Hi Elaine, Well, this is a structure I (indeed) solved and no SS information was provided. I understand that ChimeraX first assigned secondary structure element (I guess using DSSP or similar) and then assigned segment ids based on this SS assignment. Forcing the ss_is number (setattr /C res ss_id 99) does indeed overwrite that. Best Cedric Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Wednesday, 6 November 2024 at 00:24 To: GOVAERTS Cédric <Cedric.Govaerts@ulb.be> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] ChimeraX not accepting SS assignment Hi Cedric, Actually it *is* in the original PDB (or mmCIF) information. There are individual helices and individual strands: helix 1, helix 2, etc. See for example our summary of the lines in a PDB file: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fformats%2Fpdbintro.html%23secondary&data=05%7C02%7CCedric.Govaerts%40ulb.be%7Cb599f319472348f4c5f608dcfdf105ff%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638664458912179551%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=YtxoacnZaD11edQLMgfziw6rbtb%2FafiYXbaNqVfZkfQ%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html#secondary>> The only time Chimera(X) tries to figure it out is when the file doesn't have any secondary structure assignments in it, such as when somebody created their own PDB file rather than getting it from the databank. I hope this helps, Elaine
On Nov 5, 2024, at 3:13 PM, GOVAERTS Cédric via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks (once more!) One follow up question : how does Chimera establish the ss_id to start with? As far as I know this was not present in the original PDB so why where there different segments in the structure ?
Thanks
Cedrc
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, 4 November 2024 17:44 To: GOVAERTS Cédric <Cedric.Govaerts@ulb.be> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: ChimeraX not accepting SS assignment
Hi Cedric, ChimeraX is accepting the SS assignment, but.... In addition to secondary structure assignment, there is another attribute that indicates whether the residues are in the same secondary structure segment as each other -- for example there could be two strands immediately next to each other (which shows a connecting thin part no matter what) that is not the same as having one long strand (which would not show any thin part).
See residue attribute "ss_id" in addition to "ss_type": <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fattributes.html%23residue&data=05%7C02%7CCedric.Govaerts%40ulb.be%7Cb599f319472348f4c5f608dcfdf105ff%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638664458912205300%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=WCSiZj%2BIvQNU86Xs6zDWzs71Y5JJc3axf52Dd0DpxXY%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>>
So if you want a longer set of residues to be all in the same strand (or in the same helix, same issue), you would have to also tell ChimeraX they are part of the same element by assigning them the same "ss_id" value. You can just give it some high number just to make sure it isn't the same ID as some other secondary structure element in the structure, for example:
setattr /A:10-25 res ss_id 99
See also previous posts <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2Fmessage%2FP34Q6R2R3VOGGII7COZE6NWH6K4Q6OE3%2F&data=05%7C02%7CCedric.Govaerts%40ulb.be%7Cb599f319472348f4c5f608dcfdf105ff%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638664458912236583%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=2vdQtZ%2FHQW%2Fq0k58J5BSGJsnEE9QdsjZDw79sifcAFo%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/P34Q6R2R3VOGGII7COZE6NWH6K4Q6OE3/>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2Fmessage%2FAQYXJULBOURU63YPEE735T43IYHO3B5I%2F&data=05%7C02%7CCedric.Govaerts%40ulb.be%7Cb599f319472348f4c5f608dcfdf105ff%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638664458912252022%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=j9TljTnwIAX45F0M1tWQ9JuZgzmG57i2mmXMuiqPMp8%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/AQYXJULBOURU63YPEE735T43IYHO3B5I/>>
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 Nov 4, 2024, at 4:49 AM, GOVAERTS Cédric <Cedric.Govaerts@ulb.be> wrote:
Hi Team, I want to define the secondary structure assignment on an immunoglobulin domain (C chain) using setattr /C:some-selection res ss_type 2 However ChimeraX refuses to represent a few residues within the selection as strands. This is also the case if, for instance, if I try setattr /C: res ss_type 2 Most residues are shown as strands (even some which clearly are coiled, see below, the loops) but *some* residues are still shown as coiled (even inside a strand).<image001.png> Any reason for this ? Can I overcome it ? Thanks a lot Cedric Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgovaertslab.ulb.ac.be%2F&data=05%7C02%7CCedric.Govaerts%40ulb.be%7Cb599f319472348f4c5f608dcfdf105ff%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638664458912268571%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=zE0%2BbIG7gD3lR2yBY8pcfSx6Y1ly5pXCg9fiQMFHit8%3D&reserved=0<http://govaertslab.ulb.ac.be/>