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

[Marc Pusey]

The Command+V did work to paste the sequence, altho as I'm using a PC split
keyboard it turned out to be start+V.  I don't think it was the source
formatting - the paste command was totally missing from the Edit drop-down
menu that had the copy command when I went to pick up the sequence (but it
was also gone when I went to paste), so I had nothing to click on.  I was
happy to get the sequence in, then the execution stopped with messages
about being unable to access a GPU and suggestions about Colab Pro - which
when I tried to access it I was apparently blocked by institutional
limitations.  So now I'm torturing myself with trying to figure out how to
download and use AlphaFold on a Mac...

Cheers

Marc Pusey


On Wed, Nov 17, 2021 at 1:38 PM Tom Goddard <goddard at sonic.net> wrote:

> That is odd.  The "paste" menu entry on the ChimeraX AlphaFold sequence
> entry box works fine for me on macOS Big Sur (11.6).  Possibly the source
> sequence that you copied was not plain text but was in some other format
> that the ChimeraX sequence entry field cannot handle.  I am not sure what
> format that could be though, and if that is the problem then using
> Command+V to paste also should not work.
>
> Tom
>
> On Nov 17, 2021, at 9:10 AM, Marc Pusey via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> 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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-- 
Marc Pusey
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