[Chimera-users] Missing cavities

sapeptides sapeptides at gmail.com
Thu Jun 5 12:59:12 PDT 2014

Thank you very much!!! It worked. Sorry for this stupid question!


On Thu, Jun 5, 2014 at 9:15 PM, Tom Goddard <goddard at sonic.net> wrote:

> 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”.
> Tom
> 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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