[cmview-users] CMView and Phosphorylated proteins

[Henning Stehr]

> 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.

sounds good

> 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.

Hmm, I'm guessing that the PDB reader code doesn't know how to read
the atoms and falls back to unknown but then it will probably be more
involved to make this work. I don't work on the code anymore so this
was my best guess.

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

When you load a structure with multiple models, you have to choose
which one of the models to load in CMView. You could manually load the
whole ensemble in PyMol though.

At some point there was an experimental function in CMView to load
ensembles as "fuzzy" contact maps with greyscale contacts but I think
it was just for generating contact map images.

Henning

> -----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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