Thanks for the explanation. k From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, November 21, 2023 11:23 AM To: Murphy, Kenneth <kmurphy@wustl.edu> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] al2co input * External Email - Caution * Hi Ken, ChimeraX takes your alignment data and prepares a Clustal ALN format file for input to its internal version of al2co. You can save your alignment in that format with the command "save folder-path/file-name.aln". If you have more than one alignment open, you would also have to provide "alignment alignment-ID" in the command, where alignment-ID is shown in the title bar of the alignment window. --Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 21, 2023, at 5:13 AM, Murphy, Kenneth via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Thanks for ChimeraX. I've been loading multiple sequence alignments in fasta format directly into ChimeraX for mapping conservation onto a pdb and it works great. My MSA are directly from clustalo omega and in fasta format not clu formtat. My question is this. My compiled al2co.c as well as the binary I downloaded for al21co.exe doesn't work with input in fasta format. And yet ChimeraX opens and al2co window when I input my alignment. Does ChimeraX use another version of al2co that is configured to open fasta files? thanks for any info. 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. _______________________________________________ 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.