[cmview-users] CMView and Phosphorylated proteins

[Henning Stehr]

Hi Pryank,

that's true. CMView only really works with standard amino acids.

A poor workaround would be to replace SEP with standard Serine in the
PDF file, then CMView would at least recognize the residues but of
course you would lose the ability to distinguish between the two.

If you are very adventurous, there is the class
owl.core.structure.AminoAcid.java that defines the amino acid types.
You can try to add SEP at #21 but you would have to recompile the
project and I'm not sure if it would break anything.

The sources are on GitHub:

https://github.com/josemduarte/cmview
https://github.com/eppic-team/owl

Cheers,
Henning

On Fri, Aug 1, 2014 at 9:44 AM, Patel, Pryank <p.patel42 at herts.ac.uk> wrote:
> Dear CMView users,
>
> I am a new user to CMView, so my apologies if this has been asked and
> answered before. I am studying the structure of a protein which is
> phosphorylated under certain conditions. I have the structures of both the
> phosphorylated and non-phosphorylated forms, and am using CMView to generate
> contact maps and compare the contacts within each structure under each
> condition in pymol. However, CMView is not able to recognise phosphorylated
> residues (phosphoserine, SEP, specifically). Is there a fix that I am able
> to implement so it will recognise phosphoserine? It may not make too much of
> a difference overall but I think it would help me with my analysis.
>
>
>
> Best wishes,
>
> Pryank
>
>
>
> Pryank Patel
>
> School of Life and Medical Sciences
>
> University of Hertfordshire
>
> Hatfield
>
> Hertfordshire
>
> AL10 9DB
>
> p.patel42 at herts.ac.uk
>
>
>
>
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