Mark, That doesn't work...yet. Generalized wildcarding is in the works for PyMOL.
Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . 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 > Mark A Saper > Sent: Wednesday, March 09, 2005 8:01 AM > To: Pymol > Subject: [PyMOL] combine distance objects > > How about > disable _dist* > enable _dist* > > Mark > _________________________________ > Mark A. Saper, Ph.D. > Associate Professor of Biological Chemistry Biophysics > Research Division, University of Michigan Chemistry Building > Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. > > sa...@umich.edu (734) 764-3353 fax > (734) 764-3323 > http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html > On Mar 8, 2005, at 11:27 PM, pymol-users-requ...@lists.sourceforge.net > wrote: > > > Send PyMOL-users mailing list submissions to > > pymol-users@lists.sourceforge.net > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > or, via email, send a message with subject or body 'help' to > > pymol-users-requ...@lists.sourceforge.net > > > > You can reach the person managing the list at > > pymol-users-ad...@lists.sourceforge.net > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of PyMOL-users digest..." > > > > > > Today's Topics: > > > > 1. Re: combine distance objects (Robert Campbell) > > 2. [Re: [PyMOL] combine distance objects] (Viktor Hornak) > > 3. Re: combine distance objects (Michael George Lerner) > > 4. RE: combine distance objects (Garcia, Tzintzuni I.) > > > > --__--__-- > > > > Message: 1 > > Date: Tue, 8 Mar 2005 10:55:20 -0500 > > From: Robert Campbell <r...@post.queensu.ca> > > To: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] combine distance objects > > > > Hi, > > > >> Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote: > >>> > >>> I want to create a lot of distance objects (in the > hundreds) between > >>> particular atomic pairs. Obviously I can make a script like the > >>> following, inserting the exact atomic selections that I want: > >>> > >>> distance distobj12 = (atom1), (atom2) distance distobj34 > = (atom3), > >>> (atom4) ... etc. > >>> > >>> However, I will end up with hundreds of distance object > controls on > >>> the right side of the pymol viewer. I want to have just a SINGLE > >>> distance object that contains all of the individual > distance objects > >>> combined. > >>> That way I could enable/disable the entire object with a single > >>> click, or change the color, etc. Hundreds of individual objects > >>> would be unmanageable. > >>> > >>> Is there a way to do this? Thanks, > > > > * Warren L. DeLano <war...@delanoscientific.com> [2005-03-07 13:46] > > wrote: > >> > >> This is a reasonable request, but no, it isn't possible > right now -- > >> sorry. > >> > >> If it isn't necessary to be able to turn the distances on and off, > >> then you can name them using a preceeding underscore "_" > so that they > >> are omitted from the object list. > > > > But in fact one *can* still turn them on and off, with the > "enable" or > > "disable" command on the command line: > > > > enable _dist1 > > disable _dist1 > > > > And it would be straightforward to put those commands within a loop: > > > > # turn them all off: > > for i in range(100): > > cmd.disable("_dist1%s" % i) > > > > # turn them all on: > > for i in range(100): > > cmd.enable("_dist1%s" % i) > > > > Change "100" to whatever is appropriate. > > > > Cheers, > > Rob > > -- > > Robert L. Campbell, Ph.D. > > <r...@post.queensu.ca> > > Senior Research Associate phone: > > 613-533-6821 > > Dept. of Biochemistry, Queen's University, fax: > > 613-533-2497 > > Kingston, ON K7L 3N6 Canada > > http://adelie.biochem.queensu.ca/~rlc > > PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 > > C0E2 > > > > > > --__--__-- > > > > Message: 2 > > Date: Tue, 08 Mar 2005 11:31:16 -0500 > > From: Viktor Hornak <hor...@csb.sunysb.edu> > > To: pymol-users@lists.sourceforge.net > > Subject: [Re: [PyMOL] combine distance objects] > > > > > > Robert Campbell wrote: > > > >> Hi, > >> > >>> Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote: > >>> > >>>> I want to create a lot of distance objects (in the hundreds) > >>>> between particular atomic pairs. Obviously I can make a script > >>>> like the following, inserting the exact atomic selections that I > >>>> want: > >>>> > >>>> distance distobj12 = (atom1), (atom2) distance distobj34 > = (atom3), > >>>> (atom4) ... etc. > >>>> > >>>> However, I will end up with hundreds of distance object > controls on > >>>> the right side of the pymol viewer. I want to have just > a SINGLE > >>>> distance object that contains all of the individual distance > >>>> objects combined. > >>>> That way I could enable/disable the entire object with a single > >>>> click, or change the color, etc. Hundreds of individual objects > >>>> would be unmanageable. > >>>> > >>>> Is there a way to do this? Thanks, > >>>> > >> > >> * Warren L. DeLano <war...@delanoscientific.com> [2005-03-07 13:46] > >> wrote: > >> > >>> This is a reasonable request, but no, it isn't possible > right now -- > >>> sorry. > >>> > >>> If it isn't necessary to be able to turn the distances on > and off, > >>> then you can name them using a preceeding underscore "_" so that > >>> they are omitted from the object list. > >>> > >> > >> But in fact one *can* still turn them on and off, with the > "enable" > >> or "disable" command on the command line: > >> > >> enable _dist1 > >> disable _dist1 > >> > >> And it would be straightforward to put those commands > within a loop: > >> > >> # turn them all off: > >> for i in range(100): > >> cmd.disable("_dist1%s" % i) > >> > >> # turn them all on: > >> for i in range(100): > >> cmd.enable("_dist1%s" % i) > >> > >> Change "100" to whatever is appropriate. > >> > >> Cheers, > >> Rob > >> > > > > Even though the scripting of this sort is flexible and will get you > > what you want, I'd still support Daniels's suggestion. Grouping > > multiple objects (not just distances) would be extremely useful > > because one can split the objects into functional or > logical units and > > collectively manipulate their properties (e.g. color, > state, graphical > > representation) and it would be more interactive than scripting the > > same functionality. I can imagine however, that > incorporating object > > hierarchy/grouping into PyMol may not be a trivial task... > > > > Cheers, > > -Viktor > > > > -- > > ============================= > > Viktor Hornak > > Center for Structural Biology > > SUNY at Stony Brook > > ============================= > > > > > > > > > > --__--__-- > > > > Message: 3 > > Date: Tue, 8 Mar 2005 11:42:28 -0500 (EST) > > From: Michael George Lerner <mler...@umich.edu> > > To: Robert Campbell <r...@post.queensu.ca> > > cc: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] combine distance objects > > > > > > On Tue, 8 Mar 2005, Robert Campbell wrote: > > > >> Hi, > >> > >>> Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote: > >>>> > >>>> I want to create a lot of distance objects (in the hundreds) > >>>> between particular atomic pairs. Obviously I can make a > >>>> script like the following, inserting the exact atomic > >>>> selections that I want: > >>>> > >>>> distance distobj12 = (atom1), (atom2) > >>>> distance distobj34 = (atom3), (atom4) > >>>> ... etc. > >>>> > > > >> But in fact one *can* still turn them on and off, with the > "enable" or > >> "disable" command on the command line: > >> > >> enable _dist1 > >> disable _dist1 > >> > >> And it would be straightforward to put those commands > within a loop: > >> > >> # turn them all off: > >> for i in range(100): > >> cmd.disable("_dist1%s" % i) > >> > >> # turn them all on: > >> for i in range(100): > >> cmd.enable("_dist1%s" % i) > >> > >> Change "100" to whatever is appropriate. > > > > I was just about to write something like this. In fact, I > have tons of > > files called something like x.py sprinkled around that do > things like > > > > ----------------------------------------- > > from pymol import cmd > > num_dist = 100 > > > > def show_dist(): > > """ show all of my distance objects """ > > for i in range(num_dist): > > cmd.enable('_dist%s'%i) > > > > def hide_dist(): > > """ hide all of my distance objects """ > > for i in range(num_dist): > > cmd.disable('_dist%s'%i) > > > > cmd.extend('sd',show_dist) > > cmd.extend('hd',hide_dist) > > ----------------------------------------- > > > > You could also try something cute like > > > > def show_dist(): > > dists = [name for name in cmd.get_names() if > cmd.get_type(name) == > > 'object:distance'] > > for name in dists: cmd.enable(name) > > > > etc. > > > > if you don't want to have to keep track of how many there are. > > > > -michael > > > > -- > > www.umich.edu/~mlerner | _ |Michael Lerner > > This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan > > it's a cheer-ocracy. | - against HTML email X | Biophysics > > -Torrence, Bring It On| / \ | mler...@umich > > > >> Cheers, > >> Rob > >> -- > >> Robert L. Campbell, Ph.D. > >> <r...@post.queensu.ca> > >> Senior Research Associate phone: > >> 613-533-6821 > >> Dept. of Biochemistry, Queen's University, fax: > >> 613-533-2497 > >> Kingston, ON K7L 3N6 Canada > >> http://adelie.biochem.queensu.ca/~rlc > >> PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 > A8F5 F635 C0E2 > >> > >> > >> ------------------------------------------------------- > >> SF email is sponsored by - The IT Product Guide > >> Read honest & candid reviews on hundreds of IT Products from real > >> users. > >> Discover which products truly live up to the hype. Start > reading now. > >> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > >> _______________________________________________ > >> PyMOL-users mailing list > >> PyMOL-users@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > > > > > > --__--__-- > > > > Message: 4 > > Subject: RE: [PyMOL] combine distance objects > > Date: Tue, 8 Mar 2005 14:11:39 -0600 > > From: "Garcia, Tzintzuni I." <tzgar...@utmb.edu> > > To: <pymol-users@lists.sourceforge.net> > > > > > UmVhZGluZyB0aGlzIHRocmVhZCBnYXZlIG1lIHRoZSBpZGVhIHRoYXQgbWF5Ym > UgYSBnb29 > > kIGZl > > > YXR1cmUgZm9yIGFuIHVwY29taW5nIHJlbGVhc2UgbWlnaHQgYmUgdGhlIGFkZG > l0aW9uIG9 > > mIHNv > > > bWV0aGluZyBsaWtlIGZvbGRlcnMgdG8gdGhlIG9iamVjdC9zZWxlY3Rpb24gYm > FyIG9uIHR > > oZSBy > > > aWdodCwgdGhpcyB3YXkgb2JqZWN0cyBhbmQgc2VsZWN0aW9ucyBjb3VsZCBiZS > Bncm91cGV > > kIGFu > > > ZCBhZmZlY3RlZCBhbGwgYXQgb25jZS4gIEkgdGhpbmsgdGhpcyB3b3VsZCBiZS > BleHRyZW1 > > lbHkg > > > 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Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
