[phenixbb] Improving picture quality of ED map in PYMOL

Lari Lehtiö lari.lehtio at abo.fi
Tue Sep 1 23:02:30 PDT 2009


I do it like this:
First just type

> ray
> save junk.png

Read the resolution, multiply by 4 or 5 depending on the intended  
printed size. Should keep the geometry, which is nice if you have a  
stereo view.

> ray 4*x,4*y
> save highresolution.png

You can also test different mesh settings like mesh_width

There is also a pymol mailing list, you could ask more detailed questions.


Lari Lehtiö
Pharmacy, Department of Biochemistry and Pharmacy
Åbo Akademi University,
BioCity, FIN-20520 Turku
+358 2 215 4270

Quoting Pavel Afonine <PAfonine at lbl.gov>:

> Hi Raja,
> here is what I usually do to get a paper-quality picture out of PyMol:
> once I have model and maps displayed, I issues these commands:
> ray 500,500
> png file_name
> You need to play with the above numbers to get the picture you like, and
> it will be saved under file name file_name.png.
> Since I use Pymol one a year or so, I can't remember what the above
> "magic" numbers/commands mean.
> Pavel.
> On 9/1/09 11:16 AM, Raja Dey wrote:
>> Dear Friends,
>>                      Sorry, for the of topic question. Does anyone   
>> can tell how to improve the quality of a picture showing the   
>> electron density map of dna in a complex using PYMOL. I created the  
>>  figure, but not happy with the quality as it is now. Might be  
>> there  is a way to improve which I don't know. I want the lines in  
>> the  mesh to be more sharp and fine. Any suggested program to  
>> prepare a  publication quality figure to show the ED map would be  
>> of great help.
>> Thanking you in advance...
>> Raja
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