[Chimera-users] hbonds and distances movie script questions

mfellner at msu.edu mfellner at msu.edu
Fri May 5 12:42:27 PDT 2017

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

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
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