Dear Elaine Thanks for showing syntax sample. It worked - a composite may was generated from two locally refined maps. Now, scale factor was calculated based on threshold values of both maps. Best Yuro
On Aug 10, 2023, at 3:36 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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Dear Yuro, Once you get more familiar with how to read the help it is not that complicated. Example ChimeraX command for maps #1 and #2 you want to scale x1 and x2:
vol max #1,2 scaleFactors 1,2
The syntax is shown in the "volume max" help <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
volume maximum volume-spec [ scaleFactors f1,f2,... | fromlevels ] [ onGrid gridmap ] [ spacing S | Sx,Sy,Sz ] [ boundingGrid true | false ] [ gridStep N | Nx,Ny,Nz ] [ gridSubregion i1,j1,k1,i2,j2,k2 | all ] [ valueType value-type ] [ hideMaps true | false ] new-map-options
You should read the help page because there are many options and you might want to use some of them. However, they are just options, i.e. you don't need to include them if you just want the default behaviors.
The reason we have help pages is that we don't have time/resources to fully describe everything in every possible command each user needs in separate replies on this mailing list.
And there is even a help page on how to read these usage lines, which explains the meaning of "[ ]" (= an option), " | " (= separator between possible values of the option), etc. <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 10, 2023, at 11:39 AM, Takagi, Yuichiro via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine I don’t understand the instruction - it’s a bit too abstract for me to write a syntax - That is why I am positing this site. It would be nice if syntax comes with some kind of actual examples in chimera instructions.
Now let’s say, I have two maps A and B by which I want to make a composite map. Scale factor of map A is 1 and that of B is 2. What would be the syntax for this using vop maximum ?
Thanks for your help Best Yuro