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