[chimerax-users] .chimerax and PhosphoSitePlus

Wed Feb 24 11:35:52 PST 2021

Thanks Elaine, until you sent this I hadn't realized there was Uniprot
functionality in ChimeraX. Thanks!

____________________________

Daniel Gurnon, Ph. D.
Associate Professor of Chemistry and Biochemistry
DePauw University
Greencastle, IN 46135

On Tue, Feb 23, 2021 at 6:47 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Forgot to mention that for viewing UniProt features, you need ChimeraX 1.2
> daily build from December 21, 2020 or newer.  That's the approximate date
> that that capability was added, according to the Change Log:
>
> <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>
>
> Elaine
>
> > On Feb 23, 2021, at 3:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Daniel,
> > Something you and other ChimeraX users may be interested in is that you
> can fetch the UniProt sequence and then view the sequence features on both
> the sequence and the associated structure. There are several types of
> sequence features, but "modified residue" is one of them.  So for your
> purposes, I guess it depends on how well UniProt has annotated the sequence
> with its known modified sites, how often updated from the literature, etc.
> >
> > Maybe the least convenient step for this currently is that you need to
> look up the UniProt ID of the chain of interest. The simplest may be to
> look it up at the RCSB PDB website.  I couldn't think of a nice way using
> ChimeraX alone (blast nr takes too long).
> >
> > So I can open 1i10 and the corresponding UniProt sequence, according to
> the entry for that structure in the RCSB PDB:
> > <http://www.rcsb.org/structure/1I10>
> >
> > open 1i10
> > open uniprot:p00338
> >
> > ... in ChimeraX, that automatically pops up a dialog listing the uniprot
> sequence features.  Choosing some feature automatically shows it as colored
> boxes on the sequence and selects the corresponding positions on the
> structure.  In the attached images I just chose all "modified residue"
> features in the left side of the features table, but if you wanted to get
> more specific and just see for example the phosphotyrosine site, you could
> choose that on the right side of the features table.
> >
> > Here's the User Guide info on viewing UniProt features in ChimeraX:
> > <
> https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot
> >
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > <Screen Shot 2021-02-23 at 3.34.33 PM.png><Screen Shot 2021-02-23 at
> 3.34.58 PM.png><Screen Shot 2021-02-23 at 3.36.02 PM.png>
> >
> >> On Feb 23, 2021, at 11:15 AM, Daniel Gurnon <danielgurnon at depauw.edu>
> wrote:
> >>
> >> Thanks for the quick feedback Eric and Elaine.
> >>
> >> I only stumbled upon this this morning while thinking how nice it would
> be to be able to highlight all post-translational modification sites in a
> protein, to compare with variants of uncertain significance....I did a
> google search to see if something like that already existed, and at first
> glance this PSP script seemed to be the answer. But now it seems like it
> would be easier to write my own script.
> >>
> >> ____________________________
> >>
> >> Daniel Gurnon, Ph. D.
> >> Associate Professor of Chemistry and Biochemistry
> >> DePauw University
> >> Greencastle, IN 46135
> >>
> >>
> >> On Tue, Feb 23, 2021 at 1:55 PM Eric Pettersen <pett at cgl.ucsf.edu>
> wrote:
> >> Hi Daniel,
> >>      The script will actually execute if you wait several minutes.  The
> problem is that in the middle of the script it adds a surface and then
> executes many, many color commands, which causes the surface to be updated
> each time.  If you move the surface commands to the end of the script, it
> takes only several seconds to execute.  It doesn't look a lot like the
> image on the web page because for some reason the script labels every
> residue in the structure.  I have attached a script with the surface
> commands moved to the end.  You may or may not want to edit the script to
> remove the label commands.
> >>
> >> --Eric
> >>
> >>      Eric Pettersen
> >>      UCSF Computer Graphics Lab
> >>
> >>
> >>> On Feb 23, 2021, at 9:06 AM, Daniel Gurnon <danielgurnon at depauw.edu>
> wrote:
> >>>
> >>> Hi all,
> >>> I'm interested in visualizing post translational modified positions in
> Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP).
> I'm not able to get it working though, so I hope you can help:
> >>>
> >>> Here's an example of a page with an available Chimera script. From
> what I read in the documentation about web services, I should be able to
> click the script, and it will open in a locally running instance of
> Chimera. However, in Chrome, my only option is to download the script.
> >>>
> >>> When I download and then try to open the script in ChimeraX (v 1.1),
> it tells me the ".chimerax" file type is not recognized. When I try to open
> it in the original Chimera (v1.15), I get the infinite spinning wheel of
> rainbows. These things occur whether or not I have the reference PDB
> structure loaded. Just to see what would happen, I also tried pasting the
> first command from the .chimerax file (setattr a label Ser-89 :88.A at OG)
> into Chimera and ChimeraX. The command executed successfully in Chimera,
> but in ChimeraX, I get the error
> >>>
> >>> setattr a label Ser-89 :88.A at OG
> >>> Expected a keyword
> >>>
> >>> Thanks in advance for the assistance,
> >>> Dan
> >>> ____________________________
> >>>
> >>> Daniel Gurnon, Ph. D.
> >>> Associate Professor of Chemistry and Biochemistry
> >>> DePauw University
> >>> Greencastle, IN 46135
> >>> _______________________________________________
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> >>
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