[chimerax-users] [External] Re: getting sequences into the Structure Prediction

[Marc Pusey]

Hi Elaine -

I'll try that.  When I tried doing a "standard" copy and paste I could do
the copy, but the paste option disappeared from my drop-down edit
menu, which as you can imagine was very frustrating.

As I said - I was probably missing something very obvious - in this case
going the keyboard shortcut route.

Cheers

Marc


On Wed, Nov 17, 2021 at 10:19 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Marc,
> You should be able to copy the sequence as plain text from wherever you
> have it (e.g. shown in some text editor or browser window), and then paste
> it into the Paste area.  You would just use the normal copy/paste
> mechanisms of your system, e.g. command-C, command-V.  E.g. if you had a
> fasta file, open it in a text editor, copy the text, and then click into
> ChimeraX and paste it into the AlphaFold dialog Paste area.
>
> For example, I can copy the sequence of deer LDLR from this page
> <https://www.ncbi.nlm.nih.gov/protein/OWK12557.1?report=fasta>
>
> and paste it in the AlphaFold dialog.  Clicking Fetch finds the human one
> in the AlphaFold database.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Nov 17, 2021, at 7:36 AM, Marc Pusey via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hi -
> > I may be missing something very obvious, but...  I am trying to input
> and use protein sequences for structure predictions using the AlphaFold
> feature of ChimeraX.  I've not had any problems when the sequence can be
> obtained from a UniProt file, but several of the proteins I'm working with
> do not have such a file available.  Additionally, there is going to come a
> time where I will want to see what the consequences are from making
> mutations to those sequences that are available from UniProt.  The input
> gives the option of either Paste or UniProt, but I've not found a way to do
> a simple cut and paste to put in the sequence.
> > I'm using a Mac running Mojave, version 10.14.6.
> > Thanks!
> > Marc Pusey
>
>

-- 
Marc Pusey
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