Hi Is there an easy way to export the list of similar PDB structures, the % sequence ID, E-value etc that can be found using FOLDSEEK to an excel file. Thanks in advance L __________________________________________________________________________ P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
Hi Lynne, The Foldseek results are automatically cached in a JSON ".sms" file (e.g. on my Mac the default location is in ~/Downloads/ChimeraX/Foldseek/ ), but (1) there are lots of other numbers that you may not want (coordinates, perhaps) (2) I don't know how hard it would be to extract just the parts that you want and get them into Excel The sms files are described here <https://rbvi.ucsf.edu/chimerax/docs/user/formats/sms.html> ...but you should just look at the ones on your own system with a text-editor to really understand the contents. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 15, 2025, at 7:40 AM, Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Is there an easy way to export the list of similar PDB structures, the % sequence ID, E-value etc that can be found using FOLDSEEK to an excel file. Thanks in advance L __________________________________________________________________________ P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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/
Hi Lynne, In tomorrow's ChimeraX daily build and release candidate you can right click (or ctrl click) on the Foldseek results table to show a menu and choose "Save CSV or TSV File..." to save the table as a comma-separated-values or tab-separated-values text file. You should be able to read that into Excel. It saves the entire table. Currently there is not a way to save just the selected table rows. Tom
On May 15, 2025, at 7:40 AM, Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Is there an easy way to export the list of similar PDB structures, the % sequence ID, E-value etc that can be found using FOLDSEEK to an excel file. Thanks in advance L
__________________________________________________________________________
P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto
Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4
Phone: 416-813-5378 (Internal 305378)
Web page: https://lab.research.sickkids.ca/howell/
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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/
participants (3)
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Elaine Meng -
Lynne Howell -
Tom Goddard