Hi Alison,
Can you provide a sample image of what you're talking about? Feel free
to email me directly and attach an image.
A quick suggestion would be to try Grid Mode, especially if you're
viewing surfaces of aligned proteins.
See http://www.pymolwiki.org/index.php/Grid_mode.
Cheers,
-- Jason
On Tue, Sep 25, 2012 at 1:38 PM, alison cuff wrote:
> Hi there
>
> I am fairly new to pymol and am currently using it to visualise
> superpositions of 2 protein structures. However, I have noticed that a lot
> of structural detail is lost in regions where the structures are very
> similar and - instead of seeing two proteins nicely superimposed - I get
> fragments or some structural data missing altogether.
>
> Is there a way to counteract this problem please?
>
> All advice much appreciated!!!
>
>
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Jason Vertrees, PhD
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