Pymol illustration

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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marie
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Posts: 4
Joined: 2015.11.05 20:04

Pymol illustration

#1 Post by marie » 2015.12.27 19:50

Hello

I have my damfilt.pdb file and I uploaded it to Pymol. How can I increase the diameter of the protein's spheres and buffers's spheres, in order to obtain a full clean surface of the envelope?

Thank you

sasha
Active member
Posts: 46
Joined: 2014.03.05 17:56

Re: Pymol illustration

#2 Post by sasha » 2016.01.12 01:40

To modify the size of displayed spheres, you can use the 'set sphere_scale' in the pymol command line, for example:

show spheres
set sphere_scale, 1.5
set sphere_scale, 3.0

you can play around with the number until you get the desired results.

HTH,

sasha

sasha
Active member
Posts: 46
Joined: 2014.03.05 17:56

Re: Pymol illustration

#3 Post by sasha » 2016.10.06 14:28

My previous post referred to changing the size of displayed spheres, but if you want to modify the surface representation, you should change the solvent_radius parameter:

set solvent_radius, 1.8
If the surface does not change correspondingly, use:
rebuild
A larger solvent_radius would show a smoother surface.
Check out more info at:
https://pymolwiki.org/index.php/Surface

Best,

sasha

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