Hi Sam, My explanation of how ChimeraX determines the initial thresholds was meant to convey that it is a very generic rule (choose threshold so 1% of grid points are inside surface). That is never going to be an ideal level, it is just a starting point so you see some density. With cryoEM maps that there is no rule about how to set a good threshold -- it has to be chosen on a case-by-case basis by the researcher. For X-ray maps a reasonable rule like using a threshold a 3 standard deviations works because crystallographic density fills the volume bounds and so the result is not skewed by the variable padding around the structure that is seen in cryoEM maps. Tom
On Sep 13, 2023, at 1:23 AM, Samuel Haysom <Samuel.Haysom@SoseiHeptares.com> wrote:
Hi all,
Thank you for your helpful replies. Eric's suggestion of OpenCommands works for my use case. Unfortunately, I don't have access to the daily build so I'll have to wait until the “volume defaultvalues“ commands are put in a stable release but that would be my preferred solution as it doesn’t require installing anything so thanks Oli for that suggestion.
Tom, to my knowledge (although anyone can contradict me) no one working in cryoEM of membrane proteins ever uses the default threshold for viewing volumes because it will usually include the entire detergent micelle which obscures the protein features. I think people would therefore appreciate the ability to change the defaults, although by the look of Oli's reply this is already present to some extent in the daily builds.
Thanks for your help, Sam
Sent from Outlook for iOS <https://aka.ms/o0ukef> From: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> Sent: Tuesday, September 12, 2023 7:20:04 PM To: Samuel Haysom <Samuel.Haysom@SoseiHeptares.com <mailto:Samuel.Haysom@SoseiHeptares.com>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Setting default volume step and rms level
Hi Sam,
The initial volume threshold level is set to make the surface enclose 1% of the grid points. That seems like a high threshold. It encloses along a line about 1 in 5 grid points (1/100 ** 1/3) which usually is an ok starting point for cryoEM and x-ray maps. It doesn't use standard deviation or root-mean-square thresholds (although those can be used with the sdLevel and rmsLevel options of the volume command after the volume is open) because cryoEM often has very large padding around the actual structure so those statistics based levels are skewed to very low levels (unlike in X-ray where the structure extends to the edge of the volume data). ChimeraX will use grayscale display of a single plane for large data (>= 256 million grid points) and it uses a linear ramp of the gray levels from the threshold where 90% of grid values are higher up to the threshold where 1% of the grid values are higher (ie from threshold rank 10% to rank 99%).
These 1% and 90% default threshold parameters are currently not settable using a command. I could allow setting those defaults, although I think only you would use that and am reluctant to tamper with the code (and introduce new bugs) for a feature only used by one person.
Tom
On Sep 12, 2023, at 2:38 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Is it possible to change the default step and level that ChimeraX uses when it opens maps? My data (cryoEM) mostly opens at step 2 with the level set too low for useful viewing, necessitating adjusting these settings for every map I open. Is there a global setting that I can change (for instance by specifying it in a startup script) to change this behaviour so my maps always open at step 1 and at a specified level (say rmsLevel 8)?
KR, Sam Samuel Haysom <mailto:Samuel.Haysom@soseiheptares.com> | Research Scientist | Biophysics Sosei Heptares <https://eu-west-1.protection.sophos.com/?d=soseiheptares.com&u=aHR0cHM6Ly9zb...> | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom
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