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

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 15 09:23:09 PDT 2019

Hi Edel,
This all sounds like basically the same problem, MSMS surface calculation failures.  This is a commonly encountered problem in Chimera especially for weird (less well packed) structures such as may result from modeling and/or morphing.

The surface workarounds page you already looked at is exhaustive for Chimera.  

The other solution is to use ChimeraX, at least for the surface-calculation and rendering part. ChimeraX surface calculation is totally different and much more robust. You could still use Chimera for parts of your workflow if you wanted, but ChimeraX also has modeller interface (plus command-line version), matchmaker command, and morph command.  Command syntax is slightly different but generally similar, and I prefer ChimeraX’s morph command because it’s both easier to use and has more options.


I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 15, 2019, at 6:47 AM, Edel Fenix <edel.fenix at gmail.com> wrote:
> 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 appearing/disappearing.
> 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. 
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html
> Any help would be greatly appreciated, Edel
> <Screenshot 2019-07-15 at 12.05.12.png>
> <Screenshot 2019-07-15 at 14.30.00.png>
> )
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