[Chimera-users] Surface render error in MD movie for morph conformation

Edel Fenix edel.fenix at gmail.com
Mon Jul 15 06:47:13 PDT 2019

Everything works at the basic level and has produced very useful data and
animations. I am most grateful for these tools and your help. The BIG
problem I have is that for some frames no surface is rendered at all. Other
parts "magically" disappear and reappear during the transformation.

*What I would want to do:*
1. There are missing structures/regions in need of repairs in the PDB files
I work with (see attached screenshot example). The files are for the same
protein but different regions missing in different models and they differ
some, ideally they shouldn't. I am using Chimera and Modeller to repair
these with loops/refinement. Ideally I would want to match/alter the
proteins so the gaps connect correctly and their amino acid structure is
the same for all models. I feel like this may be the/one cause for the
surface errors when rendering?

I've tried using modeller both locally and the web service so I have
verified installation, integration and function. Must I generate multiple
drafts and manually review and select the one best corresponding or is
there a way to get it performed for all models loaded of the same protein?
Further, if I want them to have the same genetic makeup, can I somehow use
one as reference to alter the others?

2. Align the protein snapshots from the configurational change using
matchmaker (works great!).

3. Use morph conformation to generate an animation of the configurational
change with surface rendered. Works sort of, with errors for some frames
where no surface is rendered at all or regions magically

4. Solve the surface error I get, see attached error message :(
If I use split copying from the example page, the model looks nothing like
it should look like and more like boiling gruel. I am not experienced with
Chimera but I feel like if I ensure the files have no gaps and are
structurally identical with the same amino acid makeup it may work as is?

*The problems with existing suggested solutions:*
The link below present 4 possible solutions linked from the error message.

Solution 1 looks nothing like what I want when rendered in my test.

Solution 2 does not solve the issue of disappearing structures magically
appearing again. I am not sure of the cause but could be because the models
have different structure/missing parts. If repaired and matched across all
protein models in the animation might work? If so, might not even give an
error message? Looks viable but does not solve the problem.

Solution 3 is not viable as I am looking to render the surface in details,
not "overall" look for large structures.

Solution 4 is not applicable as I do not want CPK.


Any help would be greatly appreciated, Edel

[image: Screenshot 2019-07-15 at 12.05.12.png]

[image: Screenshot 2019-07-15 at 14.30.00.png]
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