[Chimera-users] Pseudobonds disappearing during morphing movie

Elaine Meng meng at cgl.ucsf.edu
Thu May 12 09:25:09 PDT 2011

Hi Alan,
I haven't tried the whole script yet (can you send me the PDB files?  I'll keep them private, i.e. only for the development group here if you send them just to me) but will try to address the low-hanging fruit in your set of questions:

(A) lines thinner in saved movie.  In general, lines such as silhouette edges and pseudobonds may turn out thinner in saved images and movies when you are doing "supersampling," which initially saves a larger image and samples it down to the final requested size.  You can check if this is the issue by using File... Save Image to save a single image -- the dialog should report the maximum achievable linewidth given the requested size and amount of supersampling.  The reason is that there is an upper limit to how fat your computer can draw the lines (at least via the method used by Chimera).  If you have 2x2 supersampling, for example, Chimera will try to make the lines twice as fat in the initial larger image, but may run into this upper limit.  Then when the image is sampled down to the final size, the lines may not be as thick as they appear in the interactive display.  You could try using lower supersampling.  Also make sure you are using a recent version (1.5.3 candidate or 1.6) because there was a lines-too-thin-in-images bug a couple of months ago.

(B) setattr "p" vs. "g" -- this is because some attributes are for individual pseudobonds (p) and some attributes are defined for whole pseudobond groups (g).   Individual pseudobonds don't have a linewidth attribute, it is set at the group level.  All the pseudobonds in that group (for example, hydrogen bonds) would get the same linewidth and it is not possible to make different ones in the same group have different widths.  If you are looking at the Selection Inspector or some other attributes inspector, it will show you which attributes are for individual pseudobonds and which are for groups.  The balloon help will give the attribute name and allowed values.

I will try to look at your other issues and get back to you,
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 12, 2011, at 8:54 AM, Alan Cheung wrote:

> Hi there - i'm scripting a complex movie and am having problems with
> pseudobonds during morphing.  Script is pasted at the end.
> Part of the movie contains a morph between two structures, both of
> which are missing the same amino acid segment.  Loading the two
> structures show the pseudobond for the missing residues and the
> resulting morph also contains the same pseudobond.
> I've been changing the thickness of the pseudobond with :
> setattr g lineWidth 8
> and while the two static structures and the morph in the chimera
> window have a thicker pseudobond, the resulting movie (encoded to
> .mov) does not.  Am i doing something wrong?
> Alan
> p.s. incidentally, when morphing by script, if one includes "nogui
> true" with the "morph movie" command, pseudobonds aren't kept in the
> morph at all.  A bug?
> p.p.s. can someone explain to me the difference between "setattr g"
> and "setattr p"?  I've read the manual but i don't understand why only
> the former seems to work for me.
> ## movie script
> open model1.pdb
> open model2.pdb
> morph start #0 frames 50 name morph1 method linear
> morph interpolate #1 name morph1
> morph movie name morph1
> coordset #2 1,1
> setattr g lineWidth 8
> ~modeldisplay #
> movie record supersample 3 directory ~/TEMP/
> modeldisplay #2
> coordset #2 1,51 ; wait 51
> movie stop
> movie encode output morph1.mov

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