray trace a surface, the colors on the surface appear to have a smaller color depth. In other words, there are finite boundaries between different shades of colors rather than a smooth gradient. Could the problem be color-dependent? Has anyone seen this? Any ideas how to fix it? Mark

Re: [PyMOL] Ray Trace Triangles

Hi Sean, On Fri, 09 Jul 2010 11:05:09 -0400 Sean Law wrote: > I have been tackling this problem (on and off) for quite some time now but > without any luck. I have been trying to create CGO triangles using the > following simple sample script: > > > ### > > fr

[PyMOL] Ray Trace Triangles

Hi PyMOLers, I have been tackling this problem (on and off) for quite some time now but without any luck. I have been trying to create CGO triangles using the following simple sample script: ### from pymol.cgo import * from math import * from pymol import cmd

Re: [PyMOL] ray with cuda

Quyen, Something like this may appear in alpha-form in a PyMOL 1.x release (this year or early next) and in full in the PyMOL 2.0 release (later). My guess is this will take time to do well. We'd most likely be targeting the more generic openCL over CUDA in particular. As for implementation, ch

Re: [PyMOL] ray with cuda

Dear Jason, Oh I see...In the mean time, do you have any advice as how to accomplish such a thing? What about a forecast of when an official implementation of such thing in pymol framework? Best, Quyen On Fri, Apr 2, 2010 at 4:08 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Qu

Re: [PyMOL] ray with cuda

Quyen, No, not yet. It's something I very excited to get done though. -- Jason On Fri, Apr 2, 2010 at 4:44 PM, QT wrote: > Dear all, > > Is it possible to ray using cuda?  I know VMD has some plugin that allows > cuda integration and was wondering if Pymol has a similar thing. > > Best, > Quye

[PyMOL] ray with cuda

Dear all, Is it possible to ray using cuda? I know VMD has some plugin that allows cuda integration and was wondering if Pymol has a similar thing. Best, Quyen -- Download Intel® Parallel Studio Eval Try the new software

Re: [PyMOL] Ray Tracing A Protein Gallery

Buz Barstow [mailto:b...@mac.com] > Sent: Thursday, December 18, 2008 3:27 PM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Ray Tracing A Protein Gallery > > Dear All, > > Thanks for all your suggestions on ray tracing the protein gallery. > > In the end,

Re: [PyMOL] Ray Tracing A Protein Gallery

.com] Sent: Monday, December 15, 2008 11:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ray Tracing A Protein Gallery Dear All, I'm making a gallery of protein molecules for my PhD thesis. I'd like to find an automatic way to ensure that all of the ray traced images have the

Re: [PyMOL] Ray Tracing A Protein Gallery

rceforge.net > Subject: [PyMOL] Ray Tracing A Protein Gallery > > Dear All, > > I'm making a gallery of protein molecules for my PhD thesis. > I'd like to find an automatic way to ensure that all of the > ray traced images have the same scale. Is there an easy way &g

Re: [PyMOL] Ray Tracing A Protein Gallery

On Mon, Dec 15, 2008 at 11:41 AM, Buz Barstow wrote: > I'm making a gallery of protein molecules for my PhD thesis. I'd like > to find an automatic way to ensure that all of the ray traced images > have the same scale. Is there an easy way to do this? > Translate every model so that the center i

[PyMOL] Ray Tracing A Protein Gallery

Dear All, I'm making a gallery of protein molecules for my PhD thesis. I'd like to find an automatic way to ensure that all of the ray traced images have the same scale. Is there an easy way to do this? Thanks! and all the best, --Buz

Re: [PyMOL] ray and mpng

, Douglas (NIH/NCI) [E] Sent: Thursday, July 24, 2008 9:20 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] ray and mpng Hello Everyone, Can the "ray" command be used to set a higher image quality before issuing the "mpng" command to generate image files for making movie

[PyMOL] ray and mpng

Hello Everyone, Can the "ray" command be used to set a higher image quality before issuing the "mpng" command to generate image files for making movies? I am trying to confirm this for someone else, but as I see it,t the "ray" command is best for a single high quality image and that it would n

Re: [PyMOL] ray-traced stero figurea

Hi Richard, to change wall-eyed stereo figures to cross-eyed, you can simply exchange the left and right images (in wall-eyed, the left picture is for the left eye, the right picture for the right eye, whereas in cross-eyed, the left picture is for the right eye and vice versa). Warren once

Re: [PyMOL] ray-traced stero figurea

Hi Richard, Why not set stereo_mode,3 and raytrace as it is on the screen? You can set stereo_angle and stereo_shift to modify the scene. Cheers, Tsjerk On 03 Apr 2007 10:57:36 -0500, Richard Baxter wrote: Dear All, I used the following commands to generate a nice wall-eye stereo figure (at

[PyMOL] ray-traced stero figurea

Dear All, I used the following commands to generate a nice wall-eye stereo figure (at least it seems to work for me): ray 600,900,-1,-3; png stereo_right.png ray 600,900,-1,3; png stereo_left.png figures are combined in photoshop at 300dpi with an extra 5mm between, so that images are 2 inches a

Re: [PyMOL] ray trace density

Hi, > We are, for the first time, using pymol to make figures that show > electron density in addition to the model. No problem making the > figure, but when we go to ray-trace the image, pymol crashes. This > only seems to happen when electron density is present in the figure. > We are using cc

[PyMOL] ray trace density

Hello everyone, I apologize in advance if this has been asked recently, but I could not find an answer to it on-line anywhere. We are, for the first time, using pymol to make figures that show electron density in addition to the model. No problem making the figure, but when we go to ray-tra

Re: [PyMOL] Ray-tracing inner surface backside

Paul, I'm actually quite interested in an answer to this question as well. An example of what I have been able to do is this: http://kinemage.biochem.duke.edu/~immormino/neca_new.png I like using this type of rendering to look at a protein cavity from inside the protein. For me it has been hel

[PyMOL] Ray-tracing inner surface backside

Hi folks, what I did for now is that I selected a subset of residues that sit around a cavity. Then I showed the surface of the original protein inside the selection to get only the inside surface of the cavity. Now it looks sort of like a hose with inside and outside just as I wanted. Now I'd

Re: [PyMOL] Ray, png

pymol-users-ad...@lists.sourceforge.net wrote on 01/03/2006 05:32:38 PM: > Hi, > On the subject of larger image sizes, I had a question a while back; > I'd like to know if it's been addressed or anyone has a quick(er) workaround- > Basically, is there in inverse to the viewport command? i.e., if

[PyMOL] ray

Here's another question about ray. At what level in pymol is it implemented? Is it part of what's provided by OpenGL, or done at some higher/other level? Terry

RE: [PyMOL] Ray, png

r...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > David A. Horita > Sent: Tuesday, January 03, 2006 2:39 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] R

[PyMOL] Ray, png

Hi, On the subject of larger image sizes, I had a question a while back; I'd like to know if it's been addressed or anyone has a quick(er) workaround- Basically, is there in inverse to the viewport command? i.e., if I manually resize the Pymol window to fit around the molecule I'm displaying, how

Re: [PyMOL] ray tracing problem

Thank you Warren and Jacob, I pressed stop and then ray tracing went fine. I don't know who pressed that play-button, but it wasn't me... ~Lari~ On Friday 02 September 2005 18:41, Lari Lehtio wrote: > Hello, > > I'm in a process of making a whole bunch of figures for a paper and I have > an ir

[PyMOL] ray tracing problem

Hello, I'm in a process of making a whole bunch of figures for a paper and I have an irritating problem. Some of the figures just do _not_ get ray traced. It processes the image, but the image stays normal (=ugly). I'm running 0.98 on an amd64 box with gentoo and I've tried the binary distribu

Re: Subject: [PyMOL] ray-trace stereoview

7;cmd.extend('stereo_ray',stereo_ray)'). You may have to add the line "import os" to the start of the script too. Cheers, Stephen > Subject: Subject: [PyMOL] ray-trace stereoview > From: tree > Reply-To: javer...@utmb.edu > To: PyMol Users List > Organ

Subject: [PyMOL] ray-trace stereoview

-requ...@lists.sourceforge.net wrote: > Message: 5 > Date: Fri, 10 Jun 2005 16:25:33 -0600 > From: migalepa > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] ray-trace stereoview > > Pymol community, > > I'm trying to ray-trace (ray 3000,2250) a stereoview of a molecule but

[PyMOL] ray-trace stereoview

Pymol community, I'm trying to ray-trace (ray 3000,2250) a stereoview of a molecule but the image displayed once I save the rendered figure (trough png) correspond to the normal view of the molecule (no stereoview!?). Pymol seems to do it if the figure is saved trough the GUI, which gives a lo

[PyMOL] ray-trace stereoview

Pymol community, I'm trying to ray-trace (ray 3000,2250) a stereoview of a molecule but the image displayed once I save the rendered figure (trough png) correspond to the normal view of the molecule (no stereoview!?). Pymol seems to do it if the figure is saved trough the GUI, which gives a lo

Re: [PyMOL] ray

Hi Kostas, This topic has been covered several times from a resolution stand point. Joel has a nice hint, but be sure to set your viewport to the right aspect ratio before using the ray command. viewport 700, 700 (other pymol commands to make your figure the way you want) ray 2400, 2400 png myf

Re: [PyMOL] ray

Hi Kostas, I tghink generally 300 dpi is sufficient for publication but you can ray trace to any sort of resolution and then down size your graphic. See posts on High end graphics but this should help *To get 4in by 4in figure @600dpi ray 2400, 2400* * * *Then png picture.png Then resize

[PyMOL] ray

Dear PyMolers I am about to write a paper and I want your suggestions for the pictures I am going to make. First of all I will use white background and the structure is a NMR one. So I need to display the backbone of the ensemble and the rest pictureswill be cartoons and sticks mainly. I want t

Re: [PyMOL] ray-trace stop button?

Mark, You don't have to reboot, go to the process tab of windows task manager and end the python image underlying PyMOl. Jules Mark Wilke wrote: Is there any way of stopping a ray trace once it has been started without closing pymol? Some of my ray trace jobs take too long and I want to sto

[PyMOL] ray-trace stop button?

Is there any way of stopping a ray trace once it has been started without closing pymol? Some of my ray trace jobs take too long and I want to stop them. I've also noticed that pymol doesn't close very elegently during a ray trace job. I'm working on a windows pc and the "end task" approach some

[PyMOL] Ray tracing transparent spheres

Hi, Having difficulty with the sphere_transparency and stick_transparency options in ray-traced figures. When I try to set the transparency to 1 (or close to 1) the object just appears darker in the ray trace (not transparent). The effect I'm trying to achieve is to have things fade in and ou

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

On Thu, Feb 19, 2004 at 12:24:53PM +0100, Michael Banck wrote: > On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: > > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. > > That seems to be identical to Debian Bug #229080 > (http://bugs.debian.org/229080) > >

RE: [PyMOL] ray command

: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > David A. Horita > Sent: Monday, April 05, 2004 11:30 AM > To: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] ray command > > Hi, > Regarding the use of the

RE: [PyMOL] ray command

Hi, Regarding the use of the ray command, is there a way to automatically set either the x or y value to maintain the same aspect ratio as displayed in the window? For that matter, how do you determine the number of x and y points displayed (other than making a bitmap and loading that into anot

RE: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Morri Feldman > Sent: Thursday, February 19, 2004 3:18 PM > To: Michael Banck > Cc: pymol users > Subject: Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2 > > Hi Michael, > > I download

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

Hi Michael, I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine. When I run this copy rather than the .deb version I am able to ray trace lines without a crash. Best, Morri On Thu, 19 Feb 2004, Michael Banck wrote: > On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund w

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

Michael, * Michael Banck [2004-02-19 12:24] wrote: > On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: > > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. > > That seems to be identical to Debian Bug #229080 > (http://bugs.debian.org/229080) > > > The sto

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. That seems to be identical to Debian Bug #229080 (http://bugs.debian.org/229080) > The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I > got

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

Dear Buz, > I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm > having trouble ray tracing graphics. > Each time I start the ray tracer Pymol quits with a segmentation fault > error; I guess you are running into a compiler bug (or a bug in PyMol which gets exposed only

[PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

Hi, I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm having trouble ray tracing graphics. I installed Pymol from the source file pymol-0_93-src.tgz. Each time I start the ray tracer Pymol quits with a segmentation fault error; /usr/local/pymol/pymol.com: line 2: 29720

Re: [PyMOL] Ray Tracing Crash

Package: pymol Version: 0.93-2 On Thu, Jan 22, 2004 at 08:53:37AM -0800, Morri Feldman wrote: > On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote: > > > On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: > > > Regarding my problems raytracing on my debian/testing machine. > > >

Re: [PyMOL] Ray Tracing Crash

On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote: > On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: > > Regarding my problems raytracing on my debian/testing machine. > > What is the exact version of the pymol .deb you're using? 0.93-2? pymol_0.93-2_i386.deb > What architect

Re: [PyMOL] Ray Tracing Crash

On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: > Regarding my problems raytracing on my debian/testing machine. What is the exact version of the pymol .deb you're using? 0.93-2? What architecture are you running on? i386 or something else? Do you use pymol's internal raytracer, or

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