vop subtract removing too much of my map
I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1! how can I get precise subtraction?
Hi Ahmad, To my knowledge the map subtraction is precise. But if you think there is a problem, you will need to give a precise and detailed description of exactly what you did, including the data files and all the steps needed to show the problem, and why you believe there is a problem (and possibly use menu: Help... Report a Bug, instead of sending e-mail here). If we can't reproduce a problem, we can't fix it! It may be that you need to create the molmaps with smaller grid spacing to give a more precise result. molmap details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> vop subtract details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1!
how can I get precise subtraction?
Thanks a lot for the response, I can send data if necessary, but it likely has to do with options / resolution The higher resolution of map2 is, the sharper the subtraction. I tried using a finer gridSpacing but it doesn't change much! Does the map threshold factor into the subtraction? On Tue, Sep 29, 2020 at 10:05 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, To my knowledge the map subtraction is precise. But if you think there is a problem, you will need to give a precise and detailed description of exactly what you did, including the data files and all the steps needed to show the problem, and why you believe there is a problem (and possibly use menu: Help... Report a Bug, instead of sending e-mail here). If we can't reproduce a problem, we can't fix it!
It may be that you need to create the molmaps with smaller grid spacing to give a more precise result.
molmap details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
vop subtract details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1!
how can I get precise subtraction?
I don't see anything about map threshold in the "vop subtract" link I sent you earlier, so I don't think it has an effect. So the factors you can control are the molmap resolution (as you said) and molmap grid spacing. The resolution of results from map interpolation (which is part of subtraction and several other map calculations) depend on input map resolution, grid spacing, bumpiness, and the shift between their grids, as discussed here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#notes>
On Sep 29, 2020, at 10:53 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks a lot for the response, I can send data if necessary, but it likely has to do with options / resolution
The higher resolution of map2 is, the sharper the subtraction. I tried using a finer gridSpacing but it doesn't change much!
Does the map threshold factor into the subtraction?
On Tue, Sep 29, 2020 at 10:05 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, To my knowledge the map subtraction is precise. But if you think there is a problem, you will need to give a precise and detailed description of exactly what you did, including the data files and all the steps needed to show the problem, and why you believe there is a problem (and possibly use menu: Help... Report a Bug, instead of sending e-mail here). If we can't reproduce a problem, we can't fix it!
It may be that you need to create the molmaps with smaller grid spacing to give a more precise result.
molmap details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
vop subtract details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1!
how can I get precise subtraction?
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Correct, vop subtract does not use displayed threshold levels in any way. Tom
On Sep 29, 2020, at 11:23 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I don't see anything about map threshold in the "vop subtract" link I sent you earlier, so I don't think it has an effect.
So the factors you can control are the molmap resolution (as you said) and molmap grid spacing. The resolution of results from map interpolation (which is part of subtraction and several other map calculations) depend on input map resolution, grid spacing, bumpiness, and the shift between their grids, as discussed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#notes>
On Sep 29, 2020, at 10:53 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks a lot for the response, I can send data if necessary, but it likely has to do with options / resolution
The higher resolution of map2 is, the sharper the subtraction. I tried using a finer gridSpacing but it doesn't change much!
Does the map threshold factor into the subtraction?
On Tue, Sep 29, 2020 at 10:05 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, To my knowledge the map subtraction is precise. But if you think there is a problem, you will need to give a precise and detailed description of exactly what you did, including the data files and all the steps needed to show the problem, and why you believe there is a problem (and possibly use menu: Help... Report a Bug, instead of sending e-mail here). If we can't reproduce a problem, we can't fix it!
It may be that you need to create the molmaps with smaller grid spacing to give a more precise result.
molmap details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
vop subtract details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1!
how can I get precise subtraction?
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Well I'm trying to make a mask for a part of my molecule, my strategy for this is to create a molmap of 60 A (map1) and another of 5 A (map2) and subtract map1 - map2 Usually people would suggest using volume eraser for this, but I want to go with the lazy approach of subtraction!!! Is there a way I can tweak the molmap / vop subtract settings to give me what I want? On Tue, Sep 29, 2020 at 11:41 AM Tom Goddard <goddard@sonic.net> wrote:
Correct, vop subtract does not use displayed threshold levels in any way.
Tom
On Sep 29, 2020, at 11:23 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I don't see anything about map threshold in the "vop subtract" link I sent you earlier, so I don't think it has an effect.
So the factors you can control are the molmap resolution (as you said) and molmap grid spacing. The resolution of results from map interpolation (which is part of subtraction and several other map calculations) depend on input map resolution, grid spacing, bumpiness, and the shift between their grids, as discussed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#notes>
On Sep 29, 2020, at 10:53 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks a lot for the response, I can send data if necessary, but it likely has to do with options / resolution
The higher resolution of map2 is, the sharper the subtraction. I tried using a finer gridSpacing but it doesn't change much!
Does the map threshold factor into the subtraction?
On Tue, Sep 29, 2020 at 10:05 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, To my knowledge the map subtraction is precise. But if you think there is a problem, you will need to give a precise and detailed description of exactly what you did, including the data files and all the steps needed to show the problem, and why you believe there is a problem (and possibly use menu: Help... Report a Bug, instead of sending e-mail here). If we can't reproduce a problem, we can't fix it!
It may be that you need to create the molmaps with smaller grid spacing to give a more precise result.
molmap details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
vop subtract details and options: < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1!
how can I get precise subtraction?
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
If you want to mask out part of your map, maybe it makes more sense to use a displayed surface (molmap surface or molecular surface) and the "mask" command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> Elaine
On Sep 29, 2020, at 11:46 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Well I'm trying to make a mask for a part of my molecule, my strategy for this is to create a molmap of 60 A (map1) and another of 5 A (map2) and subtract map1 - map2
Usually people would suggest using volume eraser for this, but I want to go with the lazy approach of subtraction!!!
Is there a way I can tweak the molmap / vop subtract settings to give me what I want?
On Tue, Sep 29, 2020 at 11:41 AM Tom Goddard <goddard@sonic.net> wrote: Correct, vop subtract does not use displayed threshold levels in any way.
Tom
On Sep 29, 2020, at 11:23 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I don't see anything about map threshold in the "vop subtract" link I sent you earlier, so I don't think it has an effect.
So the factors you can control are the molmap resolution (as you said) and molmap grid spacing. The resolution of results from map interpolation (which is part of subtraction and several other map calculations) depend on input map resolution, grid spacing, bumpiness, and the shift between their grids, as discussed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#notes>
On Sep 29, 2020, at 10:53 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks a lot for the response, I can send data if necessary, but it likely has to do with options / resolution
The higher resolution of map2 is, the sharper the subtraction. I tried using a finer gridSpacing but it doesn't change much!
Does the map threshold factor into the subtraction?
On Tue, Sep 29, 2020 at 10:05 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, To my knowledge the map subtraction is precise. But if you think there is a problem, you will need to give a precise and detailed description of exactly what you did, including the data files and all the steps needed to show the problem, and why you believe there is a problem (and possibly use menu: Help... Report a Bug, instead of sending e-mail here). If we can't reproduce a problem, we can't fix it!
It may be that you need to create the molmaps with smaller grid spacing to give a more precise result.
molmap details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
vop subtract details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1!
how can I get precise subtraction?
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Correction. vop subtract does not use the map threshold levels unless the minRMS option is given. As described in the vop subtract documentation: "the minRMS option can be used to scale othermap automatically to minimize the root-mean-square sum of the resulting (subtracted) values at grid points within the lowest contour of othermap." https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract> Tom
On Sep 29, 2020, at 11:41 AM, Tom Goddard <goddard@sonic.net> wrote:
Correct, vop subtract does not use displayed threshold levels in any way.
Tom
On Sep 29, 2020, at 11:23 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I don't see anything about map threshold in the "vop subtract" link I sent you earlier, so I don't think it has an effect.
So the factors you can control are the molmap resolution (as you said) and molmap grid spacing. The resolution of results from map interpolation (which is part of subtraction and several other map calculations) depend on input map resolution, grid spacing, bumpiness, and the shift between their grids, as discussed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#notes>
On Sep 29, 2020, at 10:53 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks a lot for the response, I can send data if necessary, but it likely has to do with options / resolution
The higher resolution of map2 is, the sharper the subtraction. I tried using a finer gridSpacing but it doesn't change much!
Does the map threshold factor into the subtraction?
On Tue, Sep 29, 2020 at 10:05 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, To my knowledge the map subtraction is precise. But if you think there is a problem, you will need to give a precise and detailed description of exactly what you did, including the data files and all the steps needed to show the problem, and why you believe there is a problem (and possibly use menu: Help... Report a Bug, instead of sending e-mail here). If we can't reproduce a problem, we can't fix it!
It may be that you need to create the molmaps with smaller grid spacing to give a more precise result.
molmap details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
vop subtract details and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1!
how can I get precise subtraction?
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Ahmad Khalifa -
Elaine Meng -
Tom Goddard