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