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

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

[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

oday'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 morphing > Mes

[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

[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

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

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

[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

logical threads. > Although, during PyMOL ray tracing CPU usage maxes-out at 32 treads. > > I have even tried setting max_treads to 72, but PyMOL refuses to use any > more than 32 threads. > > Why this limitation? and is the a way to overcome it? > > Thanks > > Jesper &g

[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 trying

[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

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,

[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

[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

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

Hi, Did you try with this recipe http://www.pymolwiki.org/index.php/Huge_surfaces? 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 trying

[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

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 h.adam.steinb...@gmail.com wrote: The

[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 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,

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

Paulo - Brazil - Mensagem original - De: Thomas Holder thomas.hol...@schrodinger.com Para: Ricardo O. S. Soares rsoa...@fcfrp.usp.br Cc: pymol-users pymol-users@lists.sourceforge.net Enviadas: Terça-feira, 14 de Janeiro de 2014 18:18:37 Assunto: Re: [PyMOL] Ray tracing with no GUI

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

:37 Assunto: 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

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

thomas.hol...@schrodinger.com Para: Ricardo O. S. Soares rsoa...@fcfrp.usp.br Cc: pymol-users pymol-users@lists.sourceforge.net 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

[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

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

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. I

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,

[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

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.

[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 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

[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

Re: [PyMOL] ray - volume

Hi Lina, set ray_volume, on Cheers, -- Jason On Tue, Nov 29, 2011 at 10:27 AM, lina lina.lastn...@gmail.com 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

Re: [PyMOL] ray - volume

On Tue, Nov 29, 2011 at 11:34 PM, Jason Vertrees jason.vertr...@schrodinger.com 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,

Re: [PyMOL] ray - volume

On Tue, Nov 29, 2011 at 11:56 PM, David Hall li...@cowsandmilk.net 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.

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 li...@cowsandmilk.net wrote: Since I happen to be playing with volumes right now, I tried that and it causes my

Re: [PyMOL] ray - volume

On Wed, Nov 30, 2011 at 12:25 AM, Jason Vertrees jason.vertr...@schrodinger.com 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

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 problems

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

[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

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

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 Jason.

[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

[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?

[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

Re: [PyMOL] Ray Trace Triangles

Hi Sean, On Fri, 09 Jul 2010 11:05:09 -0400 Sean Law magic...@hotmail.com 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:

[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#174; Parallel Studio Eval Try the new

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 rdirect...@gmail.com 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.

Re: [PyMOL] Ray Tracing A Protein Gallery

: 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, I used several of the techniques suggested, and everything worked out really

Re: [PyMOL] Ray Tracing A Protein Gallery

: 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 same scale

Re: [PyMOL] Ray Tracing A Protein Gallery

# and save save struct001.png Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Monday, December 15, 2008 11:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ray

[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

[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 need

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 movies? I am trying

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

[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

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 rbax...@alumni.uchicago.edu wrote: Dear All, I used the following commands to generate 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 ccp4

[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-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

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 I

[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, png

-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] Ray, png Hi, On the subject of larger

[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 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

[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

[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

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

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

[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

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) 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

RE: [PyMOL] ray command

[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 ray command, is there a way to automatically set either the x or y value

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

Michael, * Michael Banck mba...@gmx.net [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)

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

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

-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 downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine

[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 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 by

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

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 architecture

RE: [PyMOL] Ray Tracing Crash

(650)-593-4020 -Original Message- From: Morri Feldman [mailto:morrifeld...@yahoo.com] Sent: Tuesday, January 20, 2004 10:36 PM To: Warren L. DeLano; 'Matt Franklin'; 'Morri Feldman' Cc: 'pymol-users' Subject: RE: [PyMOL] Ray Tracing Crash Warren and Matt, Thanks so much

Re: [PyMOL] Ray Tracing Crash

On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote: My debian/testing system at home also has trouble ray tracing, especially with sticks. When it fails I get a segmentation fault. What architecture are you running on? i386 or something else? Do you use pymol's internal

[PyMOL] Ray Tracing Crash

I am running pymol .93. When I try to ray trace a scene, the gui shows a white status bar that moves halfway across the screen and then freezes. After this the GUI is frozen and must be killed. No error messages are shown. The computer is running RedHat 9 and has 4 processors. Has anyone else

Re: [PyMOL] Ray Tracing Crash

Morri Feldman wrote: I am running pymol .93. When I try to ray trace a scene, the gui shows a white status bar that moves halfway across the screen and then freezes. After this the GUI is frozen and must be killed. No error messages are shown. The computer is running RedHat 9 and has 4

RE: [PyMOL] Ray Tracing Crash

, 2004 6:25 PM To: Morri Feldman Cc: pymol-users Subject: Re: [PyMOL] Ray Tracing Crash Morri Feldman wrote: I am running pymol .93. When I try to ray trace a scene, the gui shows a white status bar that moves halfway across the screen and then freezes. After this the GUI is frozen

[PyMOL] Ray tracing dashed lines

Hello Pymolers, I'm using pymol 0.92. I changes some of the dash parameters - I want the distance lines to look continuous. This works fine, until I ray trace the protein. Then the dash returns to it's default settings... Any suggestions? thanks, Einat. Einat Sitbon Department of Molecular

Re: [PyMOL] Ray trace is freezing...

the command 'ray' initiates the raytracing which is not GPU-dependent, i.e. your gfx drivers won't increase your raytrace time, only upgrading your main CPU will. But it shouldn't freeze. Does it crash? Have you tried ray'ing a simple scene, i.e. just a few residue, stick representation,

[PyMOL] Ray trace is freezing...

Dear everybody, I'm using the last version of PyMOL, which is very fast (!), but I encountered a problem with ray. I found a driver for my video card which makes programs like O a lot faster, and it also makes PyMOL faster in all the *preparation* process. But as soon as I want to ray my

[PyMOL] ray trace stereo

When I ray trace with the internal renderer (default renderer), my rendered image is not kept in stereo, but instead snaps back to mono. How do I get stereo ray traced images. Also, is there a way to increase the number of passes for the anti-alias smoothing function--it seems a little low

[PyMOL] ray tracer disconnects c-terminal residue

greetings pymol universe: why does my C alpha trace lose connectivity between the c-terminal residues upon ray tracing? i can see the connection fine until i ray trace it. after raytracing i only see the c-terminal alpha carbon atom not connected to the previous alpha carbon. thanks! =

[PyMOL] ray-tracing clip's off C-terminus

I am making C-alpha ribbon traces with two different sets of coordinates. Each time, when I type ray to render, the resulting image has the C-terminal C-alpha clipped off. The missing carbon is visible in the non-ray traced image, however. Please send suggestions to fix this asap.

[PyMOL] ray and stereo

Hi all, I'm trying to have stereo image of ray traced objects but am running into a problem: If I display stereo first (cross-eye) and than ray, it renders only one (mono) image. If I render first and then try to stereo-on, it reverts back to unrendered image. ?? Thanks, n. Ruslan Sanishvili

[PyMOL] ray tracing of stereo figures

Dear All : I tried to ray trace the cross-eyed stereo figure. On the screen, I saw the nice stereo figure. However, when I opened the .png file using Adobe Illustrator after ray tracing and saving the file in PyMol, I don't see the stereo figure but only one image. Did I do something wrong?

RE: [PyMOL] ray tracing and cross-eyed stereo

, 2002 18:04 To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] ray tracing and cross-eyed stereo Pymolers, I am trying to make an image (png file) in cross-eyed stereo, but it seems that I cannot make the stereo image and ray trace. Does anyone know either how to do this or how

RE: [PyMOL] ray doubts

Ricardo, Yes, ray makes a huge difference in quality. You get true specular reflections (not just OpenGL interpolations), you get perfectly round spheres, you get shadows, you get clean transparent surfaces (without artifacts), and you get better depth-cue fogging (although with light