[Chimera-users] hbonds and distances movie script questions

Elaine Meng meng at cgl.ucsf.edu
Fri May 5 13:41:02 PDT 2017


You’re welcome!  I often start with “focus” but then make subsequent scale and X/Y-move adjustments since (as you saw) focus often leaves large margins.  If you work out the series of scale and move commands needed after windowsize and focus, you could put them in your script and avoid having to save a session with the position…but if you were already starting with a saved session anyway, generating the position by hand and saving it is easier.
Best,
Elaine


> On May 5, 2017, at 12:42 PM, mfellner at msu.edu wrote:
> 
> Dear Elaine
> 
> Thank you for the promt reply and the detailed suggestions.
> The semicolon separator is a nice hint, I will use that a lot from now on and that fixed my hbonds issue.
> 
> I used the setattr p labelColor 0.9,0.9,0.0,0.0 suggestion to deal with the labels, thanks for that trick. I did not try to move the labels, undisplaying them at some point is good enough for me.
> 
> And lastly I am now using windowsize to get rid of edges, had to adjust the script a little bit when stuff didnt fit anymore, but it worked out well. I normally use "focus" to get to a nice centered position but I will consider the savepos in the future.
> 
> Thanks again, best wishes
> Matthias
> 
> Quoting Elaine Meng <meng at cgl.ucsf.edu>:
> 
> > Hi Matthias,
> > Thanks for the kind words!  Sounds like an impressive movie, not to
> > mention a very long script!
> >
> > The ?hbond? option ?lineType? was added after the 1.11 release, so
> > you?d need a 1.12 daily build to have it available.
> > <http://www.rbvi.ucsf.edu/chimera/docs/relnotes/snapshot.html>
> >
> > In your current script, if you combine two commands on the same line
> > with semicolon separator, that avoids showing the intermediate state.
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
> >
> > One way to show/hide pre-existing hbonds is with setattr, for example
> >
> > setattr g display false
> > setattr g display true
> >
> > However, that includes ALL pseudobonds, so you may need to experiment
> > with including an atomspec at the end to get only the pseudobond
> > group of interest.  You can also set the distance labels to nothing,
> > but that loses their contents:
> >
> > setattr g label ?"
> >
> > (that was two double quotation marks at the end? again may want to
> > append some atomspec to limit scope).  Here?s a sneaky idea, you
> > could make the labels 100% transparent to hide them and then recolor
> > to show them again.
> >
> > setattr p labelColor 0.9,0.9,0.0,0.0
> > setattr p labelColor 0.9,0.9,0.0,1.0
> >
> > Although the label/rlabel commands have an offset, I don?t know of
> > any command way to adjust offset of a pseudobond label, sorry.  You
> > could control position in 2D exactly and fade in/out with a 2D label,
> > but depends how many there are? could be a lot of work.
> >
> > As for minimizing whitespace, I use ?windowsize? to make sure I?m
> > using a constant size, and  ?scale? and ?move x? and ?move y?
> > commands to make the molecules fill it to my satisfaction (or if you
> > are starting with a session, you can use these until you get what
> > want, then ?savepos? and re-save session? later, as in after
> > restoring the session to run the script, you can ?reset? to that
> > named position.  Often I have multiple saved positions and can use
> > ?reset? to glide from one to the other in a movie.)
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> >
> >> On May 4, 2017, at 2:52 PM, mfellner at msu.edu wrote:
> >>
> >> Good day
> >> I am making a movie by writing a chimera command script and I
> >> searched through existing chimera topics but I could not find a
> >> solution for these issues:
> >>
> >> Is there a command to display hbonds, I have made a script now to
> >> select residues and find the hbonds, even color + line width them
> >> and then I get rid of them later by ~hbonds.
> >>
> >> What I would prefer is to have them premade (so I dont need to
> >> select residues during the movie) but not displayed, later I then
> >> displayed and undisplayed them with a scipt command.
> >>
> >> Also I could not get the lineType command to work inside the hbond
> >> script (lineWidth worked fine), I had to use the setattribute
> >> command in a second script line, so for a splitsecond I have a
> >> different linetype displayed.
> >>
> >> The second question is about distance labelling. I can set the
> >> options in the gui and then distances are displaed by a script with
> >> the distance in Angstrom shown. Is there a way to undisplay the
> >> distance label later but keep the dashed line, so change the gui
> >> option with a script?
> >>
> >> Also I assume this is not possible, is there a script to change
> >> where the label will show up next to the line? I have not looked
> >> into displaying and undisplaying 2D labels with scripts, maybe that
> >> is a possibility?
> >>
> >> Lastly which is not that important, is there any way to trim the
> >> corners easily? I think I am recording a lot of white space to the
> >> left and right throughout the movie, if I resize the window the
> >> molecule gets focused, so its no longer exactly where I had it
> >> related to the corners and I think I would have to adjust the script.
> >>
> >> Thank you so much, I hope I made my questions clear, chimera is an
> >> awesome program, movie is 21 minutes at the moment.
> >>
> >> Best wishes
> >> Matthias Fellner Michigan State University
> >
> >




More information about the Chimera-users mailing list