Re: [PyMOL] (small) Pymol feature request--filter for edit settings window
Hey Michelle, Ezequiel Panepucci wrote grepset, a little script that allows you to do exactly what you want and even more. No need even to open the edit settings menu, just type 'grepset ray', and you're cruising. Get grepset from http://www.pymolwiki.org/index.php/Grepset and put it into your .pymolrc file as 'run /path/to/grepset.py'. Life is good. Andreas Michelle Gill wrote: While we're discussing ways to make our favorite program a little better, I had an idea I thought I'd throw out there... While making some figures the other day, I found myself scrolling endlessly through the edit settings menu (under Setting --> Edit All) a number of times, mostly to locate a relatively small number of settings related to ray tracing. This got me thinking about a way to improve access to the many wonderful features that have been added to PyMOL. The solution I came up with is a filter line which could be placed directly above the window listing all the settings. Users could then type a word, say "ray" or "cartoon", and only the settings containing this word would be shown. The best example of a program containing this feature is the "about:config" window in Firefox. When you open a browser and type "about:config" instead of an address, a window containing hundreds of settings appears. At the top is a filter bar which you can use to pare down the number of settings listed below. I think this would be a great addition to PyMOL and would help users familiarize themselves with the many new settings which have been (and will be) implemented. :) Perhaps others have even better solutions to this problem. The use of a filter is just the first idea which came to my mind. I think it would be relatively easy to implement, although my python programming skills are somewhat limited. Thanks, Michelle Gill -- --> Andreas Förster <-- 8 rue Doudart de Lagrée, 38000 Grenoble ++33.(0)438.866201 and ++33.(0)456.452000 www.biochem.utah.edu/~andreas docandreas.blogspot.com
RE: [PyMOL] align and iterate residues
Andrea, This feature will be present with alignment visualization, but that is not quite ready yet... 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 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Andrea Spitaleri > Sent: Wednesday, April 19, 2006 5:04 AM > To: pymol-users > Subject: [PyMOL] align and iterate residues > > Hi all, > I found very nice the align command in order to align domains > within huge complex. However, I was wondering whether is it > possible to iterate on the superimposed structure in order to > know "which with wich" residues. Creating the object, I > cannot iterate on it. > Thanks for any suggestion > > Regards > > andrea > -- > "La conoscenza libera il genere umano dalla superstizione" > J. Watson > > > --- > This SF.Net email is sponsored by xPML, a groundbreaking > scripting language that extends applications into web and > mobile media. Attend the live webcast and join the prime > developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642 > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
Re: [PyMOL] a scaling question
Fei, The easiest way would be to use get_view/set_view. 1. Move your first frame pdb around until you're happy with the view 2. type get_view (pymol viewer window, or pymol gui window), and save the output in a new text file (I'd call it view.pml, but that's just me) 3. Load all of your frames in a script (which you're probably doing already), change "load frame2.pdb" to load frame2.pdb ; @view.pml" for all of your frames (or change whatever loop structure you're using). This way all of your frames will be in the same scale, as well as orientation (which may not be what you're looking for). If you only want to control scale (not orientation), then you could probably work something up that only takes the scale parameters out of the orientation matrix. Hope this helps, Pete > Hi!: > I met a scaling problem. > I created many pdb files along one trajectory of DNA movement. I loaded each pdb file in pymol to create a picture, that is, one frame of the trajectory. Pymol shows each molecule in an optimal size automatically according the general shape of the molecular. The shape of the molecule along trajectory kept changing so that the size of the molecule also kept > changing. When I connected all the time frames together, I saw the funny effect that the molecule was jumping back and forth. > How can I put the molecule in the different time frames in exactly the same size? > Thanks! > Fei > > > > > > --- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] Pymol / C
Hi! I must develop a program in language C, in which I have to execute Pymol and to invocate functions as select or translate inside my program. I am writing to enquire how can I do it, how can I invocate the Pymols functions. Thanks! __ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com
[PyMOL] a scaling question
Hi!: I met a scaling problem. I created many pdb files along one trajectory of DNA movement. I loaded each pdb file in pymol to create a picture, that is, one frame of the trajectory. Pymol shows each molecule in an optimal size automatically according the general shape of the molecular. The shape of the molecule along trajectory kept changing so that the size of the molecule also kept changing. When I connected all the time frames together, I saw the funny effect that the molecule was jumping back and forth. How can I put the molecule in the different time frames in exactly the same size? Thanks! Fei
[PyMOL] align and iterate residues
Hi all, I found very nice the align command in order to align domains within huge complex. However, I was wondering whether is it possible to iterate on the superimposed structure in order to know "which with wich" residues. Creating the object, I cannot iterate on it. Thanks for any suggestion Regards andrea -- "La conoscenza libera il genere umano dalla superstizione" J. Watson
Re: [PyMOL] RE: povray image mapping and default pigments
Hi,
Actually, one of the first of these images I made was of conotoxin floating
above a see. Will that do? I'd still have to add the sunset though ;) O, and
the checkered beach...
In regards the problem of Seth, it's good you've solved it. It is possible
though to remove all statements about textures from a mesh2 object. You have
to remove both the texture_list as well as the references to the textures.
If you don't know what I'm talking about, you can check out the povray
manual on mesh2. Besides, you may be better off using statements like
union { #include "moleculedef.inc" pigment {image_map{ " mypicturehere.gif"
}} }
rather than changing the #default for that. Especially handy if you can find
a snowboarder object you want to merge with your kinase piste...
By the way, I may try to write a script to process the mesh2 file from Pymol
to strip out texture statements (and add them as #declares) if I can find
some time. Also, it would be so nice to have a tidied up mesh2 file, rather
than an endless set of triangles. mesh2 can be so much better (smaller, more
efficient, easier to handle).
Cheers,
Tsjerk
On 4/19/06, Thomas Stout wrote:
>
>
>
> I'm glad you solved your problem, but more importantly when are we going
> to get to see this picture of an easter bunny on some wood-textured
> rendition of a half-submerged albumin glowing softly in the warm lights of a
> double sunset over an infinite lake lapping at the shores of a checkered
> beach???
>
> :)
>
> -Tom
>
>
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net on behalf of Seth Harris
> Sent: Tue 4/18/2006 2:45 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] RE: povray image mapping and default pigments
>
> To answer my own question...instead of entirely taking out the
> pigment{blah
> blah blah} statements from the texture_lists in the povray input as used
> to
> work, I found that in this case replacing them with "pigment {}"
> statements
> was still a permissible syntax and also allowed a #default pigment
> declaration in the header file to override the molecular scene
> descriptions.
>
> If you have no idea what I'm talking about, it's probably for the best.
>
> Funny how often just describing your problem to someone else allows you to
> lay it out logically enough to lead you to a solution...thanks for
> listening!
>
> -Seth
>
> -- Forwarded message --
> From: Seth Harris
> Date: Apr 18, 2006 2:18 PM
> Subject: povray image mapping and default pigments
> To: pymol-users@lists.sourceforge.net
>
>
> This is for the povray gurus out there...
>
> Occasionally I muck around with the time-consuming practice of trying to
> map
> pictures onto molecular surfaces with povray.
>
> I had this working to some extent, but something has changed (I think with
> the povray file format produced by pymol & make_pov where now there are
> fancy texture_list texture and pigment statements, rather than simple
> "pigment" ones.)
>
> In the past, I set it up so that the povray file has a header (cameras,
> lights, etc.) separate from the molecular scene description. Then I would
> usually edit the header to apply some #default texture or pigment to use
> the
> povray parlance. So the approach I used to use was to strip out all the
> pigment {} statements from the molecular scene descriptor povray input
> with
> a perl script, and then use the #default pigment {image_map{ "
> mypicturehere.gif" }} syntax in the header to map the image on to the
> surface...the practical uses of having a picture of someone, say,
> snowboarding down a mountain mapped onto the surface of some kinase are
> just
> endless. But that aside, the problem now is that these newer texture_list
> statements aren't so amenable to this global pigment removal thing, and I
> haven't quite figured out how best to get around this. (Couldn't remove
> them
> entirely and putting in the image_map pigment thing didn't seem to work,
> although maybe I just didn't get the right combination of open and closed
> brackets {?}}})
>
> Anyone have any experiences along these lines? As near as I can tell,
> there
> was some switch in smooth triangle definitions with Povray 3.5 which was
> capitalized on by some pymol 0.98 edition. Perhaps I have to go back to an
> old archived version of pymol? Or, more sensibly, perhaps I should
> recognize
> that pictures of easter bunnies or whatever don't belong on some
> wood-textured rendition of a half-submerged albumin, glowing softly in the
> warm light(s) of a double sunset over an infinite lake lapping at the
> shores
> of a checkered beach. But for some reason journal editors seem to enjoy
> this.
>
> Thanks,
> Seth
>
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