RE: [PyMOL] How to apply state-specific colours?
Hubert, The trick for doing this is to load each state into a "discrete" object, which maintains separate atoms for each state. load $TUT/1hpv.pdb, discrete=1 load $TUT/1hpv.pdb, discrete=1 color red, state 1 color blue, state 2 Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC 400 Oyster Pt. Blvd., Ste 213 South San Francisco, CA 94080 (650)-346-1154 Fax:(650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Hubert Kettenberger > Sent: Friday, October 15, 2004 4:59 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] How to apply state-specific colours? > > Dear all! > > I would like to prepare a an animation in which I would like > to follow one certain residue on its journey through an > enzyme in a stepwise manner. To do so, I would like to color > a certain residue, say, red in state one and grey in all > other frames. In frame 2, the next residue should be red, all > others grey. Frame three has the third residue red, all > others grey etc. > > Is there a command like > > color red, residue 1 and state 1 > color red, residue 2 and state 2 > etc., > > i.e. is there a way to apply colours selectively to a certain state? > > Thanks in advance for your ideas! > > Hubert > > > > > > --- > This SF.net email is sponsored by: IT Product Guide on > ITManagersJournal Use IT products in your business? Tell us > what you think of them. Give us Your Opinions, Get Free > ThinkGeek Gift Certificates! Click to find out more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] How to apply state-specific colours?
Hubert,
You need to use the mdo command, e.g.
cmd.mclear()
cmd.mset("1 x10")
# Set all residues to white
cmd.mdo(1, "color white")
# Colour a residue
cmd.mdo(2, "color red, (i;51)")
# Clear colour of previous residue, and highlight a new one
cmd.mdo(3, "color white, (i;51); color red, (i;184)")
I tried to do this using the script language, but
mdo 2, color red, (i;51)
causes an error on my version (Linux 0.98beta05) - I think this is a bug.
Gareth
On Fri, 15 Oct 2004, Hubert Kettenberger wrote:
> Dear all!
>
> I would like to prepare a an animation in which I would like to follow
> one certain residue on its journey through an enzyme in a stepwise
> manner. To do so, I would like to color a certain residue, say, red in
> state one and grey in all other frames. In frame 2, the next residue
> should be red, all others grey. Frame three has the third residue red,
> all others grey etc.
>
> Is there a command like
>
> color red, residue 1 and state 1
> color red, residue 2 and state 2
> etc.,
>
> i.e. is there a way to apply colours selectively to a certain state?
>
> Thanks in advance for your ideas!
>
> Hubert
>
>
>
>
>
> ---
> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> Use IT products in your business? Tell us what you think of them. Give us
> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
> http://productguide.itmanagersjournal.com/guidepromo.tmpl
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
---
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548 http://www.ebi.ac.uk/~gareth
[PyMOL] How to apply state-specific colours?
Dear all! I would like to prepare a an animation in which I would like to follow one certain residue on its journey through an enzyme in a stepwise manner. To do so, I would like to color a certain residue, say, red in state one and grey in all other frames. In frame 2, the next residue should be red, all others grey. Frame three has the third residue red, all others grey etc. Is there a command like color red, residue 1 and state 1 color red, residue 2 and state 2 etc., i.e. is there a way to apply colours selectively to a certain state? Thanks in advance for your ideas! Hubert
