[Chimera-users] problem with surface representation

[Miriam Gochin]

Outstanding!  That worked perfectly!  Thank you so much, Tom.
Miriam Gochin
Touro University - CA
miriam.gochin at tu.edu
707-638-5463
________________________________________
From: Tom Goddard [goddard at cgl.ucsf.edu]
Sent: Monday, November 09, 2009 10:07 PM
To: Miriam Gochin
Subject: Re: [Chimera-users] problem with surface representation

Hi Miriam,

  I think the cusps (two points) are just parts of the surface.  The
surface is obtained by rolling a sphere of a 1.4A radius over the
molecule and the surface is all points reached by that rolling sphere.
The cusps happen because that sphere does not fit between the residue 36
and 104 HE2 atoms.  If you reduce the probe radius to 1.2 A then you get
rid of the cusp but the surface is slightly different.  You would change
probe radius in the same dialog where you changed vertex density.

    Tom


-------- Original Message --------
Subject: Re: [Chimera-users] problem with surface representation
From: Miriam Gochin <miriam.gochin at tu.edu>
To: Tom Goddard <goddard at cgl.ucsf.edu>
Date: 11/9/09 9:31 PM
> Hi Tom,
>
> Thanks for the suggestions.  That does improve things a bit, but not completely.  Maybe I just have bad geometry at that position?  I attach the pdb file.  The residues involved are #36 and #104, if you have time to take a look at it.
>
> Best,
>
> Miriam
> Touro University - CA
> miriam.gochin at tu.edu
> 707-638-5463
> ________________________________________
> From: Tom Goddard [goddard at cgl.ucsf.edu]
> Sent: Monday, November 09, 2009 8:50 PM
> To: Miriam Gochin
> Cc: Chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] problem with surface representation
>
> Hi Miriam,
>
>   I guess the surface is being divided into two few triangles.  You can
> increase the number of triangles by increasing the "vertex density"
> parameter.  To do this, select the surface (ctrl-click it), use
> inspection selector (menu Actions / Inspect), set the "Inspect" menu in
> the inspector dialog to MSMS Surface, increase the "vertex density"
> parameter, say from 2 to 5, and press the Enter key after typing in the
> new number.  That should give a smoother surface.
>
>   Another step that can improve the lighting of the surface is to enable
> glossy lighting in the Lighting panel.  Menu Tools / Viewing Controls /
> Lighting, quality -> glossy.  Some old graphics cards don't support this.
>
>     Tom
>
> -------- Original Message --------
> Subject: [Chimera-users] problem with surface representation
> From: Miriam Gochin
> To: Chimera-users
> Date: 11/9/09 8:07 PM
>
>> I am having trouble with some pointed edges to my surface (attached).  It only happens in one location - everywhere else the surface is smooth.  I appreciate any suggestions.
>>
>> Thanks,
>> Miriam Gochin
>> Touro University - CA
>> miriam.gochin at tu.edu
>>
>>
>
>
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