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
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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cgl.ucsf.edu> To: Stapleton kevin2017/4/3 <kevin.aug@protein.osaka-u.ac.jp> Cc: chimerax-users@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi Kako, It should generalize to your values, just substitute them into the command. We also need to know what value you want to substitute for those below .0337 and what value you want to substitute for those above 0.0405. If the answer to both of those is zero, meaning you want all the points outside that range to be zero, then it's just similar to what I sent before. E.g. if your input map is #2: volume threshold #2 min 0.0337 set 0 max 0.0405 setmax 0 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#threshold> (I believe "vop threshold" is same as "volume threshold") If the answers to what new values you want were not zero then substitute in your answer values instead. There might be an alternative way by showing isosurfaces at 0.0337 and 0.0405 and using masking (volume mask) but I'm not sure about it, whereas I'm pretty sure the "volume threshold" command will work because I tested it before sending my previous answer. I hope this helps, Elaine
On Nov 10, 2021, at 6:47 PM, Stapleton kevin2017/4/3 <kevin.aug@protein.osaka-u.ac.jp> wrote:
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@cgl.ucsf.edu> To: Stapleton kevin2017/4/3 <kevin.aug@protein.osaka-u.ac.jp> Cc: chimerax-users@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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participants (2)
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Elaine Meng -
Stapleton kevin2017/4/3