[cmview-users] CMView and Phosphorylated proteins

[Patel, Pryank]

Dear Henning,
Thank you for your very quick response. Strangely (but happily), when I checked out an SVN version of cmview and owl, pymol was able to read SEP, which it wasn't able to in the binary version.

Having looked at the code (although I am not a Java programmer by any means), merely adding in SEP as amino acid 21 doesn't look like being enough. It doesn't break anything in the compilation, but it is still read as an unknown amino acid. I just don't have a lot of free time at the moment to start hacking through the code. So your original suggestion of just replacing SEP with SER in the PDB file looks like being the best one for now, which is fine since I can still distinguish between the two in Pymol and see the different interactions.

On a separate note, I am assuming ensembles of structures in a PDB file will not be recognised by CMView (eg: NMR structure file)?

Best wishes,
Pryank

Pryank Patel
School of Life and Medical Sciences
University of Hertfordshire
Hatfield
Hertfordshire
AL10 9DB
p.patel42 at herts.ac.uk


-----Original Message-----
From: h.stehr at gmail.com [mailto:h.stehr at gmail.com] On Behalf Of Henning Stehr
Sent: 01 August 2014 19:43
To: Patel, Pryank
Cc: cmview-users at bioinformatics.org
Subject: Re: [cmview-users] CMView and Phosphorylated proteins

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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