Re: [PyMOL] Color starting midway between adjacent chains
Hi David, Thanks. But what about between all chains? I mean, so between chains B and C and so on. I need a generic script that can be applied for any protein. Thanks! ?? ??: David Hallmailto:li...@cowsandmilk.net ?? ??: ?2014?? ?3?? ?4?? ?2?:?57 ?? ??: I-Ji Jungmailto:u5205...@anu.edu.au ??: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net set_bond line_color, color_name, n. CA+CB will color all bonds between CA and CB whatever color you put in as color_name If you're doing sticks instead of lines, you should use set_bond stick_color, color_name, n. CA+CB -David On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung u5205...@anu.edu.aumailto:u5205...@anu.edu.au wrote: Hi everyone, I have just started learning Pymol and PyMol seems to use a different colour convention than Molmol, i.e. the colour of a side chain starts half way between the CA and CB atoms (instead of starting at the CA). Do you know whether there would there be a way to start the side chain colour at the CA without changing the colour of the backbone? Any help will be greatly appreciated! Thank you. I-Ji -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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.nethttp://www.mail-archive.com/pymol-users%40lists.sourceforge.net -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk___ 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] forward and backward keyboard shortcuts
Hi, Is there any keyboard shortcut to move to the next or the previous state of an object, namely something equivalent to forward and backward commands? -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk___ 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] forward and backward keyboard shortcuts
Thomas, Right and left arrow keys. Cheers, Jason On Tuesday, March 4, 2014, Thomas Evangelidis teva...@gmail.com wrote: Hi, Is there any keyboard shortcut to move to the next or the previous state of an object, namely something equivalent to forward and backward commands? -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.grjavascript:_e(%7B%7D,'cvml','tev...@pharm.uoa.gr'); teva...@gmail.comjavascript:_e(%7B%7D,'cvml','teva...@gmail.com'); website: thomasevangelidishomepagehttps://sites.google.com/site/thomasevangelidishomepage/ -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk___ 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] command to deactivate/hide an object
Hi, Is there some command that deactivates an object, namely something equivalent to clicking on an object name at the object panel? I am loading multiple files and render them as sticks but the memory overflows. If there was a command to keep the stick representation but deactivate the object (hide it) then I could visualize the structures one by one once they are all loaded -which is actually what I want. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk___ 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] command to deactivate/hide an object
Hi Thomas, sure, it's enable and disable. http://pymolwiki.org/index.php/Enable http://pymolwiki.org/index.php/Disable Cheers, Thomas On 04 Mar 2014, at 13:25, Thomas Evangelidis teva...@gmail.com wrote: Hi, Is there some command that deactivates an object, namely something equivalent to clicking on an object name at the object panel? I am loading multiple files and render them as sticks but the memory overflows. If there was a command to keep the stick representation but deactivate the object (hide it) then I could visualize the structures one by one once they are all loaded -which is actually what I want. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk ___ 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] command to deactivate/hide an object
A super hack way is this:
hide all
python
my_list = cmd.get_object_list() # gets all objects loaded
index = 0
def next_thing():
global index
cmd.show('sticks', my_list[index])
cmd.hide('sticks', my_list[index - 1])
index += 1
def last_thing():
global index
index -= 1
cmd.show('sticks', my_list[index - 1])
cmd.hide('sticks', my_list[index])
cmd.extend('next_thing', next_thing)
cmd.extend('last_thing', last_thing)
python end
Then you can type “next_thing” or “last_thing” to cycle through your objects.
Jordan
On Mar 4, 2014, at 4:03 PM, Thomas Holder thomas.hol...@schrodinger.com wrote:
Hi Thomas,
sure, it's enable and disable.
http://pymolwiki.org/index.php/Enable
http://pymolwiki.org/index.php/Disable
Cheers,
Thomas
On 04 Mar 2014, at 13:25, Thomas Evangelidis teva...@gmail.com wrote:
Hi,
Is there some command that deactivates an object, namely something
equivalent to clicking on an object name at the object panel? I am loading
multiple files and render them as sticks but the memory overflows. If there
was a command to keep the stick representation but deactivate the object
(hide it) then I could visualize the structures one by one once they are all
loaded -which is actually what I want.
thanks,
Thomas
--
==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.
--
Subversion Kills Productivity. Get off Subversion Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
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--
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[PyMOL] Pseudo AxPyMol
I’m using powerpoint for mac, so I don’t have the luxury of Axpymol (any plans for OSX?) I wanted to make a movie that iterates through scenes of a PyMol session and pauses there until I hit the “next” button on powerpoint. My workaround was to simply make a movie that went trough all scenes and break them up into separate movies. When I hit “next” on the clicker for powerpoint, it would make that movie appear on the slide and it would be appear to be a continuation of the last movie. I was wondering if there is a way to render movies by frame. For instance only tell PyMol to render frames 1-30. Then in another movie 31-60 etc. Perhaps the simplest way would be to dump every frame as a separate .png, and reconstruct manually. Any thoughts on this? How to make it easier, or does this seem like the easiest way. Jordan -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk ___ 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] Pseudo AxPyMol
Hi Jordan, I don't know if this helps you, but you can start pymol in presentation mode (by saving a session with scenes and then edit the name to psw instead of pse). Then you will immediately go full-screen and hitting space (or the clicker I presume) will let you move to the next scene. This might not be fancy enough, but I thought I'd mention it. One other thing you could do is to save the files in the movie (instead of making a movie directly) and then make small movies from the output png's. Hope this helps, Folmer 2014-03-04 23:41 GMT+01:00 Jordan Willis jwillis0...@gmail.com: I'm using powerpoint for mac, so I don't have the luxury of Axpymol (any plans for OSX?) I wanted to make a movie that iterates through scenes of a PyMol session and pauses there until I hit the next button on powerpoint. My workaround was to simply make a movie that went trough all scenes and break them up into separate movies. When I hit next on the clicker for powerpoint, it would make that movie appear on the slide and it would be appear to be a continuation of the last movie. I was wondering if there is a way to render movies by frame. For instance only tell PyMol to render frames 1-30. Then in another movie 31-60 etc. Perhaps the simplest way would be to dump every frame as a separate .png, and reconstruct manually. Any thoughts on this? How to make it easier, or does this seem like the easiest way. Jordan -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk ___ 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 -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk___ 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
