Re: [ccp4bb] surface drawings

Protein crystallography Programs for crystallography X-ray detectors
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CCP4bb <-- 2007 <-- March 2007 <-- 12 March 2007

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Subject: Re: surface drawings
From: James Whisstock James {- dot -} Whisstock {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2007-03-12

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From: "Stojanoff, Vivian" stojanof {- at -} BNL {- dot -} GOV
Date: 2007-03-12

Subject: Re: surface drawings
From: Maneesh Yadav yadavm {- at -} SCRIPPS {- dot -} EDU
Date: 2007-03-12

When I've wanted to show an internal cavity I've found the best route is:

pdb file->voidoo->mapman->ccp4 map->pymol

(play with your probe size in voidoo to prevent thr probe from "rolling out" of your cavity)

You can load the ccp4 formatted cavity maps into xfit/coot, you get your volume measurements and draw a nice picture (you cavity is now an "object" in pymol, and you have a little more flexibility as to how it is rendered).

The different surfacing algorithms between programs behave differently, I always get weird face normals when trying to use pymol surface for internal cavities. A lab I used to be in had a copy on insightII which seemed to do a better job with those...

-----Original Message-----
From: CCP4 bulletin board on behalf of Green, Todd
Sent: Mon 3/12/2007 8:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] surface drawings

Hello All,

I would like to make an illustration which has a semi-transparent surface rendering for a large cavity. I just want the suface to cover the cavity not the entire protein (which will most likely exist as a ribbon drawing). Is there a way to set a boundary for a surface drawing? By that, I mean pick a point within the cavity and set a radius to draw a solvent accessible surface and thusly only those points falling within the radius are shown. Seems simple enough, but I haven't quite figured it out as of yet.

Thanks in advance for any advise.
Todd

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 12 March 2007

Previous message:
Subject: Re: surface drawings
From: James Whisstock James {- dot -} Whisstock {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2007-03-12

Next message:
Subject: The X6A workbench is back!
From: "Stojanoff, Vivian" stojanof {- at -} BNL {- dot -} GOV
Date: 2007-03-12