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From: Huiying Li <hl...@br...> - 2003-10-29 23:52:01
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I am wondering how to load the O/BRIX maps into Pymol using version 0.92. Is there a default file extension, say *.dsn6, for O map, or need to define the map format with a keyword? Thanks for any help. -------------------------------------------------- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: hl...@br... -------------------------------------------------- |
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From: <rb...@uc...> - 2003-10-30 01:14:29
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Dear All, I want to look at my structure in PyMOL and, having centered on something defined by my selection script, pick atoms nearby and see what residues they belong to. That is, I want to pick select an atom with the mouse and have its name, residue name and residue number appear on screen, like it does in O. I figured out that [Ctrl] + Left-Mouse-Button selects the atom as "lb", and that the command 'label (lb),"%s %s %s" % (name,resn,resi)' gives me the label I want. Now how could I get something like that to appear as a menu function in the GUI so I don't have type it in all the time? Can it be a command executed as part of my startup script? Maybe some function like this already exists, otherwise I think it is a very useful thing. regards, Richard Baxter |
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From: Warren L. D. <wa...@de...> - 2003-11-01 02:37:18
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Richard,
It's not GUI, but you could simply bind a function key such as F1 to
that command:
cmd.set_key('F1',lambda :cmd.label("(lb)",'"%s %s
%s"%(name,resn,resi)'))
You might then want to bind 'F2' to something which hides all labels.
cmd.set_key('F2',cmd.label)
Cheers,
Warren
--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of
> rb...@uc...
> Sent: Wednesday, October 29, 2003 5:14 PM
> To: pym...@li...
> Subject: [PyMOL] labeling atoms in GUI
>
>
> Dear All,
>
> I want to look at my structure in PyMOL and, having centered
> on something defined by my selection script, pick atoms
> nearby and see what residues they belong to. That is, I want
> to pick select an atom with the mouse and have its name,
> residue name and residue number appear on screen, like it does in O.
>
> I figured out that [Ctrl] + Left-Mouse-Button selects the
> atom as "lb", and that the command 'label (lb),"%s %s %s" %
> (name,resn,resi)' gives me the label I want. Now how could I
> get something like that to appear as a menu function in the
> GUI so I don't have type it in all the time? Can it be a
> command executed as part of my startup script?
>
> Maybe some function like this already exists, otherwise I
> think it is a very useful thing.
>
> regards,
>
> Richard Baxter
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.
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> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>
|
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From: <rb...@uc...> - 2003-11-01 17:56:20
|
Thank Warren, that works great -RB
Quoting "Warren L. DeLano" <wa...@de...>:
> Richard,
>
> It's not GUI, but you could simply bind a function key such as F1 to
> that command:
>
> cmd.set_key('F1',lambda :cmd.label("(lb)",'"%s %s
> %s"%(name,resn,resi)'))
>
> You might then want to bind 'F2' to something which hides all labels.
>
> cmd.set_key('F2',cmd.label)
>
> Cheers,
> Warren
>
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of
> > rb...@uc...
> > Sent: Wednesday, October 29, 2003 5:14 PM
> > To: pym...@li...
> > Subject: [PyMOL] labeling atoms in GUI
> >
> >
> > Dear All,
> >
> > I want to look at my structure in PyMOL and, having centered
> > on something defined by my selection script, pick atoms
> > nearby and see what residues they belong to. That is, I want
> > to pick select an atom with the mouse and have its name,
> > residue name and residue number appear on screen, like it does in O.
> >
> > I figured out that [Ctrl] + Left-Mouse-Button selects the
> > atom as "lb", and that the command 'label (lb),"%s %s %s" %
> > (name,resn,resi)' gives me the label I want. Now how could I
> > get something like that to appear as a menu function in the
> > GUI so I don't have type it in all the time? Can it be a
> > command executed as part of my startup script?
> >
> > Maybe some function like this already exists, otherwise I
> > think it is a very useful thing.
> >
> > regards,
> >
> > Richard Baxter
|
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From: Warren L. D. <wa...@de...> - 2003-10-30 18:17:35
|
Huiying, PyMOL will recognize the following extensions for O maps: .o .omap .brix The following will render the entire brick at 1 sigma: load map.o isomesh m1, map, 1 Or if you have a pdb load model.pdb isomesh m1, map, 1, 100/, 8 will give you an 8 A brick around residue 100, etc. Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Huiying Li > Sent: Wednesday, October 29, 2003 3:52 PM > To: pym...@li... > Subject: [PyMOL] How to load O/BRIX map > > > > I am wondering how to load the O/BRIX maps into Pymol using > version 0.92. Is there a default file extension, say *.dsn6, > for O map, or need to define the map format with a keyword? > > Thanks for any help. > > -------------------------------------------------- > Huiying Li, Ph. D > Department of Molecular Biology and Biochemistry > Natural Sciences I, Rm 2443 > University of California at Irvine > Irvine, CA 92697, USA > Tel: 949-824-4322(or -1953); Fax: 949-824-3280 > email: hl...@br... > -------------------------------------------------- > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/p> ymol-users > |
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