Re: [PyMOL] image metadata plugin
Am Dienstag, 13. Februar 2007 schrieb DeLano Scientific: We have much work to do to make annotations more general and more accessible... Personally, i just store the session with the scene to reget an impression what I did, but you're right this does not explain what you actually see. Cheers Martin -- Liberty is always dangerous, but it is the safest thing we have. (Harry Emerson Fosdick)
[PyMOL] image metadata plugin
Hello everybody, I just had an idea for a plugin, but I know I won't have time to make it, so...I thought I would mention it in the hope someone else can. :) Basically, I often make snapshot images (pngs) of scenes. The problem with doing this is that I have learned to be careful to make the filename tell me what it is. For example : nacatgrip_1fmn_201_203.png. Otherwise, I look at the picture 6 months later and wonder what it was. This would be a lot easier if there was a snapshot plugin that could store an image and metadata about the image - the path to the structure file, structure names, comments, etc. In fact, a truly clever thing would be to store the session along with the image, and you could browse sessions by looking at thumbnail images... Anyway, just a thought. gilleain torrance
Re: [PyMOL] image metadata plugin
I was actually thinking about a related approach. Could one include a feature in PyMOL allowing the user to save notes with a session? I've really come to like saving sessions but going back to them later I often wonder what the objects are exactly, what the views were meant to represent, which views are saved, which color scheme I used. Briefly, details that help recreate scenes or images. I've sent emails not too long ago arguing that one should simply write scripts, and all will be obvious. I stand corrected (thanks, Warren) because it won't. If you're pdb file is gone, your script will only take you on a long search through the dark corners of all available hard disks but not to brilliant figures. Gilleain, I'm not sure you would want to save a session with every png because that would inflate the size of your image significantly. But it'd sure be cool to have a snapshot saved in the session file to have a thumbnail to look at. Andreas On 2/12/07, gilleain torrance gilleain.torra...@gmail.com wrote: Hello everybody, I just had an idea for a plugin, but I know I won't have time to make it, so...I thought I would mention it in the hope someone else can. :) Basically, I often make snapshot images (pngs) of scenes. The problem with doing this is that I have learned to be careful to make the filename tell me what it is. For example : nacatgrip_1fmn_201_203.png. Otherwise, I look at the picture 6 months later and wonder what it was. This would be a lot easier if there was a snapshot plugin that could store an image and metadata about the image - the path to the structure file, structure names, comments, etc. In fact, a truly clever thing would be to store the session along with the image, and you could browse sessions by looking at thumbnail images... Anyway, just a thought. gilleain torrance
Re: [PyMOL] image metadata plugin
Andreas, Gilleain, others, Agreed -- there is strong demand for annotations within scenes session files. Currently this is only possible when you define (or redefine a scene) using the command line: scene 001, store, This is the view of the binding site. And note that you can pass in a multi-line string using Python: cmd.scene(001,store,This is the view of the binding site.\nPlease note the ligand in yellow.) We have much work to do to make annotations more general and more accessible... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Andreas Forster Sent: Monday, February 12, 2007 3:32 AM To: gilleain torrance Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] image metadata plugin I was actually thinking about a related approach. Could one include a feature in PyMOL allowing the user to save notes with a session? I've really come to like saving sessions but going back to them later I often wonder what the objects are exactly, what the views were meant to represent, which views are saved, which color scheme I used. Briefly, details that help recreate scenes or images. I've sent emails not too long ago arguing that one should simply write scripts, and all will be obvious. I stand corrected (thanks, Warren) because it won't. If you're pdb file is gone, your script will only take you on a long search through the dark corners of all available hard disks but not to brilliant figures. Gilleain, I'm not sure you would want to save a session with every png because that would inflate the size of your image significantly. But it'd sure be cool to have a snapshot saved in the session file to have a thumbnail to look at. Andreas On 2/12/07, gilleain torrance gilleain.torra...@gmail.com wrote: Hello everybody, I just had an idea for a plugin, but I know I won't have time to make it, so...I thought I would mention it in the hope someone else can. :) Basically, I often make snapshot images (pngs) of scenes. The problem with doing this is that I have learned to be careful to make the filename tell me what it is. For example : nacatgrip_1fmn_201_203.png. Otherwise, I look at the picture 6 months later and wonder what it was. This would be a lot easier if there was a snapshot plugin that could store an image and metadata about the image - the path to the structure file, structure names, comments, etc. In fact, a truly clever thing would be to store the session along with the image, and you could browse sessions by looking at thumbnail images... Anyway, just a thought. gilleain torrance
