Re: [PyMOL] Mac OS X 10.4.3
Warren, with 0.99beta25 the problem still exists. After loading a molecule there's no flickering but if I do a ray trace then the flickering starts when I rotate. Shifting the window stops the flickering. By running show cartoon after loading I can also get the flickering. Again, moving the window stops it. Brian On Nov 4, 2005, at 3:40 AM, Warren DeLano wrote: Brian, Can you confirm that this problem exists in the very latest beta? I can't reproduce on my iMac G5 http://delsci.com/beta Is there any special trick to get it to happen? 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 Brian J Goodfellow Sent: Thursday, November 03, 2005 2:17 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mac OS X 10.4.3 Hi Mac users, has anyone noticed an annoying flickering appearing when rotating a molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If the window is moved then the flickering disappears. However, if a ray trace is then drawn the problem starts again until the window is moved again - very annoying! Brian Goodfellow *** Brian J Goodfellow Departamento de QuÌmica Universidade de Aveiro 3810-193 Aveiro, Portugal Tel: +351 234 401506, Fax: +351 234 370084 http://www.dq.ua.pt/ingles/index_mem.htm *** --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] problem with CASTp plugin
Hello, We are running Python v2.2.3 on Red Hat Enterprise 3 which is almost like Red Hat 9 and/or Fedora Core 1. Our RedHat version seems to be choking on the pyc file. The following is the error we get. Exception in plugin 'CASTpyMOL' -- Traceback follows... Traceback (most recent call last): File modules/pmg_tk/PMGApp.py, line 109, in initialize_plugins ImportError: Bad magic number in /usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/startup/CASTpyMOL. pyc Error: unable to initialize plugin 'CASTpyMOL'. We have contacted the plugin authors but have been unable to solve this problem. Thanks, JJ Hello, We use CASTpyMOL.pyc file, for Linux, on Suse. It works fine. The .pyc files are python compiled code and they should work only for python and PyMOL versions they have been compiled for. So, CASTpyMOL.pyc file is for PyMOL 0.98 and must be moved in the PYMOL_HOME/modules/pmg_tk/startup/ directory. Try a binary version of PyMOL, it embeds its own python interpreter. Maybe this will resolve your problem. -- Sébastien Moretti http://www.igs.cnrs-mrs.fr/ CNRS - IGS 31 chemin Joseph Aiguier 13402 Marseille cedex
[PyMOL] Re: PyMOL-users digest, Vol 1 #1049 - 6 msgs
HI Mac users, Brian Goodfellow wrote: has anyone noticed an annoying flickering appearing when rotating a =20 molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present =20 under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If =20 the window is moved then the flickering disappears. However, if a ray =20= The 10.4.3 update included a display driver update. Just go to ati's homepage (http://ati.com) and download the latest driver for you card. After this everything should be back to normal. Jesper Karlsen
[PyMOL] Re: macpymol beta 21 bug?
Hi Warren, Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that still has a problem. I then booted into my back up clone which is at 10.4.2 and 99beta21 and 99beta25 work just fine. So the 64MB ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI ones are OK. Will try and find a nVidia 64MB equipped mac for comparison. Having just read Jesper's email regarding getting drivers at ATI's website, I had a look and there are no mac drivers available as far as I can see. Only the ATI Displays software. After installing this on my machine, nothing has changed. The molecule loads fine and the window behaves in default line representation but when I change to cartoon (or any other) representation, the window flickers badly. Cheers MGM On 4 Nov 2005, at 03:48, Warren DeLano wrote: Martin, 10.4.3 is one ingredient in this problem -- ATI may be another...still trying to reproduce it here, but so far all our nVidia-based 10.4.3 machines are doing just fine. 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: Martin Montgomery [mailto:m...@mrc-dunn.cam.ac.uk] Sent: Thursday, November 03, 2005 5:08 AM To: Warren DeLano Subject: macpymol beta 21 bug? Hi Warren, I'm having a problem with 0.99 beta 21. I get an occasional glitch where the graphics pane and GUI flickers badly when I move/zoom the molecule. This can be temporarily corrected by resizing the window and typing reset. However sometimes, after a little while, the flicker returns. The brushed metal surround of the window does not flicker nor does the text pane. One possible cause is that I have updated to 10.4.3 and am not sure whether the problem also occurred in 10.4.2 but I could boot into my backup clone and check. 10.4.3 has meant that the fans are running more often even when the computer is doing very little. I've got a Dual 2Ghz G5 with 3.5G RAM and the stock Radeon 9600 Pro 64mB RAM graphics card into a Cinema 20 display. Cheers MGM Martin Montgomery Director's Group MRC Dunn Human Nutrition Unit Hills Road Cambridge CB2 2XY
Re: [PyMOL] Re: macpymol beta 21 bug?
On Nov 4, 2005, at 12:38, Martin Montgomery wrote: Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that still has a problem. I then booted into my back up clone which is at 10.4.2 and 99beta21 and 99beta25 work just fine. So the 64MB ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI ones are OK. Will try and find a nVidia 64MB equipped mac for comparison. On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not noticed any change after updating to 10.4.3. I use a self-compiled PyMol 0.98. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr -
Re: [PyMOL] Re: macpymol beta 21 bug?
I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and macpymol 99beta21/25 and it works fine with 10.4.3. It seems the problem is limited to ATI graphics cards with less than 256 RAM. nVidea cards are not affected. Will try an ATI card with 128MB RAM if I can find one here. I have also used my powerbook which has an ATI card and has the flicker problem to boot (via target mode firewire) a G5 iMac with an nVidea card and there is no problem when the powerbook system uses the iMac graphics. Cheers MGM On 4 Nov 2005, at 12:08, khin...@cea.fr wrote: On Nov 4, 2005, at 12:38, Martin Montgomery wrote: Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that still has a problem. I then booted into my back up clone which is at 10.4.2 and 99beta21 and 99beta25 work just fine. So the 64MB ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI ones are OK. Will try and find a nVidia 64MB equipped mac for comparison. On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not noticed any change after updating to 10.4.3. I use a self-compiled PyMol 0.98. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr - --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Re: macpymol beta 21 bug?
Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under 10.4.3 however, if I launch X11 and run PyMol under that - (version 0.97), then there's no problem Chris On Nov 4, 2005, at 7:26 AM, Martin Montgomery wrote: I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and macpymol 99beta21/25 and it works fine with 10.4.3. It seems the problem is limited to ATI graphics cards with less than 256 RAM. nVidea cards are not affected. Will try an ATI card with 128MB RAM if I can find one here. I have also used my powerbook which has an ATI card and has the flicker problem to boot (via target mode firewire) a G5 iMac with an nVidea card and there is no problem when the powerbook system uses the iMac graphics. Cheers MGM On 4 Nov 2005, at 12:08, khin...@cea.fr wrote: On Nov 4, 2005, at 12:38, Martin Montgomery wrote: Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that still has a problem. I then booted into my back up clone which is at 10.4.2 and 99beta21 and 99beta25 work just fine. So the 64MB ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI ones are OK. Will try and find a nVidia 64MB equipped mac for comparison. On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not noticed any change after updating to 10.4.3. I use a self-compiled PyMol 0.98. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr - --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Christopher M. Yip, Ph.D., P.Eng. Associate Professor - Canada Research Chair in Molecular Imaging Department of Chemical Engineering and Applied Chemistry Department of Biochemistry Institute of Biomaterials and Biomedical Engineering The Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Room 404 160 College St. Toronto, ON, CANADA M5S 3E1 (416) 978-7853 (416) 978-4317 (fax) christopher@utoronto.ca http://bigten.ibme.utoronto.ca
[PyMOL] Re: PyMOL-users digest, Vol 1 #1050 - 7 msgs
Hi Mac users, MGM wrote: Having just read Jesper's email regarding getting drivers at ATI's website, I had a look and there are no mac drivers available as far as I can see. Only the ATI Displays software. After installing this on my machine, nothing has changed. The molecule loads fine and the window behaves in default line representation but when I change to cartoon (or any other) representation, the window flickers badly. Wups! I quess I did to many things at ones, if was the later configuration that did the trick sorry! I downloaded the ATI Display software from ati.com. I configured the ATI Display (in System Prefs.) to use antialiasing (FSAA=2x) for MacPyMOL.app and the flickering stoped. Jesper Karlsen
Re: [PyMOL] Re: macpymol beta 21 bug in 10.4.3?
I've given it a quick run on a new Powerbook with the ATI Radeon 9700 w/128 MB, and I can't reproduce the flicker. Same thing with a G5 with a 9800 with 256 MB. My dual G4 with a Radeon 9000 (128 MB) does show the flicker, however, and Jespers trick does the trick. No more flicker. Dan -- Dr. Daniel Moriarty Siena College Chemistry and Biochemistry Dept. 515 Loudon Road Loudonville, NY 12211 (518) 783-2472 fax: (518) 276-4887 From: Martin Montgomery m...@mrc-dunn.cam.ac.uk Date: Fri, 4 Nov 2005 13:05:10 + To: pymol-users pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Re: macpymol beta 21 bug in 10.4.3? Just for completeness, I've now checked a 20 G5 iMac with a 128MB ATI card and it is fine. Also, I can confirm that there is not a problem whilst using X11 pymol on a 64MB ATI card. Cheers MGM Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under 10.4.3 however, if I launch X11 and run PyMol under that - (version 0.97), then there's no problem Chris On 4 Nov 2005, at 12:26, Martin Montgomery wrote: I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and macpymol 99beta21/25 and it works fine with 10.4.3. It seems the problem is limited to ATI graphics cards with less than 256 RAM. nVidea cards are not affected. Will try an ATI card with 128MB RAM if I can find one here. I have also used my powerbook which has an ATI card and has the flicker problem to boot (via target mode firewire) a G5 iMac with an nVidea card and there is no problem when the powerbook system uses the iMac graphics. Cheers MGM On 4 Nov 2005, at 12:08, khin...@cea.fr wrote: On Nov 4, 2005, at 12:38, Martin Montgomery wrote: Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that still has a problem. I then booted into my back up clone which is at 10.4.2 and 99beta21 and 99beta25 work just fine. So the 64MB ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI ones are OK. Will try and find a nVidia 64MB equipped mac for comparison. On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not noticed any change after updating to 10.4.3. I use a self-compiled PyMol 0.98. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr - --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] .xyz file loading problem from chempy module
Hello everyone It seems to be a problem with loading an .xyz file as a chempy model. For example doing from chempy import io m = io.xyz.fromFile(some.xyz) gives: chempy: reading some.xyz. Traceback (most recent call last): File stdin, line 1, in ? File /home/dmitriy/pymol/lib/python2.4/site-packages/chempy/__init__.py, line 185, in fromFile TypeError: fromList() takes exactly 1 argument (2 given) If I've got the right idea whats going on, there should be fromList(self,list) function in xyz.py which will hide the Storage one. Like it's done in pdb.py (it works fine for io.pdb.fromFile) I'm trying to establish a communication between my program and pymol in a simple .xyz format. Sending a list of strings, creating a chempy model and loading it into pymol will work. If there is some workaround or a fix for problem mention above. Warren, Is it possible to implement a way of passing .xyz file as a string, not as a list of strings or a file? I've seen molstr, pdbstr etc. but not xyzstr. And a short description how to load pdbstr for example it in this way will be great. Thanks Dmitriy
RE: [PyMOL] .xyz file loading problem from chempy module
Dmitriy, The very latest beta versions of PyMOL can read .xyz files directly (via the load or load_raw commands). http://delsci.com/beta load_raw usage: my_xyz=open(some.xyz).read() cmd.load_raw(my_xyz, 'xyz', my_xyz) I suspect the chempy XYZ file is limited to reading Tinker's fixed-column XYZ format. 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 Dmitriy Sent: Friday, November 04, 2005 6:34 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] .xyz file loading problem from chempy module Hello everyone It seems to be a problem with loading an .xyz file as a chempy model. For example doing from chempy import io m = io.xyz.fromFile(some.xyz) gives: chempy: reading some.xyz. Traceback (most recent call last): File stdin, line 1, in ? File /home/dmitriy/pymol/lib/python2.4/site-packages/chempy/__init__.py, line 185, in fromFile TypeError: fromList() takes exactly 1 argument (2 given) If I've got the right idea whats going on, there should be fromList(self,list) function in xyz.py which will hide the Storage one. Like it's done in pdb.py (it works fine for io.pdb.fromFile) I'm trying to establish a communication between my program and pymol in a simple .xyz format. Sending a list of strings, creating a chempy model and loading it into pymol will work. If there is some workaround or a fix for problem mention above. Warren, Is it possible to implement a way of passing .xyz file as a string, not as a list of strings or a file? I've seen molstr, pdbstr etc. but not xyzstr. And a short description how to load pdbstr for example it in this way will be great. Thanks Dmitriy --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Independent Rotation axis...
The rotate and translate commands can do this *if* you append the object=object-name to the command: Try typing in the following sequence of commands: fragment arg fragment glu translate [5,0,0], object=arg translate [-5,0,0], object=glu origin arg, object=arg origin glu, object=glu rotate y, 10, object=arg rotate y, -10, object=glu Note that these movements are accomplished via matrix and not coordinate transformations, so interacting with the molecules after they have been moved is currently a bit problematic (bugs to fix...). However, you can move complex geometries like surfaces without forcing recalcuation using this approach. Normally for movies, you'd embed commands like the above into movie commands. For that to work, you'll also need commands like: reset object=arg reset object=glu in the first movie frame. Cheers, Warren PS. Coming down the pipe: automatic 'tweening for object motion! -- 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 Nathaniel G. Butlin Sent: Friday, November 04, 2005 6:34 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] Independent Rotation axis... Hi All, I was wondering if anyone know if there is anyway to assign independent rotation axis to two different proteins within Pymol. Specifically, I amintersted in having two molecules rotate about individual axis in a movie sequence. Thanks, Nate Butlin UCDavis - Chemistry ngbut...@ucdavis.edu --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Superimpose
Hi everyone, I have two similar (closely related) multi-chain structures. I want to merge them and highlight the regions that do not superimpose. However, I do not know how to superimpose these two structures and how to select non-intersecting residues. Any help will be appreciated. Thanks. __ Yahoo! FareChase: Search multiple travel sites in one click. http://farechase.yahoo.com
Re: [PyMOL] Mac OS X 10.4.3
I see the same flickering problem (iMac G5, OSX 10.4.3). Opening as pymol -M doesn't help. Best, Morri On 11/3/05, Sabuj Pattanayek sabuj.pattana...@vanderbilt.edu wrote: I don't know if it will make a difference (I don't even have a Mac) but try opening it from a console using: pymol -M -- Morri Feldman Shokat Lab UCSF Biophysics Graduate Program
[PyMOL] OS 10.4.3
Hi I also have the flickering problem with my 15 g4 powerbook (ATI Radeon 9700 card). Some mentioned a pymol -M command but I don't use the x11 window to open pymol...I just click on a pdb file. Anybody know how to setup the pymol command (alias) ? Thanks, Mark Collins
