Re: [PyMOL] Saving high resolution images
Hi Thomas, You can also zoom out to get everything in view. You can also change the field of view. And then you can ray just the way you want, based on what you have in sight, in as high a resolution you want. Cheers, Tsjerk On Thu, Oct 22, 2009 at 9:35 PM, Thomas Stout wrote: > > But isn't it true that only the objects that are visible in the viewport are > what are written to the rendered image file? I was proposing rendering a > poster-sized image in "tiles" and stitching them back together post facto to > create a very large, high resolution image. > > something like: > --- > | | | > | | | > | render 1 | render 2 | > | | | > | | | > |-- > | | | > | | | > | render 3 | render 4 | > | | | > | | | > --- > > I feel like I'm missing something important here! > -Tom > > -Original Message- > From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] > Sent: Thursday, October 22, 2009 11:45 AM > To: Thomas Stout > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Saving high resolution images > > Hi Thomas, > > The viewport is not important for rendering. You can render at whatever > resolution/dimensions you want with whatever viewport. You can even make a > panorama using a wide angle lens if you want to have something for on your > wall ;) > > Cheers, > > Tsjerk > > On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout wrote: >> >> >> Here's a crazy idea: if someone out there were clever at both python >> and manipulating orientation matrices, I would bet that a "scene" >> could be quartered or cut into eighths and "translated" such that each >> portion filled the viewport for rendering; then the individual images >> could be spliced back together in one's favorite image handling >> program a la panoramas in photography Is this way too complex to >> be bothered with? I suspect parallax may be a problem... >> >> -Tom >> >> >> >> -Original Message- >> From: Eva Vanamee [mailto:eva.vana...@mssm.edu] >> Sent: Monday, October 19, 2009 1:51 PM >> To: pymol-users@lists.sourceforge.net >> Subject: [PyMOL] Saving high resolution images >> >> Hi, >> >> I'd like to save an image in high resolution for a poster. >> The requested size is 20" by 30". I calculated that it would >> correspond to a 6000 x 9000 pixel image. >> How can I create such a large ray traced image without crashing the >> computer? >> Many thanks in advance for the help. >> >> Best, >> >> - Eva >> >> >> -- >> -- >> -- >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart >> your developing skills, take BlackBerry mobile applications to market >> and stay ahead of the curve. Join us from November 9 - 12, 2009. >> Register now! >> http://p.sf.net/sfu/devconference >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: >> http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> This email (including any attachments) may contain material that is >> confidential and privileged and is for the sole use of the intended >> recipient. Any review, reliance or distribution by others or >> forwarding without express permission is strictly prohibited. If you >> are not the intended recipient, please contact the sender and delete >> all copies. >> Exelixis, Inc. reserves the right, to the extent and under >> circumstances permitted by applicable law, to retain, monitor and >> intercept e-mail messages to and from its systems. >> >> >> -- >> Come build with us! The BlackBerry(R) Developer Conference in >> SF, CA is the only developer event you need to attend this year. >> Jumpstart your developing skills, take BlackBerry mobile applications >> to market and stay ahead of the curve. Join us from November 9 - 12, >> 2009. Register now! >> http://p.sf.net/sfu/devconference >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: >> http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > This email (including any attachments) may contain material > that is confidential and privileged and is for the sole use of > the intended recipient. Any review, reliance or distribution by > others or forwarding witho
[PyMOL] Upgraded computer, PyMol now unusable :^(
Hi folks, I was using PyMol with no problems about a year ago. I believe that my PyMol version was in the 0.9x series. I was using Ubuntu Linux 6.06 on a Pentium IV machine. Since then I have upgraded to a new multi-core motherboard, and Ubuntu Linux 8.04. The Linux repository has a PyMol v1.0 package, so I downloaded that first. It installed with no apparent errors. Running it, though, is another matter. The command window appears, but the molecule display frame appears for just an instant, and then vanishes. If I load a PDB file, again the molecule display frame will appear -- and then disappear again. I uninstalled PyMol v 1.0 and installed PyMol v 1.1 directly from the PyMol web site. This made no difference to the program's behavior. When I run PyMol from the terminal, here's what appears in the terminal window: - ...$ pymol PyMOL(TM) Evaluation Product - Copyright (C) 2008 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Executable Build beyond a finite evaluation period. Please visit http://www.pymol.org/funding.html for more information and contact sa...@delsci.com when you are ready to purchase a Subscription. This Executable Build integrates and extends Open-Source PyMOL 1.1eval. OpenGL graphics engine: GL_VENDOR: ATI Technologies Inc. GL_RENDERER: ATI Radeon HD 3200 Graphics GL_VERSION: 2.1.7412 Release Detected 3 CPU cores. Enabled multithreaded rendering. - Most of the same text appears in the text frame of the PyMol command window, except for the four lines concerning OpenGL. As you can see, no errors have been reported. What could possibly be wrong??? Thanks for any suggestions! -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] [Solved] Upgraded computer, Pymol usable again. :^)
Hello again, With some hints from Ubuntu Forums, I tracked down and corrected my problem. Hopefully this will be of help to someone else. The fancy new desktop rendering schemes which are part of Ubuntu v.8, but which were not part of Ubuntu v.6, use 3D graphics to grow, shrink, and move windows and icons. Apparently, this conflicts with the way that PyMol wants to talk to OpenGL. The solution is to tell the desktop to behave simply. From the Ubuntu main menu, select System > Preferences > Appearance > Visual Effects. Change the setting from Normal to None. Then PyMol works as expected! -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Upgraded computer, PyMol now unusable :^(
John, We have seen such problems with OpenGL-based applications, including PyMOL, running under ATI Radeon hardware & graphics with older versions of the OpenGL-based Compiz window manager. The easiest solution is to reconfigure Linux to disable compositing and/or use a conventional window manager. It might also be possible to upgrade the Window manager and OpenGL driver to recent versions, which may or may not still exhibit the same problems. Cheers, Warren From: John Ladasky [mailto:blind.watchma...@yahoo.com] Sent: Fri 10/23/2009 5:03 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Upgraded computer, PyMol now unusable :^( Hi folks, I was using PyMol with no problems about a year ago. I believe that my PyMol version was in the 0.9x series. I was using Ubuntu Linux 6.06 on a Pentium IV machine. Since then I have upgraded to a new multi-core motherboard, and Ubuntu Linux 8.04. The Linux repository has a PyMol v1.0 package, so I downloaded that first. It installed with no apparent errors. Running it, though, is another matter. The command window appears, but the molecule display frame appears for just an instant, and then vanishes. If I load a PDB file, again the molecule display frame will appear -- and then disappear again. I uninstalled PyMol v 1.0 and installed PyMol v 1.1 directly from the PyMol web site. This made no difference to the program's behavior. When I run PyMol from the terminal, here's what appears in the terminal window: - ...$ pymol PyMOL(TM) Evaluation Product - Copyright (C) 2008 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Executable Build beyond a finite evaluation period. Please visit http://www.pymol.org/funding.html for more information and contact sa...@delsci.com when you are ready to purchase a Subscription. This Executable Build integrates and extends Open-Source PyMOL 1.1eval. OpenGL graphics engine: GL_VENDOR: ATI Technologies Inc. GL_RENDERER: ATI Radeon HD 3200 Graphics GL_VERSION: 2.1.7412 Release Detected 3 CPU cores. Enabled multithreaded rendering. - Most of the same text appears in the text frame of the PyMol command window, except for the four lines concerning OpenGL. As you can see, no errors have been reported. What could possibly be wrong??? Thanks for any suggestions! -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] [Solved] Upgraded computer, Pymol usable again. :^)
Hi John, I have a similar problem with my ubuntu 8.10. When I use a command window, I get the error message: Traceback (most recent call last): File "/var/lib/python-support/python2.5/pymol//__init__.py", line 167, in import pymol File "/var/lib/python-support/python2.5/pymol/__init__.py", line 412, in from pymol import _cmd ImportError: /var/lib/python-support/python2.5/pymol/_cmd.so: undefined symbol: PyUnicodeUCS4_SetDefaultEncoding I have installed another PyMol in a different place. When I give a full path to that PyMol, I get it open for a split second a dissapear with a message PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation period. Please visit http://www.pymol.org/funding.html for more information. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc1. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: GeForce 9800 GTX+/PCI/SSE2 GL_VERSION: 2.1.2 NVIDIA 177.82 Segmentation fault I can open PyMol only from the applications/education menu. I checked the Visual Effects, they are none. Maia John Ladasky wrote: > > Hello again, > > With some hints from Ubuntu Forums, I tracked down and corrected my > problem. Hopefully this will be of help to someone else. > > The fancy new desktop rendering schemes which are part of Ubuntu v.8, > but which were not part of Ubuntu v.6, use 3D graphics to grow, > shrink, and move windows and icons. Apparently, this conflicts with > the way that PyMol wants to talk to OpenGL. > > The solution is to tell the desktop to behave simply. From the Ubuntu > main menu, select System > Preferences > Appearance > Visual Effects. > Change the setting from Normal to None. > > Then PyMol works as expected! > > > > > -- > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Export trajectory
Andrea, I use MD quite a lot myself and we have some "in-house" tools that perform this function (converting a set of PDB files into a trajectory). However, I took it upon myself as a challenge to see if I could implement this into PyMOL as a Python script. Thus, last night I worked feverishly and created a script (now posted on the PyMOL-Wiki) called "save2traj". Do the following: 1) Save the script from the PyMOL-Wiki page 2) Load a PDB structure (let's assume that this pdb file is called "struct.pdb") 3) Load other states into this same PDB object (let's assume this object is called "struct") 4) Then, to save the states as a trajectory, use the following command: run save2traj save2traj struct, trajectory The syntax for the command is save2traj selection, name The "name" denotes the output file and will automatically have ".dcd" appended to it. In the future, there will be additional support for other file formats but that may be in the distant future. As well, please be aware that due to PyMOL's RESID renumbering that the trajectory being produced will be numbered differently than your original PDB. There are two ways around this, 1) Save a corresponding PDB file for that trajectory that is renumbered by PyMOL or 2) Retain the RESID (see PyMOL-Wiki) Since this was done on a whim, please use at your own risk until it is further developed. Hope this helps! Sean Law Michigan State University _ Lots of fantastic Windows 7 offers, in one convenient place. Get the perfect deal for you now. http://go.microsoft.com/?linkid=9691633-- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Replace Coordinates in State
Hi All, I was wondering if there was a faster way to replace all coordinates. I've used commands such as iterate_state and alter_state before but they are far too slow since they have to iterate over each atom. Instead, I want to replace one set of coordinates that correspond to a specific state with a different set. Here's what I have to work with: I have a list that contains x, y, z coordinates. Of course, this list can be manipulated and/or separated if necessary. I'm assuming that the coordinates for a specific state are stored somewhere in memory and I would basically like to replace one set of coordinates with the other. I would think that something like "pointers or references" would work a lot faster than having to copy the coordinates over (which is typically slow and is likely what alter_state is doing?). In addition, I am dealing with 100+ states using alter_state for each state would be far too slow. Any suggestions would be greatly appreciated. Thanks in advance! Sean _ CDN College or University student? Get Windows 7 for only $39.99 before Jan 3! Buy it now! http://go.microsoft.com/?linkid=9691636-- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL-users Digest, Vol 41, Issue 8
Tsjerk, I think you are missing the point of Tom's post, which was a suggestion to aid someone who's computer could NOT deliver the image in "as high a rsolution as you want', so Tom was proposing a way to break the image down into bite-size chunks that the computer COULD then handle. So the suggestion was to take one scene desired at 9000x6000 which would make the computer crash and instead mathematically figure the necessary transpositions to render it in tiles such as upper left quadrant, upper right, etc. each at 4500x3000 or whatever the computer could handle (and then you could put them all back together in photoshop, e.g.). So for someone with deep coding skills they could likely teach pymol to ray just the segments they wanted and deal with the overall perspective of the whole scene, but for a hack like myself I'd likely start the work around of trying to figure out the camera position and where I'd have to put it to get just a quarter of the scene at a time in the viewport (or an eighth, or whatever). As Warren said, you'd likely have to set orthoscopic to get rid of the perspective for starters (at least in the hack approach, but there would be more direct better ways for the skilled). As a side point, Povray (if I remember correctly) in fact allows you to break a large rendering job up into tiles pretty much just like Tom suggests, so not so crazy of an idea! I think in that case you can specify starting and ending x,y pixel coordinates from your large scene. But not in Pymol as far as I know. Sorry if I've now gone stepping in and misinterpreting someone's points myself, but it seemed like there was a lot of cross-purpose talk either from assumptions or extra politeness! -Seth > > The requested size is 20" by 30". I calculated that it would > > correspond > > to a 6000 x 9000 pixel image. > > How can I create such a large ray traced image without crashing the > > computer? > > > Message: 2 > Date: Fri, 23 Oct 2009 11:27:47 +0200 > From: Tsjerk Wassenaar > Subject: Re: [PyMOL] Saving high resolution images > To: Thomas Stout > Cc: pymol-users@lists.sourceforge.net > Message-ID: ><8ff898150910230227k12719cedv8656233c7e67d...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Thomas, > > You can also zoom out to get everything in view. You can also change > the field of view. And then you can ray just the way you want, based > on what you have in sight, in as high a resolution you want. > > Cheers, > > Tsjerk > > On Thu, Oct 22, 2009 at 9:35 PM, Thomas Stout wrote: > > > > But isn't it true that only the objects that are visible in the viewport > are what are written to the rendered image file? ?I was proposing rendering > a poster-sized image in "tiles" and stitching them back together post facto > to create a very large, high resolution image. > > > > something like: > > --- > > | ? ? ? ? ?| ? ? ? ? ?| > > | ? ? ? ? ?| ? ? ? ? ?| > > | render 1 | render 2 | > > | ? ? ? ? ?| ? ? ? ? ?| > > | ? ? ? ? ?| ? ? ? ? ?| > > |-- > > | ? ? ? ? ?| ? ? ? ? ?| > > | ? ? ? ? ?| ? ? ? ? ?| > > | render 3 | render 4 | > > | ? ? ? ? ?| ? ? ? ? ?| > > | ? ? ? ? ?| ? ? ? ? ?| > > --- > > > > I feel like I'm missing something important here! > > -Tom > > > > -Original Message- > > From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] > > Sent: Thursday, October 22, 2009 11:45 AM > > To: Thomas Stout > > Cc: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] Saving high resolution images > > > > Hi Thomas, > > > > The viewport is not important for rendering. You can render at whatever > resolution/dimensions you want with whatever viewport. You can even make a > panorama using a wide angle lens if you want to have something for on your > wall ;) > > > > Cheers, > > > > Tsjerk > > > > On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout > wrote: > >> > >> > >> Here's a crazy idea: ?if someone out there were clever at both python > >> and manipulating orientation matrices, I would bet that a "scene" > >> could be quartered or cut into eighths and "translated" such that each > >> portion filled the viewport for rendering; then the individual images > >> could be spliced back together in one's favorite image handling > >> program a la panoramas in photography ?Is this way too complex to > >> be bothered with? ?I suspect parallax may be a problem... > >> > >> -Tom > >> > >> > >> > >> -Original Message- > >> From: Eva Vanamee [mailto:eva.vana...@mssm.edu] > >> Sent: Monday, October 19, 2009 1:51 PM > >> To: pymol-users@lists.sourceforge.net > >> Subject: [PyMOL] Saving high resolution images > >> > >> Hi, > >> > >> I'd like to save an image in high resolution for a poster. > >> The requested size is 20" by 30". I calculated that it would > >> correspond to a 6000 x 9000 pixel image. > >> How can I create such a large ray traced image without crashing the > >> computer? > >> Many thanks in advance for the help.
