[Chimera-users] on chimera vop threshold

[Elaine Meng]

Dear Smith,
For your first question: I'm guessing that for the purposes of isosurface display only (not affecting the actual values) that there is interpolation between 0 and 0.17, and between 0.18 and 1. However, our volume data expert may be able to say more.  I see that for even a map with only values 0,1 moving the slider between 0 and 1 does change the display.

For your second question, just use the map surface as the surface.  E.g. after you put the threshold level where you want it, you can give the model number of the volume model (the map) as the surface model.  If you are showing map model #0 as a surface and you want to make a new map with values of 1 inside that current surface and values of 0 outside, something like:

mask ones #0

The example above uses "ones" as the volume-model because you want the 1,0 values in the new map, not the inside-surface values of the current map.  If you wanted the inside-surface values, then it would be something like:

mask #0 #0

Threse are explained in the documentation:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 12, 2021, at 12:01 AM, Smith Lee <smith_lee123 at yahoo.com> wrote:
> 
> Dear Elaine,
> 
> Thanks, and "vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1" should be what I intend to do.
> 
> B the way, I think I still have something which I do not understand so well. For the map I got by "vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1", as for all values above 0.18 will be set to 1 and all values lower than 0.17 will be set to 0, will you please explain to me, why the got map by "vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1", which was displayed in the chimera window, changes its appearance gradually when I modulate the "Level" in the whole Range from 0 to 1, rather than displayed in only 2 appearances, one fixed appearance with all Level values lower than 0.17, and another fixed appearance with all Level values higher than 0.18?
> 
> Besides, I also intend to learn how to realize the above aim as by "vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1" with the chimera "mask" command. The "mask" command needs a surf-models file. For a specific A.mrc which I intend to get its mask.mrc, will you please explain to me step by step how to get the "mask" command requested surf-models file at specific threshold Level of A.mrc?
> 
> I am looking forward to getting your reply.
> 
> Smith
> 
> 
> On Thursday, February 11, 2021, 11:37:55 PM GMT+8, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 
> HI Smith,
> Your process makes no sense to me.  It is not possible to do both of these things (1) make values below 0.18 = 0 and (2) make values above 0.17 = 1, because values in the range 0.17-0.18  cannot equal both 0 and 1 at the same time.
> 
> Also, your second command didn't work as expected because you need the "setMaximum" keyword to set a new maximum.  As shown in the help, the "set" keyword just sets a a new minimum.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#threshold>
> 
> Did you instead mean (1) make values below 0.17 = 0 and (2) make values above 0.18 =1 ?  If so, instead try:
> 
> vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1
> 
> However, it is unclear why you even want to do that.  If you just want to make a new map with values inside the current map isosurface as 1 and values outside the isosurface as 0 (or vice versa) just use the "mask" command instead.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Feb 11, 2021, at 3:11 AM, Smith Lee <smith_lee123 at yahoo.com> wrote:
> > 
> > Dear All,
> > 
> > I have a map (A.mrc). When I open it in chimera (the map should be #0), the Volume Viewer shows the Range is -0.618 to 1.63, the default Level is 0.175.
> > 
> > With command "vop threshold #0 minimum 0.18 set 0" I got another map (let us call it B.mrc, should be #1), the Volume Viewer shows the Range is 0 to 1.63 (understandable, the maximum value is still 1.63 as in A.mrc, the minimum value is 0 as for all values not higher than 0.18 has been set to 0), the default Level is still 0.175.
> > 
> > Immediately I run the command "vop threshold #1 maximum 0.17 set 1". Before I running the command, I guess all the density value should be either "0" or "1", because all the value lower than 0.18 has been set to "0", and all value higher than 0.17 has been set to "1".
> > 
> > However after I run the command "vop threshold #1 maximum 0.17 set 1", I got another map (let us call it C.mrc, should be #2),the Volume Viewer shows the Range is 0 to 0.17 rather than 0 to 1, and wen I change the Level, the image of #2 changes correspondingly with the Level from 0 to 0.17.
> > 
> > Here I would ask, why the command "vop threshold #1 maximum 0.17 set 1" did not lead to a map with all values greater than 0,17 as 1? How to get a map based on A.mrc so that all values less than 0.18 as 0 and all values greater than 0.17 as 1 (please tell me the specific method)? Is any significance for the obtained C.mrc with range from 0 to 0.17? 
> > 
> > I am looking forward to getting your reply.
> > 
> > Smith