[Chimera-users] surface

Gesa Volkers gesa.volkers at gmx.de
Mon May 13 18:31:18 PDT 2013


Hi Tom,

deleting the other monomers from the pdb file solved the issue, thanks! 
I usually only select and hide what I don't need to show and wasn't 
aware that the interfaces produced this effect.

I am not a big fan of sending out huge attachemnts to mailing lists 
because this can be very annoying for some. Also my image did show the 
surface but with a high transparency. I used another screen on my 
computer today and then realized it was indeed very tough to see!

Thanks for your advice,
Gesa

-- 
Gesa Volkers, PhD
DFAIT Postdoctoral Fellow
Department of Biochemistry and Molecular Biology
University of British Columbia
Life Sciences Centre
2350 Health Sciences Mall
Vancouver BC V6T 1Z3
Canada

Tel: (001-) 604-822-7729
gesa at byron.biochem.ubc.ca

Am 13.05.2013 19:37, schrieb Tom Goddard:
> Hi Gesa,
>
>    I don't understand what your "chewed up" surface looks like.  The image you linked to just showed a ribbon and no surface at all as far as I could see.  So I'll just take a guess at what the problem might be.  If you send a picture (you can just attach it in email to chimera-users) I'll have a better idea.
>
>    One possible problem is that you have 2 or more chains (for 2 or more monomers) in one PDB model and just want your surface to enclose a single chain.  By default Chimera puts a surface on all the chains (not including ligands and solvent) and if you ask it to show just chain A it only shows the part of that full surface that touches chain A.  That leaves a hole where chain A contacts chain B.  A simple way to avoid this is just delete all the atoms except chain A (menu Select / Chain / A, menu Select / Invert, menu Actions / Atoms / Delete) then create your surface.  If you don't want to delete the other chains look at the "surfcat" command.
>
>    A second possibility for a "chewed up" surface is that your computer graphics driver is buggy and messing up the surface.  The best hope of fixing that is updating the driver.
>
> 	Tom
>
>
> On May 12, 2013, at 8:46 PM, Gesa Volkers wrote:
>
>> Hi chimera users/developers,
>>
>> I have a problem with a surface calculation from one monomer of a structure that I want to show. As you can see in this image
>>
>> http://imageshack.us/photo/my-images/801/testss.png/
>>
>> it looks like the surface calculation failed (?) because the surface is missing in the middle (note the chewed up structure of the surface). Most of the surface is smooth but for whatever reason not this part of the structure. I have played around with probeRadius, vertex density and zone and they all increase quality but do not add the missing surface part (I'm not even sure if zone is applicable to surfaces at all or only to electron density maps).
>>
>> Any suggestions which parameter I am missing?
>>
>> Thanks for suggestions,
>> Gesa
>>
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>>
>



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