[cmview-users] CMView and Phosphorylated proteins

[Jose Manuel Duarte]

Hi Pryank

Just a couple of comments. First about having non-standard amino-acids 
read properly: indeed the latest development version obtainable from 
github will most likely cope better with them as support for 
non-standard amino-acids has now been developed in the underlying OWL 
library.

It seems that you already managed to get the code from SVN and compile 
it, but just to let you know this would be the process to get the latest 
from github and compile the package (it has become a lot easier thanks 
to maven):

(You will need both the maven and git packages installed locally for the 
"git" and "mvn" command to work)

$ mkdir owl; cd owl
$ git clone https://github.com/eppic-team/owl.git
$ mvn install -DskipTests
$ mkdir cmview; cd cmview
$ git clone https://github.com/josemduarte/cmview.git
$ mvn install -DskipTests

This will give you a final jar file under cmview/target that you can 
then use to run cmview with "java -jar cmview.jar".

About the NMR structures indeed as Henning says we do have an 
experimental feature to show all NMR models in gray scale. To try it out 
you simply need to set USE_EXPERIMENTAL_FEATURES=true in the cmview.cfg 
file, then you'll get a checkbox to load all models in the structure 
loader dialog.

Hope this helps

Jose



On 05/08/14 17:30, Henning Stehr wrote:
>> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> cmview-users mailing list
>>> cmview-users at bioinformatics.org
>>> http://www.bioinformatics.org/mailman/listinfo/cmview-users
>>>
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