Re: [PyMOL] Missing parts in cartoon mode
Well ill be d..! The .pse file you send me shows the loops just fine. I´m still puzzled as to why PyMol 0.98 on win2000 fails to show those loops but now I can just use your .pse file as a template and work my way around it. Ill also try upgrading as Warren suggest. Anyways, thanks a lot for the help, it is greatly appreciated! Cheers kasper -Original Message- From: Joel Tyndall Sent: 10/18/2005 10:17:30 PM To: randkas...@icqmail.com Subject: Re: [PyMOL] Missing parts in cartoon mode Hi again, Hmmm had a look and it looks fine to me. I'm assuming you're looking at chain H. See if you can open this pse file which is displaying the cartoon. The only strange thing is that there is no residue 218. sorry I can't be of any more help. might be worth sending Warren/me a pse of the problem? See ya J PS thats a windows pse file and should work randkas...@icqmail.com wrote: Hi Joel The two missing loops of the 1DAN structure when in cartoon mode are located to res. 183-189 and 220-220. I´m using a standard PC with Windows 2000. Any suggestions? A fellow collegue in my lab is having identical troubles but he´s also using a PC with win2000. Its quite frustrating because the rest of the structure looks great in PyMol! Cheers Kasper The two missing loops of the 1DAN structure when in cartoon mode are located to res. 183-189 and 220-220. I´m using a standard PC with Windows 2000. Any suggestions? A fellow collegue in my lab is having identical troubles but he´s also using a PC with win2000. Its quite frustrating because the rest of the structure looks great in PyMol! Cheers Kasper -Original Message- *From: Joel Tyndall* Sent: 10/17/2005 12:07:00 AM To: randkas...@icqmail.com Subject: Re: [PyMOL] Missing parts in cartoon mode Hey Kasper, which loops can't you see (amino acid nos./chain/)? what OS are you on (OSX, PC, Linux?) I have had a look and it looks ok on windows Cheers J randkas...@icqmail.com wrote: Hi everybody I am getting quite desperate! For some strange reason PyMol do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon display mode. When I display the structure in lines or sticks everything is ok. Other pdb-viewers dont have this problem with the same .pdb file. I have tried several things: 1. Upgraded to the newest version og PyMol. 2. Redefined secondary structure using the alter command. 3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl. None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!) Cheers Kasper ___ ICQ - You get the message, anywhere! Get it @ http://www.icq.com -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin NNew Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 . ___ ICQ - You get the message, anywhere! Get it @ http://www.icq.com -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 Pfont face=Arial, Helvetica, sans-serif size=2 style=font-size:13.5px___BRfont face=Arial, Helvetica, sans-serif size=2 style=font-size:13.5pxICQ - You get the message, anywhere!brGet it @ a href=http://www.icq.com; target=newhttp://www.icq.com/a/fontbrbrnbsp;/font/font
Re: [PyMOL] Need testers for new MacPyMOL on Tiger
On Oct 14, 2005, at 17:50, Warren DeLano wrote: For cutting-edge Mac users, there is a new MacPyMOL for Tiger that integrates into a single window and links to the system Python instead of bringing its own copy (in part this is necessary preparation for Intel...). http://delsci.com/beta Please let me know how it works for you! It works fine on the few quick tests that I did. It looks fine as well, I much prefer the single window approach. Using the system Python is also a step in the right direction... now... if it also came with NumPy support compiled in... I might actually use it! 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 -
[PyMOL] Mac Stereo 3D: Breaking News
See New Power Macs on http://www.macworld.com/news/2005/10/19/liveupdate/index.php The first Quad-core Mac and the the first with a Quadro FX 4500 graphics card! Do you know what this implies? 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
[PyMOL] PyMOL featured on Apple Store site?
So, that sure looks like PyMOL to me (actually, four instances of it) running on the display of a PowerMac G5 on the newly-updated Apple Store website today. My question is, which structure is that? -- D. Joe Anderson, Asst. Sci.2252 Molecular Biology Bldg Biochem, Biophys, Mol Bio Iowa State Univ, Ames, IA 50010 How to Report Bugs Effectively http://www.chiark.greenend.org.uk/~sgtatham/bugs.html
Re: [PyMOL] PyMOL featured on Apple Store site?
Do you have the URL? D. Joe Anderson wrote: So, that sure looks like PyMOL to me (actually, four instances of it) running on the display of a PowerMac G5 on the newly-updated Apple Store website today. My question is, which structure is that?
Re: [PyMOL] PyMOL featured on Apple Store site?
nm, I found the url: http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/72303/wo/iG1ZdpmENibK2kKdLwyNuAAR9NW/0.SLID?nclm=PowerMacmco=586014F6 D. Joe Anderson wrote: So, that sure looks like PyMOL to me (actually, four instances of it) running on the display of a PowerMac G5 on the newly-updated Apple Store website today. My question is, which structure is that?
RE: [PyMOL] PyMOL featured on Apple Store site?
They've got MacPyMOL two places on this site: http://www.apple.com/powermac/graphics.html Be sure to note the explicit mention of stereo 3D in a window down near the bottom. Amazing! The Stereo 3D Matters to Me campaign actually worked. Apple really *is* serious about meeting our needs. Cheers, Warren PS. IL2 on top, hexameric insulin in the bottom right. -- 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 Sabuj Pattanayek Sent: Wednesday, October 19, 2005 10:38 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL featured on Apple Store site? Do you have the URL? D. Joe Anderson wrote: So, that sure looks like PyMOL to me (actually, four instances of it) running on the display of a PowerMac G5 on the newly-updated Apple Store website today. My question is, which structure is that? --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] CRT vs flat panel stereo on Mac question
Warren Exciting news. Any thoughts on whether it will be possible to run stereo on a flat panel? At minimum seems like we can retire SGIs and use the CRT monitors? Also, quad processors are nice, but for those of us with recent G5s is all we need the new graphics card? -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892
[PyMOL] Stereo 3D Monitors Equipment
Here is some current information for those of you ordering yourself a new Quad Quadro-based Mac for doing Stereo 3D visualization. You will also need a good CRT, a stereo signal emitter, and shutter glasses. Stereo 3D glasses emitters: - More expensive: StereoGraphics http://www.stereographics.com/products/crystaleyesworkstation/index.htm l - Less expensive: NuVision3D http://www.nuvision3d.com/the60gx.html Thanks to LCD dominance, it is getting mucher harder to find a good CRT. You may need to hunt around a bit and perhaps buy pre-owned. The critical monitor specifications for Stereo 3D are: - Must be a CRT (not an LCD). - Should be as big as you can afford (20-22). - HD15 VGA input (DVI very rare). - Vertical refresh must be at least 120 Hz. - Horizontal sync frequency must be at least 130 kHz (ideally 140 kHz). Note that the last point is CRITICAL. Do not buy a CRT monitor for stereo 3D until you have confired that it can do a horizontal sync of at least 130 kHz. Beware of consumer monitors have horizontal sync limits of 80-120 kHz and thus cannot do stereo well. Good stereo-capable CRT displays still available NEW: - Philips 202P73 http://www.cdw.com/shop/products/specs.aspx?EDC=812337 http://www.insight.com/site/product/detail/index.cfm?item_number=201B45 74 - Iiyama Vision Master Pro 514 / HM204DT http://www.cdw.com/shop/products/default.aspx?EDC=453522 Good stereo-capable displays that are discontinued (buy USED on eBay, etc.): - IBM ThinkVision C220p (discontinued) - HP p1230 CRT Monitor (P9613W) (discontinued) - DELL p1230 (discontinued) - Sony GDM-C520K (discontinued) - NEC FP2141SB-BK (discontinued) - NEC-Mitsubishi Diamond Pro 2070SB-BK (discontinued) - Sun X7149A (discontinued) Borderline displays: - ViewSonic, P225FB (H-sync: 127 kHz - good for 1280x960 @ ~110 Hz) - Samsung SyncMaster 1100 DF (H-sync: 121 kHz) - Sun X7149A (H-sync: 121 kHz) Unsuitable displays: - ViewSonic G220f/fb, G810, G90f/fb - Philips 201B40, 201B45 - NEC Accusync 120 - Mitsubishi Diamond Pro 930SB - Samsung SyncMaster 1000 P, 997DF/997MB See: http://monitors.alege.net for info on tons of monitors, old new. 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
[PyMOL] Stereo
Not sure I understand Warren's post: Also, quad processors are nice, but for those of us with recent G5s is all we need the new graphics card? I hope -- that along with an OS / OpenGL driver upgrade... Does this mean that until Apple release an OS / OpenGL driver upgrade, stereo is still not possible on OS X even with new hardware? Mark
[PyMOL] Query variable value
PyExperts: When inside PyMOL, how do I find out the value of a variable without using 'set'? For example, I can type: set specular, 1 and then I know, specular = 1. But how do I find out specular's (or ANY variable's) value without changing it? Thanks, Olivier -- Olivier Julien PhD prov student Dr Brian D. Sykes Lab Department of Biochemistry 4-19 Medical Sciences Building University of Alberta Edmonton (AB) Canada T6G 2H7 (780) 492-3006 Email: ojul...@ualberta.ca Web: http://pelican.rsvs.ulaval.ca/oli/olivier.html
RE: [PyMOL] edgelines between molecules
Balaji: I've done this by making a surface of just the domain I want to highlight, then bring it into Photoshop. Select the background, then invert the selection. Then convert selection to path and then stroke the path. Here is an example: [ Attachment only sent to Balaji, available on request ] Layer 0 is a regular surface of the residues involved in a dimer interface. Layer 1 is the stroked path. Layer 2 is a surface with charge potential of the entire region. Displaying Layer 1 and Layer 2 gives the desired figure. Have fun, Mark Date: Wed, 19 Oct 2005 15:44:35 -0400 From: Balaji Bhyravbhatla balaji.bhyravbha...@umassmed.edu To: pymol-users@lists.sourceforge.net Subject: [PyMOL] edgelines between molecules Hello All, I have a large mega-dalton multi chain structure that I would like to make an overview (surface) figure. Instead of using many colors (13subunits) I would like to use one color and demarcate the subunits by some other means.One way would be to generate some sort of edge lines between the molecules. Is that possible, if so how? If anyone has any other suggestions please send them my way, it would be highly appreciated. Thanks Balaji _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
[PyMOL] Re: PyMOL-users digest, Vol 1 #1032 - 3 msgs
Oliver, I know it'll sound crazy but -- get. :-) For example, get two_sided_lighting or get bg_rgb I think this is covered on the Wiki somewhere, too. (http://www.pymolwiki.org/) HTH, -- Jason On Wed, 2005-10-19 at 20:24 -0700, pymol-users-requ...@lists.sourceforge.net wrote: Message: 3 Date: Wed, 19 Oct 2005 16:12:25 -0600 From: Olivier Julien ojul...@rsvs.ulaval.ca To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] Query variable value PyExperts: When inside PyMOL, how do I find out the value of a variable without using 'set'? For example, I can type: set specular, 1 and then I know, specular = 1. But how do I find out specular's (or ANY variable's) value without changing it? Thanks, Olivier -- Olivier Julien PhD prov student Dr Brian D. Sykes Lab Department of Biochemistry 4-19 Medical Sciences Building University of Alberta Edmonton (AB) Canada T6G 2H7 (780) 492-3006 Email: ojul...@ualberta.ca Web: http://pelican.rsvs.ulaval.ca/oli/olivier.html -- Jason Vertrees (javer...@utmb.edu) BSCB Graduate Student @ UTMB, Galveston http://www.bscb.utmb.edu :: BSCB @ UTMB http://best.utmb.edu :: B.E.S.T. @ UTMB http://pymolwiki.org :: PyMol Wiki
