[PyMOL] ImportError
Dear developers, just to inform, after some reinitializations of Pymol 0.99rc6 (pre-compiled) in a same session, I have got the message bellow (restarted the program and it was ok again). (I don't know if its due to my Linux installation or Pymol). Cheers, Ricardo Error: 3 ImportError Exception in Tk callback Function: function lambda at 0xb6b97a04 (type: type 'function') Args: () Traceback (innermost last): File /home/aparicio/test_pymol2/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, line 1747, in __call__ None File /home/aparicio/test_pymol2/pymol/modules/pmg_tk/skins/normal/__init__.py, line 1520, in lambda None File /home/aparicio/test_pymol2/pymol/modules/pmg_tk/SetEditor.py, line 78, in __init__ None File /home/aparicio/test_pymol2/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwLoader.py, line 145, in __getattr__ None File /home/aparicio/test_pymol2/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwLoader.py, line 71, in _getmodule None ImportError: No module named PmwSelectionDialog
[PyMOL] AMD64 X2+Quadro FX1300+Fedora5
Dear all, I thought to be worth posting this message for those who experience problems with dual core+quadro FX. It seems that only recently kernel and compatible driver became available. We succeeded installing PyMOL in a AMD64 X2+Quadro FX1300+Fedora5. After installing Fedora 5 (which seems to recognize FX1300 automatically but without working properly), we followed a recipe (2-May-2006) from http://www.fedorafaq.org/ (Problems and Their Solutions, Q3) We used yum install kmod-nvidia (yum install kmod-nvidia-smp did not work) Kernel 2.6.16-1.2122_FC5 was installed by this last command line. (21-May-2006 - http://download.fedora.redhat.com/pub/fedora/linux/core/updates/5/i386/) After that, we have followed the rest of the recipe and changed /etc/X11/xorg.conf (Driver nvidia) PyMOL 0.99 runs beautifully although stereo mode was not tested yet. Kind regards, Ricardo Aparicio http://www.iqm.unicamp.br/profs/aparicio.html
Re: [PyMOL] stereo: should wait for LCD solutions in near future?
Warren, Thank you for replying. Cheers, Ricardo Warren DeLano wrote: Ricardo, A 20+ 1600-1920 by 1200 pixel switchable stereo LCD display based on Parallax Barrier at a $2-3,000 price point would have a good shot at displacing shutter glasses -- but I don't know that any such product yet exists. In my experience: - Lenticular displays work fine for video but are unsuitable for technical graphics where thin lines must be rendered cleanly and without artifacts or anisotropy. - Polarization and/or mirror-based displays are too bulky, complex, and expensive. - Only Parallax Barrier provides both stereo and non-stereo display modes in the space of a desktop LCD monitor without unreasonable visual artifacts. But losing 2X in horizontal resolution means one needs to start with a very high resolution display (1920 or higher). The $500 Sharp 3D autostereoscopic display is a great proof of concept, and if it had 3X more pixels, I think it would be a viable option. Incidentally, Dimension Technologies has a 19 autostereoscopic display for $3,695 with about twice as many pixels as the Sharp 15 http://www.dti3d.com/component/page,shop.product_details/flypage,shop.f lypage/product_id,7/option,com_virtuemart/Itemid,1/, but I think it will still take 50% more pixels for ~33% less money in order to tap the full potential of this market. For now, I'd stick with CRTs and shutter glasses. 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 Ricardo Aparicio Sent: Monday, March 20, 2006 2:17 PM To: pymol-us...@lists.sf.net Subject: [PyMOL] stereo: should wait for LCD solutions in near future? Dear all, After reading many messages from last January, I would like to have a better idea if the best option for stereo continues to be the one kindly indicated at http://pymol.sourceforge.net/stereo3d.html (some messages mentioned alternatives like those listed bellow). Is there a chance that in near future a technology based on LCD monitors may become available at reasonable price and competitive image quality? (intrinsic horizontal low resolution of LCD 3D options seems to be a problem) Comments are welcomed. Cheers, Ricardo Aparicio http://store.sharpsystems.com/product.asp?sku=2555920 http://www.sharp3d.com/technology/howsharp3dworks/ http://www.inition.co.uk/inition/open_week_stereoscopic.htm http://www.inition.co.uk/inition/compare.php?SubCatID=1 http://www.inition.co.uk/inition/product.php?URL_=product_ster eovis_planar_sd1710SubCatID_=3 http://www.crystalcanyons.net/abouts/3dc9_DualMonitorComplete.shtm --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=kkid0944bid$1720dat1642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users .
[PyMOL] stereo: should wait for LCD solutions in near future?
Dear all, After reading many messages from last January, I would like to have a better idea if the best option for stereo continues to be the one kindly indicated at http://pymol.sourceforge.net/stereo3d.html (some messages mentioned alternatives like those listed bellow). Is there a chance that in near future a technology based on LCD monitors may become available at reasonable price and competitive image quality? (intrinsic horizontal low resolution of LCD 3D options seems to be a problem) Comments are welcomed. Cheers, Ricardo Aparicio http://store.sharpsystems.com/product.asp?sku=2555920 http://www.sharp3d.com/technology/howsharp3dworks/ http://www.inition.co.uk/inition/open_week_stereoscopic.htm http://www.inition.co.uk/inition/compare.php?SubCatID=1 http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_planar_sd1710SubCatID_=3 http://www.crystalcanyons.net/abouts/3dc9_DualMonitorComplete.shtm
[PyMOL] labels again
Dear colleagues: I've been looking for a way to add labels to my figures. After a search in the e-mail list files, I could draw cgo labels, although it would be a pain to orient them by hand using cmd.rotate and cmd.translate (too many figures). So, in the case of mono, I have used photoshop to include labels (superposing figures from PyMOL). The main problem, however, is that I need stereo now and I see two possibilities: to use cgo labels in both figures or to use labels (photoshop) in only one figure of the stereo par. My questions are: 1a) are there news about labels within PyMOL? Any recent improvement? (last e-mail in this issue was from august/25)? Any other clue I didn't see? 1b) are there news concerning automatic orientation? 2) is there a way to change color of cgo labels? 3) is there a way to change font of cgo labels? 4) do you have any reference (paper published or web) where I can see PyMOL-made figures containing labels? Thank you very much for your help. Regards, Ricardo Aparicio PhD Student Sao Paulo - BR
Re: [PyMOL] transparent sphere
Hi, the PyMOL Current Capabilities (v0.80) include Transparent surfaces and spheres (http://pymol.sourceforge.net/) Another option would be use NCSMASK (ccp4) and control the transparency level by changing the GRID, it worked for me. Good luck, Ricardo Aparicio PhD Student Brazil Michael Sorich wrote: Hi I wish to draw a sphere with either a semi-transparent or mesh surface. I can create a sphere as a cgo, however this has an opaque surface. Any help would be appreciated Michael Sorich PhD Student School of Pharmaceutical, Molecular and Biomedical Sciences University of South Australia Email: michael.sor...@postgrads.unisa.edu.au mike_sor...@hotmail.com --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.351 / Virus Database: 197 - Release Date: 19/04/2002
[PyMOL] util.mroll movie rate
Dear users: Sorry if these are trivial questions for you but I am in trouble and any help is very welcomed: 1) How to use util.mroll to rotate around another axis other than Y axis ? 2) how to control the speed of a movie? (it is possible to change size and number of images but I think there is an easier answer to this question) Thank you in advance, Ricardo Aparicio PhD Student Brazil
Re: [PyMOL] Selecting objects to move
I'm new too but I think on-line manual can help you. http://pymol.sourceforge.net/html/toc.html Good luck, Ricardo Leslie Hall wrote: Hello, I have just started using PyMol and had a question about moving selected objects in an animation. Here is basically what I want to do. 1.Load two separate pdb files. 2.Be able to move the two molecules independently of each other. 3.Show a conformational change in one of the molecules. 4.Move the two molecules independently and show them docking with each other. Thanks, Les ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
