getting sequences into the Structure Prediction
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
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@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
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@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@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
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@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@cgl.ucsf.edu <mailto:meng@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 <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@cgl.ucsf.edu <mailto:chimerax-users@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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@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@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@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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Marc Pusey
Hi Marc, I never saw Google Colab say it could not get a GPU, although I am not surprised that their free Colab service is probably being more and more heavily used, so at peak times you will not be able to get a GPU. Colab Pro might fix that by giving you higher priority (although there are no guarantees). I am surprised you cannot reach the Colab Pro sign up page https://colab.research.google.com/signup <https://colab.research.google.com/signup> If your university is blocking google sites how can you get anything done? AlphaFold will not run on a Mac, only on Linux, and you'll need a high-end GPU, with at least 8 Gbytes of memory. I'd suggest you try Google Colab a bit later -- I think it is rare that it cannot give you a GPU. You might have better luck directly using Google's AlphaFold Colab server from a web browser instead of via ChimeraX https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebo... Tom
On Nov 17, 2021, at 12:25 PM, Marc Pusey via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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@sonic.net <mailto:goddard@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@cgl.ucsf.edu <mailto:chimerax-users@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@cgl.ucsf.edu <mailto:meng@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 <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@cgl.ucsf.edu <mailto:chimerax-users@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-- Marc Pusey _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Marc Pusey -
Tom Goddard