[Chimera-users] Missing cavities

Tom Goddard goddard at sonic.net
Thu Jun 5 12:15:28 PDT 2014

Hi Susanna,

  I think you mean that the solid tan surface where you cut the molecule is blocking your view inside.  That is a feature added to Chimera many years ago to make the cut object look solid.  To undisplay that flat surface in the Side View dialog press the “Surface capping…” button and click off “Cap surfaces at clip planes”.


On Jun 5, 2014, at 11:58 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> On Jun 5, 2014, at 7:38 AM, sapeptides <sapeptides at gmail.com> wrote:
>> Hi Erik,
>> I'm writing because I have noticed that in the new versions of chimera when I create a surface and then try to "cut" it (with the side view tool) to see inside the model I obtain this weird picture (attached), whereas in the old versions (how old I do not remember but I created a stunning images of various active sites) it was possible to check all the cavities inside the molecular structures.
>> I was wondering if you could suggest how to visualize pockets and clefts when the vdw or solvent accessible surface is present.
>> Thanks a lot!
>> Susanna
> <test1.png>
> Hi Susanna,
> 	It's best to send questions like this to the chimera-users list rather than me directly so that others can benefit from the answer and since I may not actually be the best person to answer the question.  For instance, I have no good ideas about showing cavities effectively with VDW or solvent-accessible surfaces and hope someone else can chime in there.
> 	As for the lack of cavities in your image, did Chimera issue a warning when it computed the surface saying that "[c]alculation of some surface components failed" and that "[a] single component of the surface was calculated"?  If so, that means that calculation of interior cavities failed and Chimera is showing the exterior surface only (which the error message does say if you read it in its entirety).  That would produce the lack of interior cavities you observed.  If you didn't get such a message, can you supply the PDB ID for this structure (or PDB file) so I can investigate?  Thanks!
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
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