Re: [PyMOL] Question on rotation
Hi Terry, There's a bit more to it. In the pymol view, the camera is located at the origin, so to rotate your coordinates you first have to move the center to the origin, do the rotation and move the thing back. I've scripted this in Povray. If you're interested, I can send you the script. You can then rescript it in python or you can output your scene to povray and do the rest there. In addition (although you may already know this), the meaning of all elements of the result of get_view (python index) is 0:9 - rotation matrix 9:12 - camera position 12:15 - origin of rotation 15:17 - slab near and far 17 - orthoscopic flag Cheers, Tsjerk On 4/25/06, Terry Jones wrote: > > I wrote a pymol plugin that produces a bunch of cgo. The images I generate > have a cube drawn around them. > > I've been asked if it's possible to allow the user to initially rotate the > image to their heart's content and then have the plugin draw the > surrounding cube. I.e., once the image is rotated, the cube will be drawn > in a way that always looks good to the viewer, not at some random angle. > In > other words, the cube will always have the same orientation, no matter how > much the image has been rotated before the cube is drawn. > > OK, having said the same thing 3 times, and hopefully made sense at least > once, I'll say something new... > > I imagine this can be done easily enough. I guess I should be able to call > get_view and get the current rotation matrix (elements 0-8 of the returned > list) and apply this to all points that I plan to draw between when making > the cube. > > My questions: Is this right? Do I need to do anything more than just > multiply the old point by the rotation matrix? What's the easiest way to > do > this in Pymol or Python, or should I just code it (it's very simple after > all). And, of course, is there a better way to do what I want? > > Thanks for any help. Don't assume I know what I'm doing, because I > probably > don't. So the more details, the better. > > Regards, > Terry > > > --- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
Re: [PyMOL] Question on rotation
Hi Tsjerk > "Tsjerk" == Tsjerk Wassenaar writes: Tsjerk> There's a bit more to it. In the pymol view, the camera is located Tsjerk> at the origin, so to rotate your coordinates you first have to move Tsjerk> the center to the origin, do the rotation and move the thing Tsjerk> back. I've scripted this in Povray. If you're interested, I can Tsjerk> send you the script. Yes, that sounds great, thanks. Tsjerk> You can then rescript it in python or you can Tsjerk> output your scene to povray and do the rest there. If it's not too complex, I'll rewrite for python so I can run it interactively. Tsjerk> In addition (although you may already know this), the meaning of Tsjerk> all elements of the result of get_view (python index) is Yes, thanks a lot. Terry
RE: [PyMOL] pse/session files increase memory usage?
Pete, It is a PyMOL fact of life that session files take more memory, because all state information must transient exist in both Python and C while the session is being loading. However, we should get that memory back after the session is fully loaded. If not, then you may be right about a memory leak. A good way to test this is to see what happens if you load the same session over and over again without restarting PyMOL. Does memory usage consistently increase or does it level off? The most likely cause of this would be PyMOL failing to decrement the reference counts on certain session data. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Peter Adrian Meyer > Sent: Tuesday, April 25, 2006 3:15 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pse/session files increase memory usage? > > Hi all, > > For complex scenes, I've noticed that pymol 0.99rc6 (with > ext0.99rc1) on linux appears to use more memory when started > from a pse file than it does when loading the models/maps > manually or from a pml script (based on the fact that I get > out of memory errors during ray-tracing after starting from a > pse, but not after starting from pml scripts). > > The easy work-around is to use pml scripts instead of pse > files, but I was curious if anyone else had run into this > (or, for that matter if it's a known issue...my best guess > would be that there's a memory leak somewhere, or that the > configuration flags I used to build python were causing problems). > > Pete > > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University > > > > --- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier Download IBM WebSphere Application Server > v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; dat=121642 > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
RE: [PyMOL] pse/session files increase memory usage?
Warren, I did a bit of testing (memory figures from top VIRT column, after pymol had finished executing commands and was responsive to input): >pymol set.pml (316MB) save test.pse (537MB) reinitialize ; load test.pse (539MB after load) reinitialize ; load test.pse (540MB after load) reinitialize ; load test.pse (542MB after load) quit > pymol test.pse (532MB) It looks to me like there's a small memory leak when reloading the same session file, but that this is fairly minor compared to the difference between loading objects from a script and loading from a session file. Pete > Pete, > > It is a PyMOL fact of life that session files take more memory, because > all state information must transient exist in both Python and C while the > session is being loading. However, we should get that memory back after > the session is fully loaded. If not, then you may be right about a memory > leak. A good way to test this is to see what happens if you load the same > session over and over again without restarting PyMOL. Does memory usage > consistently increase or does it level off? > > The most likely cause of this would be PyMOL failing to decrement the > reference counts on certain session data. > > Cheers, > Warren > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > >> -Original Message- >> From: pymol-users-ad...@lists.sourceforge.net >> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of >> Peter Adrian Meyer >> Sent: Tuesday, April 25, 2006 3:15 PM >> To: pymol-users@lists.sourceforge.net >> Subject: [PyMOL] pse/session files increase memory usage? >> >> Hi all, >> >> For complex scenes, I've noticed that pymol 0.99rc6 (with >> ext0.99rc1) on linux appears to use more memory when started >> from a pse file than it does when loading the models/maps >> manually or from a pml script (based on the fact that I get >> out of memory errors during ray-tracing after starting from a >> pse, but not after starting from pml scripts). >> >> The easy work-around is to use pml scripts instead of pse >> files, but I was curious if anyone else had run into this >> (or, for that matter if it's a known issue...my best guess >> would be that there's a memory leak somewhere, or that the >> configuration flags I used to build python were causing problems). >> >> Pete >> >> >> Pete Meyer >> Fu Lab >> BMCB grad student >> Cornell University >> >> >> >> --- >> Using Tomcat but need to do more? Need to support web >> services, security? >> Get stuff done quickly with pre-integrated technology to make >> your job easier Download IBM WebSphere Application Server >> v.1.0.1 based on Apache Geronimo >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; > dat=121642 >> ___ >> PyMOL-users mailing list >> PyMOL-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> >> > Pete Meyer Fu Lab BMCB grad student Cornell University
RE: [PyMOL] pse/session files increase memory usage?
Pete, Thanks -- I ran some tests too and wasn't able to find any convincing memory leaks either. Instead, it appears that Python simply caching memory previously used, all of which appears to remain available to Python for loading of subsequent session. As it turns out, this inefficiency in Python is something people are aware of and thinking about: http://evanjones.ca/memoryallocator Since we are currently dependent upon Python for our platform-independent session save & restore capability, we are stuck with this behavior until Python itself is fixed. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Peter Adrian Meyer > Sent: Wednesday, April 26, 2006 9:02 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] pse/session files increase memory usage? > > Warren, > > I did a bit of testing (memory figures from top VIRT column, > after pymol > had finished executing commands and was responsive to input): > > >pymol set.pml (316MB) > save test.pse (537MB) > reinitialize ; load test.pse (539MB after load) > reinitialize ; load test.pse (540MB after load) > reinitialize ; load test.pse (542MB after load) > quit > > > pymol test.pse (532MB) > > It looks to me like there's a small memory leak when > reloading the same > session file, but that this is fairly minor compared to the difference > between loading objects from a script and loading from a session file. > > > Pete > > > Pete, > > > > It is a PyMOL fact of life that session files take more > memory, because > > all state information must transient exist in both Python > and C while the > > session is being loading. However, we should get that > memory back after > > the session is fully loaded. If not, then you may be right > about a memory > > leak. A good way to test this is to see what happens if > you load the same > > session over and over again without restarting PyMOL. Does > memory usage > > consistently increase or does it level off? > > > > The most likely cause of this would be PyMOL failing to > decrement the > > reference counts on certain session data. > > > > Cheers, > > Warren > > -- > > Warren L. DeLano, Ph.D. > > Principal Scientist > > > > . DeLano Scientific LLC > > . 400 Oyster Point Blvd., Suite 213 > > . South San Francisco, CA 94080 USA > > . Biz:(650)-872-0942 Tech:(650)-872-0834 > > . Fax:(650)-872-0273 Cell:(650)-346-1154 > > . mailto:war...@delsci.com > > > > > >> -Original Message- > >> From: pymol-users-ad...@lists.sourceforge.net > >> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > >> Peter Adrian Meyer > >> Sent: Tuesday, April 25, 2006 3:15 PM > >> To: pymol-users@lists.sourceforge.net > >> Subject: [PyMOL] pse/session files increase memory usage? > >> > >> Hi all, > >> > >> For complex scenes, I've noticed that pymol 0.99rc6 (with > >> ext0.99rc1) on linux appears to use more memory when started > >> from a pse file than it does when loading the models/maps > >> manually or from a pml script (based on the fact that I get > >> out of memory errors during ray-tracing after starting from a > >> pse, but not after starting from pml scripts). > >> > >> The easy work-around is to use pml scripts instead of pse > >> files, but I was curious if anyone else had run into this > >> (or, for that matter if it's a known issue...my best guess > >> would be that there's a memory leak somewhere, or that the > >> configuration flags I used to build python were causing problems). > >> > >> Pete > >> > >> > >> Pete Meyer > >> Fu Lab > >> BMCB grad student > >> Cornell University > >> > >> > >> > >> --- > >> Using Tomcat but need to do more? Need to support web > >> services, security? > >> Get stuff done quickly with pre-integrated technology to make > >> your job easier Download IBM WebSphere Application Server > >> v.1.0.1 based on Apache Geronimo > >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; > > dat=121642 > >> ___ > >> PyMOL-users mailing list > >> PyMOL-users@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > >> > > > > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University > > > > --- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier > Download IBM WebSphere Application Server v.1.0.1 based on
[PyMOL] run out of memory problem
Hi all, The binary distribution (macpymol-0_99rc6.tar.gz) of PyMol 0.99 was installed in Mac 10.4.6. This Mac has 1.5G memory. When doing ray, it was using about 1.2G memory, it stopped in the middle and at last it died. The error message is about running out of memory. Did anybody meet the same problem? Thanks. -Donglu
Re: [PyMOL] run out of memory problem
pymol-users-ad...@lists.sourceforge.net wrote on 04/26/2006 08:03:40 PM: > Hi all, > > The binary distribution (macpymol-0_99rc6.tar.gz) of PyMol 0.99 was > installed in Mac 10.4.6. This > Mac has 1.5G memory. When doing ray, it was using about 1.2G memory, > it stopped in the middle and > at last it died. The error message is about running out of memory. > > Did anybody meet the same problem? Thanks. > > -Donglu > Hi Donglu - We need more information to figure out what happened. How much memory was Pymol using when you first launched it? What about right before you started the raytracing? Are you rendering an unusually large or complex image? You can try adjusting the memory settings for raytracing: in the "Setting" menu, go to "Rendering" then "Memory". Try the various options and see if you still run out of memory. If your image is complex, try reducing the quality. In the "Display" menu, go to "Quality". You may be able to reduce the quality a bit without noticeably affecting the image and it should reduce memory usage. Reducing the size of the raytraced image will also reduce memory usage, but of course your image will be smaller... Hope these suggestions help, Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
[PyMOL] Nvidia Quadro/stereo emitter sync problem on Fedora 5
This is off-topic on this list, but I figured someone among the subscribers might have an idea about what is going on. I posted a question on the Nvidia nVnews forum, but got no replies so far. We are using version 8756 of the Nvidia driver on Fedora Core 5. There are several machines with various versions of the Quadro chip. The driver seems to work, except for Stereographics emitter sync on older NV25 and NV28 cards. On NV25 the emitter led does not light at all, and on NV28 it lights, but the synchronization is off (the picture flickers badly and there is no proper stereo effect when looking through the glasses). Newer NV36 cards work as advertised. This happens with the 8756 and 8178 (requires patching to work at all on FC5) drivers when using the latest kernels, 2.6.16-1.2096_FC5 or 2.6.16-1.2080_FC5. The machines have x86 Pentium 4 processors. Has anyone else seen this? Does stereo work using these drivers on older kernels/distributions and this is just kernel/compiler incompatibility on Fedora 5? Mikko Huhtala
