From: Mark S. <sa...@um...> - 2012-08-30 03:59:03
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Jason et al., I've noticed some strange behavior launching MacPyMOL. I'm running v 1.5.0.4 on OSX 10.8.1, but I don't think the version or OS is at fault. I discovered this problem when opening a session (.pse) file in a folder whose name is "pMM12(His6-EcLpoA(28-678)" (without quotes). Note the unmatched parenthesis before the "His". If I launch MacPyMOL by double-clicking the session file in that folder, MacPyMOL launches but detects a syntax error in the file pathname and doesn't open the file. If I again double-click the same session file again, a new MacPyMOL window opens and the session file is successfully opened! If I change the name of the enclosing folder to remove the unmatched parenthesis, the problem goes away. I know this is a consequence of the layered architecture, but I thought you should know about it. Regards, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. sa...@um... phone (734) 764-3353 fax (734) 764-3323 |
From: Jason V. <jas...@sc...> - 2012-08-30 16:28:08
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Hi Mark, Thanks for the note. We've recorded the bug and will look into it. Cheers, -- Jason On Wed, Aug 29, 2012 at 10:58 PM, Mark Saper <sa...@um...> wrote: > Jason et al., > > I've noticed some strange behavior launching MacPyMOL. I'm running v 1.5.0.4 on OSX 10.8.1, but I don't think the version or OS is at fault. I discovered this problem when opening a session (.pse) file in a folder whose name is "pMM12(His6-EcLpoA(28-678)" (without quotes). Note the unmatched parenthesis before the "His". > > If I launch MacPyMOL by double-clicking the session file in that folder, MacPyMOL launches but detects a syntax error in the file pathname and doesn't open the file. If I again double-click the same session file again, a new MacPyMOL window opens and the session file is successfully opened! If I change the name of the enclosing folder to remove the unmatched parenthesis, the problem goes away. I know this is a consequence of the layered architecture, but I thought you should know about it. > > Regards, > Mark > _________________________________ > Mark A. Saper, Ph.D. > Associate Professor of Biological Chemistry, University of Michigan > Ann Arbor MI 48109-1055 U.S.A. > sa...@um... phone (734) 764-3353 fax (734) 764-3323 > > > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: H. A. S. <ad...@st...> - 2012-11-20 02:54:06
|
Hi all, If you run the script below to get a nice blob type surface (great for illustrations) in 1.4 it all works perfectly, and you can color the new map surface any color you want. If you run the same script in 1.5 it all works perfectly too, but no matter what you do you cannot change the color of the new map surface from the default white to any other color. Not via the settings, the command line, nor the gui menus. Is there a command I can add to the script below that will allow me to change the color of map surface (surfA)? or are there new commands that I should use in this script to make this work in 1.5? or is this now broken in 1.5.0.4? --------------- set surface_quality, 1 alter all, b=50 alter all, q=1 set gaussian_resolution,5 map_new mapA, gaussian, 1, sele or pdb, 6 isosurface surfA, mapA ----------------- Thanks in advance for the help! H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |
From: Thomas H. <sp...@us...> - 2012-11-23 12:32:01
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Hi Adam, this seems to be not yet fully implemented with the new shader rendering. So you may turn shaders off for now: PyMOL> unset use_shaders Ray tracing is not affected, so you still can generate high quality figures with correct colors: PyMOL> ray Hope that helps. Cheers, Thomas H. Adam Steinberg wrote, On 11/20/12 03:40: > Hi all, > > If you run the script below to get a nice blob type surface (great for illustrations) in 1.4 it all works perfectly, and you can color the new map surface any color you want. > If you run the same script in 1.5 it all works perfectly too, but no matter what you do you cannot change the color of the new map surface from the default white to any other color. Not via the settings, the command line, nor the gui menus. > > Is there a command I can add to the script below that will allow me to change the color of map surface (surfA)? or are there new commands that I should use in this script to make this work in 1.5? or is this now broken in 1.5.0.4? > > --------------- > set surface_quality, 1 > alter all, b=50 > alter all, q=1 > set gaussian_resolution,5 > map_new mapA, gaussian, 1, sele or pdb, 6 > isosurface surfA, mapA > ----------------- > > Thanks in advance for the help! > > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: H. A. S. <ad...@st...> - 2012-11-23 16:15:23
|
Thanks Thomas, that does work. On Nov 23, 2012, at 6:31 AM, Thomas Holder wrote: > Hi Adam, > > this seems to be not yet fully implemented with the new shader > rendering. So you may turn shaders off for now: > > PyMOL> unset use_shaders > > Ray tracing is not affected, so you still can generate high quality > figures with correct colors: > > PyMOL> ray > > Hope that helps. > > Cheers, > Thomas > > H. Adam Steinberg wrote, On 11/20/12 03:40: >> Hi all, >> >> If you run the script below to get a nice blob type surface (great for illustrations) in 1.4 it all works perfectly, and you can color the new map surface any color you want. >> If you run the same script in 1.5 it all works perfectly too, but no matter what you do you cannot change the color of the new map surface from the default white to any other color. Not via the settings, the command line, nor the gui menus. >> >> Is there a command I can add to the script below that will allow me to change the color of map surface (surfA)? or are there new commands that I should use in this script to make this work in 1.5? or is this now broken in 1.5.0.4? >> >> --------------- >> set surface_quality, 1 >> alter all, b=50 >> alter all, q=1 >> set gaussian_resolution,5 >> map_new mapA, gaussian, 1, sele or pdb, 6 >> isosurface surfA, mapA >> ----------------- >> >> Thanks in advance for the help! >> >> >> H. Adam Steinberg >> 7904 Bowman Rd >> Lodi, WI 53555 >> 608/592-2366 > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > ------------------------------------------------------------------------------ > Monitor your physical, virtual and cloud infrastructure from a single > web console. Get in-depth insight into apps, servers, databases, vmware, > SAP, cloud infrastructure, etc. Download 30-day Free Trial. > Pricing starts from $795 for 25 servers or applications! > http://p.sf.net/sfu/zoho_dev2dev_nov > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |