[chimerax-users] vop min/max threshold

[Stapleton kevin2017/4/3]

Elaine, 

Thanks for the help.  And I must apologies.   I think my example with molmap was a bad one. It was an honest attempt at making the problem simpler.    

I am actually working with EM density volume and I want to keep the "good" threshold range as an output .mrc.    I thought by using that example I wouldn't over complicate things.  Apologies.

The real story is that I have density map with a threshold range of -0.000558 to 0.0405.  I want to keep only a range of 0.0337 to 0.0405. Then, save that map.  The resulting histogram would then show only those value ranges.

Hope you are well
KAko



----- Original Message -----
>> From: Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
>> To: Stapleton kevin2017/4/3 <kevin.aug at protein.osaka-u.ac.jp>
>> Cc: chimerax-users at cgl.ucsf.edu
>> Date: 2021-11-10 09:50:42
>> Subject: Re: [chimerax-users] vop min/max threshold
>> 
>> Hi Kevin,
>> If you really want to set every value that is outside the 0.26-0.27 range to zero,  the command is:
>> 
>> vop threshold #2 min 0.26 set 0 max 0.27 setmax 0
>> 
>> The "set" keyword is for setting the new minimum, not the new maximum, as shown in the usage:
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#threshold>
>> 
>> Also, be aware that your molmap map includes solvent, ligands, ions, etc.  If you don't want those, you'd need a narrower specification in the molmap command, e.g.
>> 
>> molmap #1 & protein 10
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>> > On Nov 9, 2021, at 4:31 PM, Stapleton kevin2017/4/3 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> > 
>> > Hello everyone! 
>> > 
>> > just trying to get my head around a small problem, but one my brain turns into spaghetti.   I am trying to save a density from molmap with a threshold range of given values.   
>> > 
>> > for example:
>> > 
>> > open 2gbp
>> > molmap #1 10
>> > 
>> > From the resulting density (now ID #2) I want to save the map at a very narrow threshold range.  for example the current range is 0.0-0.528.  But I would like to save the map with a "restricted" level of 0.26-0.27.  
>> > 
>> > I have been playing with the vop min/max threshold xxx set 0/1 commands but I keep getting turned around.  
>> > 
>> > here is what I did:
>> > 
>> > open 2gbp
>> > molmap #1 10  - produces a new map ID #2
>> > 
>> > vop threshold #2 minimum 0.26 set 0
>> > vop threshold #3 maximum 0.27 set 1
>> > 
>> > I used the set 0/1 because I want the range 0.26-0.27 to have the density values and anything outside of that to have zero.  Like a mask in relion.  But for my specific case relion_mask wont work as well. 
>> > 
>> > Somewhere I am turning the options around and it has my brain flattened.  Any help is appreciated. 
>> > 
>> > All the best and thanks for making my science life 1Million times easier with your wonderful program :-)
>> > 
>> > Kako
>> > 
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