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). [cid:image001.png@01DB2EC0.1E7E3DF0] 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<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/ From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Sunday, 3 November 2024 at 18:33 To: mishra.ananya.163@gmail.com <mishra.ananya.163@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: Generating quantitative values for electrostatic potential and molecular lipophilicity potential Dear Ananya, These features are meant for visual analysis, such as for understanding the general properties of binding sites for comparison between similar structures. As such, the exact quantities are generally not that meaningful and you may be overestimating their relevance. The values are calculated on a 3D grid of points. What you see on the surface coloring is just interpolated values from the grid to the surface points (sometimes projected away from the surface rather than exactly at the surface (see the "offset" parameter of "coulombic" command), and mapped to the colors. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoulombic.html&data=05%7C02%7Ccedric.govaerts%40ulb.be%7C7cdd38f469db4eab32fb08dcfc2d9f29%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638662520099727971%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=gej%2FSNg%2F0Aqj1sFEUqgHB7F%2BKExYkBdnmjXYgJvu2tY%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html>> Given this explanation that the specific values may not be that meaningful, with the "coulombic" (electrostatic coloring) command, you can create the grid as a separate volume model with the "map true" option: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoulombic.html%23map-options&data=05%7C02%7Ccedric.govaerts%40ulb.be%7C7cdd38f469db4eab32fb08dcfc2d9f29%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638662520099758363%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Y5vUDlqVb5v%2BxBtcL88oN1yj5CObflZQxJ1XztesAYQ%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html#map-options>> Then you can save the map (volume model) with the "save" command: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fsave.html%23map&data=05%7C02%7Ccedric.govaerts%40ulb.be%7C7cdd38f469db4eab32fb08dcfc2d9f29%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638662520099774701%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=yDVv2jbh2h0I0ddPg65rnz0is2jFgDmB%2BMhorqhmbPU%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>> Similarly, the "mlp" command (lipophilicity coloring) also has a "map true" option: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmlp.html&data=05%7C02%7Ccedric.govaerts%40ulb.be%7C7cdd38f469db4eab32fb08dcfc2d9f29%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638662520099790621%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=O2ZKnktcLDz8ccfsVabMiKuQUhbGxqogc5u%2FepDPT%2Fw%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html>> Again, these are just the values on a regularly spaced 3D grid and not the values on the surface of the molecule. The only way I can think of to get the values on the surface of the molecule (which will again be very many points and very many values) is with several additional steps: (1) with the map model still open (created with "map true" option of either command), you would need to color the surface again using the Surface Color tool (menu: Tools... Volume Data... Surface Color) <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fsurfacecolor.html&data=05%7C02%7Ccedric.govaerts%40ulb.be%7C7cdd38f469db4eab32fb08dcfc2d9f29%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638662520099806440%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=0BAqlg1s5TyE0Y%2FF3p3lCOgDDqf6WmyTz4%2BqqfBihD8%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html>> (2) in that tool, of course you need to color the molecular surface of interest by that map model (3) in that tool, click Options and turn on "Report value at mouse position" .... and that will give a pop-up balloon reporting the value at the surface point where you put the mouse. Of course, that is only one point and there are probably thousands on your molecular surface. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2Fmessage%2FDC7U2AFCJEYNE4QFXWOI6ZX4MYXD435A%2F&data=05%7C02%7Ccedric.govaerts%40ulb.be%7C7cdd38f469db4eab32fb08dcfc2d9f29%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638662520099821751%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=waNQbkBpp6KLqWyHNPTTsMtDUbxAh5q%2F9oFoylhbhPo%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/DC7U2AFCJEYNE4QFXWOI6ZX4MYXD435A/>> Again, the coloring you got in the first place (without using Surface Color) is the best way to understand the distribution of values on the surface. I hope this clarifies the situation, 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 2, 2024, at 10:12 PM, mishra.ananya.163--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Sir/Madam,
I hope this message finds you well.
My name is Ananya, and I am an undergraduate student working on a project analysing protein structures. I am currently exploring the tools available in ChimeraX to measure structural parameters of protein models. I find the visualization features for surface electrostatic potential and molecular lipophilicity potential especially valuable for my research, as they provide essential insights for my analyses.
However, I have encountered some difficulty in locating a way to export quantitative values for these surface properties. Could you please advise if there is a method within ChimeraX to generate and export these values?
Thank you for your time and I would greatly appreciate any guidance you could offer. Hope you have a great day ahead!
Best regards, Ananya
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