Re: [PyMOL] Saving setting in PyMol
Recently I've tried to find pymolrc but couldn't do it ( I have pymol 1.5 installed from binarries package manager ) own@starlight ~/Desktop $ locate pymolrc own@starlight ~/Desktop $ locate .pymolrc own@starlight ~/Desktop $ locate *.pymolrc How I could locate it ? Akso I'm looking for detailed options of the possible settings in that file ( e.g I didnt find how to set maximum quality of images as the default option ) Thanks for help James 2013/1/26 James Starlight : > Recently I've tried to find pymolrc but couldn't do it ( I have pymol > 1.5 installed from binarries package manager ) > > own@starlight ~/Desktop $ locate pymolrc > own@starlight ~/Desktop $ locate .pymolrc > own@starlight ~/Desktop $ locate *.pymolrc > > How I could locate it ? > Akso I'm looking for detailed options of the possible settings in that > file ( e.g I didnt find how to set maximum quality of images as the > default option ) > > Thanks for help > > James > > 2012/8/16 Folmer Fredslund : >> Hi James >> >> Check out the information about how to load custom settings and functions: >> http://www.pymolwiki.org/index.php/Pymolrc >> >> Hope this helps, >> Folmer >> >> >> 2012/8/16 James Starlight : >>> Dear PyMol users! >>> >>> >>> I wounder to know about possible way to save settings of the PyMol >>> after LogOut from it. >>> >>> E.g I've defined some basic settings like fetch_host and fetch_patch >>> for uploading of new pdb files as well as set new background colour. >>> Also I've changed some advanced settings - e.g I defined to unchange >>> atom order in the processed pdb by the below commands >>> set retain_order,1 set pdb_retain_ids,1 >>> >>> >>> After exiting from PyMol and starting of the new session I must to >>> define this settings each time again. Is there any way to save this >>> parameters for each new pymol session ? >>> >>> JAmes >>> >>> -- >>> 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 (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> >> -- >> Folmer Fredslund -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] names of the residues
Hi Ahmet, If your PDB is named "1foo" and has one chain this should work: iterate first 1foo and poly, resn iterate last 1foo and poly, resn Otherwise you'll need to specify the selection more carefully, but first and last should still be appropriate. Cheers, -- Jason On Fri, Jan 25, 2013 at 4:16 PM, Ahmet yıldırım wrote: > Dear users, > > How can I learn the names of the residues that make up the N- and C- > terminals of a structure using Pymol? > > Thanks in advance > -- > Ahmet Yıldırım > > > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnnow-d2d > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] names of the residues
Dear users, How can I learn the names of the residues that make up the N- and C- terminals of a structure using Pymol? Thanks in advance -- Ahmet Yıldırım -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Piecewise rotations while viewing in surface
Hi Alex, We'll look into making this faster/smarter. To let you know, whenever you move an atom, it deforms the surface and causes a recalculation. The bigger your structure and higher quality the surface the longer this takes. Cheers, -- Jason On Tue, Jan 22, 2013 at 10:34 AM, Alex Truong wrote: > Hi All, > > This isn't really a problem per se, I'm just wondering. Is there any way > to more efficiently code the rotation protocol when the items being viewed > are in surface view? Maybe my computer isn't fast/strong enough or > something, but it seems whenever I try tweaking the position of one > subunits in relation to other subunits while everything is in surface view, > two redraws occur, and it's difficult for me to adjust with precision > because there's so much latency between positionings. Just a thought. > again, it's not really much of an issue, because I can just retoggle a new > view or something as a workaround, but it seems like manipulations while in > surface view can get a little GPU/CPU intensive. Are the redraws necessary? > > Alex > > > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnnow-d2d > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Active stereo on an iMac?
Hi Joachim, To my knowledge Apple does not support stereoscopic 3D. This has been a longstanding issue they still refuse to address. Cheers, -- Jason On Fri, Jan 25, 2013 at 11:34 AM, Joachim Reichelt < joachim.reich...@helmholtz-hzi.de> wrote: > Dear Mac-User > > is it possible to use active stereo, e.g. NVIDIA shutter glasses + ASUS > 3D Monitor on the latest iMac? > The GT 640M/650M are on the list under > http://www.nvidia.de/object/3d-vision-requirements-de.html > > -- > Joachim Reichelt > > > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnnow-d2d > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
