Hi, Would there be a way to save convservation scores from a large multiple sequence alignment into a file that could be re-loaded later instead of having to reload the actual alignment file? In looking at WDFY4, the alignment of the 3124 residue protein from 523 different species, the alignment fasta file takes around 10 minutes to load. After calculating the scores, the program shows the alignment and then the showing the convervations of residues in the protein is my goal of analysis. But it takes the same 10 minutes every time I open the session. I haven't found a way to save the scores themselves and load that in directly. Is there a way to do that? thanks it's a great program. ken murphy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Hi Ken, Once your protein residues have the seq_conservation attribute, you don't need the sequences anymore. You would only need to open the large sequence alignment once initially, along with the protein structure to get the conservation attribute assigned to the protein residues. Then you can close the sequence alignment, but don't close the protein structure until you save a ChimeraX session (*.cxs file). Later when you open the session again it will just have the protein with the conservation assignments, but not the large sequence alignment that takes a long time to open. You can save a session from the File menu or with the "save" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> If you really really wanted to save the seq_conservation attribute values to a separate file you could: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> ...but if the goal is only to color the protein, it would be simpler just to save the session with the protein structure that already has the conservation values assigned to it. 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 23, 2023, at 6:34 PM, Murphy, Kenneth via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Would there be a way to save convservation scores from a large multiple sequence alignment into a file that could be re-loaded later instead of having to reload the actual alignment file?
In looking at WDFY4, the alignment of the 3124 residue protein from 523 different species, the alignment fasta file takes around 10 minutes to load. After calculating the scores, the program shows the alignment and then the showing the convervations of residues in the protein is my goal of analysis. But it takes the same 10 minutes every time I open the session. I haven't found a way to save the scores themselves and load that in directly. Is there a way to do that?
thanks
it's a great program.
ken murphy
Also, if the only reason you're opening the alignment is to get conservation scores (so you are not also using the alignment tool to do other things), then you can significantly speed up opening the alignment by not actually starting the alignment-display tool, which takes a long time to display the million+ characters of the alignment. You need to be using the 1.7 release candidate (or current daily build) to have this capability. If you are, then "open path-to-alignment-file viewer false" will open the alignment but not start the tool. The conservation scores will still be assigned to the residues. There are a couple of handy ways to not have to type out the file path by hand. One is to use "open browse viewer false", which will bring up a file browser for you to specify the alignment file. The other is to type "open " and then drag the alignment file from your system file browser onto the command line, which will put the path to the file into the command line, then add " viewer false" and hit Return. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 24, 2023, at 9:52 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Ken, Once your protein residues have the seq_conservation attribute, you don't need the sequences anymore. You would only need to open the large sequence alignment once initially, along with the protein structure to get the conservation attribute assigned to the protein residues. Then you can close the sequence alignment, but don't close the protein structure until you save a ChimeraX session (*.cxs file). Later when you open the session again it will just have the protein with the conservation assignments, but not the large sequence alignment that takes a long time to open.
You can save a session from the File menu or with the "save" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session>
If you really really wanted to save the seq_conservation attribute values to a separate file you could: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>
...but if the goal is only to color the protein, it would be simpler just to save the session with the protein structure that already has the conservation values assigned to it.
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 23, 2023, at 6:34 PM, Murphy, Kenneth via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Would there be a way to save convservation scores from a large multiple sequence alignment into a file that could be re-loaded later instead of having to reload the actual alignment file?
In looking at WDFY4, the alignment of the 3124 residue protein from 523 different species, the alignment fasta file takes around 10 minutes to load. After calculating the scores, the program shows the alignment and then the showing the convervations of residues in the protein is my goal of analysis. But it takes the same 10 minutes every time I open the session. I haven't found a way to save the scores themselves and load that in directly. Is there a way to do that?
thanks
it's a great program.
ken murphy
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thanks, I will give it a try, you guys rock Ken From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Sunday, November 26, 2023 at 1:05 PM To: Murphy, Kenneth <kmurphy@wustl.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Keeping conservation scores without alignment * External Email - Caution * Also, if the only reason you're opening the alignment is to get conservation scores (so you are not also using the alignment tool to do other things), then you can significantly speed up opening the alignment by not actually starting the alignment-display tool, which takes a long time to display the million+ characters of the alignment. You need to be using the 1.7 release candidate (or current daily build) to have this capability. If you are, then "open path-to-alignment-file viewer false" will open the alignment but not start the tool. The conservation scores will still be assigned to the residues. There are a couple of handy ways to not have to type out the file path by hand. One is to use "open browse viewer false", which will bring up a file browser for you to specify the alignment file. The other is to type "open " and then drag the alignment file from your system file browser onto the command line, which will put the path to the file into the command line, then add " viewer false" and hit Return. --Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 24, 2023, at 9:52 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Ken, Once your protein residues have the seq_conservation attribute, you don't need the sequences anymore. You would only need to open the large sequence alignment once initially, along with the protein structure to get the conservation attribute assigned to the protein residues. Then you can close the sequence alignment, but don't close the protein structure until you save a ChimeraX session (*.cxs file). Later when you open the session again it will just have the protein with the conservation assignments, but not the large sequence alignment that takes a long time to open. You can save a session from the File menu or with the "save" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> If you really really wanted to save the seq_conservation attribute values to a separate file you could: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> ...but if the goal is only to color the protein, it would be simpler just to save the session with the protein structure that already has the conservation values assigned to it. 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 23, 2023, at 6:34 PM, Murphy, Kenneth via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi, Would there be a way to save convservation scores from a large multiple sequence alignment into a file that could be re-loaded later instead of having to reload the actual alignment file? In looking at WDFY4, the alignment of the 3124 residue protein from 523 different species, the alignment fasta file takes around 10 minutes to load. After calculating the scores, the program shows the alignment and then the showing the convervations of residues in the protein is my goal of analysis. But it takes the same 10 minutes every time I open the session. I haven't found a way to save the scores themselves and load that in directly. Is there a way to do that? thanks it's a great program. ken murphy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
participants (3)
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Elaine Meng -
Eric Pettersen -
Murphy, Kenneth