Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
Hi MJ, There is a different value for each surface vertex (it is not per atom), and there is not a one-to-one relationship between surface vertices on two different structures. So it wouldn't be clear what to subtract from what, and also messy because there are a large number of surface vertices. For properties that vary continuously on the molecular surface, my opinion is that they are best understood by side-by-side visual interpretation of coloring according to the surface values. Maybe if the structures are superimposed, you could use the "map" option of the "mlp" to command to create a map model of the MLP values (values at points on a grid) for each one and then "volume subtract" to create a difference map from the two MLP maps, and then color one of their molecular surfaces by the difference map with "color sample" ... however, I am not convinced that the result would be meaningful, at least in part because of the different shapes of the two molecular surfaces. For details of how to use these commands and their options, see their respective help pages: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 8, 2024, at 12:39 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
Hi Elaine, Got your point! Thank a lot! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
On Jan 8, 2024, at 14:52, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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Hi MJ, There is a different value for each surface vertex (it is not per atom), and there is not a one-to-one relationship between surface vertices on two different structures. So it wouldn't be clear what to subtract from what, and also messy because there are a large number of surface vertices.
For properties that vary continuously on the molecular surface, my opinion is that they are best understood by side-by-side visual interpretation of coloring according to the surface values.
Maybe if the structures are superimposed, you could use the "map" option of the "mlp" to command to create a map model of the MLP values (values at points on a grid) for each one and then "volume subtract" to create a difference map from the two MLP maps, and then color one of their molecular surfaces by the difference map with "color sample" ... however, I am not convinced that the result would be meaningful, at least in part because of the different shapes of the two molecular surfaces.
For details of how to use these commands and their options, see their respective help pages:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 8, 2024, at 12:39 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
Hi MJ, Maybe coloring residues by change in per-residue solvent exposed surface area would get at what you are trying to show. ChimeraX can compute the per-residue exposed surface area with the "measure sasa" command https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa and if you subtracted the values for the two conformations you could see which residues are becoming more exposed and which less. You could focus on hydrophobic residues only if you are interested in hydrophobic patches becoming exposed. Tom
On Jan 8, 2024, at 2:58 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Got your point! Thank a lot! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
On Jan 8, 2024, at 14:52, Elaine Meng <meng@cgl.ucsf.edu> wrote:
!-------------------------------------------------------------------| This Message Is From an External Sender This message came from outside your organization. |-------------------------------------------------------------------!
Hi MJ, There is a different value for each surface vertex (it is not per atom), and there is not a one-to-one relationship between surface vertices on two different structures. So it wouldn't be clear what to subtract from what, and also messy because there are a large number of surface vertices.
For properties that vary continuously on the molecular surface, my opinion is that they are best understood by side-by-side visual interpretation of coloring according to the surface values.
Maybe if the structures are superimposed, you could use the "map" option of the "mlp" to command to create a map model of the MLP values (values at points on a grid) for each one and then "volume subtract" to create a difference map from the two MLP maps, and then color one of their molecular surfaces by the difference map with "color sample" ... however, I am not convinced that the result would be meaningful, at least in part because of the different shapes of the two molecular surfaces.
For details of how to use these commands and their options, see their respective help pages:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 8, 2024, at 12:39 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Tom, This also sounds good, I will try to make it, thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
On Jan 8, 2024, at 16:14, Tom Goddard <goddard@sonic.net> wrote:
This Message Is From an External Sender This message came from outside your organization. Hi MJ,
Maybe coloring residues by change in per-residue solvent exposed surface area would get at what you are trying to show. ChimeraX can compute the per-residue exposed surface area with the "measure sasa" command
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa
and if you subtracted the values for the two conformations you could see which residues are becoming more exposed and which less. You could focus on hydrophobic residues only if you are interested in hydrophobic patches becoming exposed.
Tom
On Jan 8, 2024, at 2:58 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Got your point! Thank a lot! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
On Jan 8, 2024, at 14:52, Elaine Meng <meng@cgl.ucsf.edu> wrote:
!-------------------------------------------------------------------| This Message Is From an External Sender This message came from outside your organization. |-------------------------------------------------------------------!
Hi MJ, There is a different value for each surface vertex (it is not per atom), and there is not a one-to-one relationship between surface vertices on two different structures. So it wouldn't be clear what to subtract from what, and also messy because there are a large number of surface vertices.
For properties that vary continuously on the molecular surface, my opinion is that they are best understood by side-by-side visual interpretation of coloring according to the surface values.
Maybe if the structures are superimposed, you could use the "map" option of the "mlp" to command to create a map model of the MLP values (values at points on a grid) for each one and then "volume subtract" to create a difference map from the two MLP maps, and then color one of their molecular surfaces by the difference map with "color sample" ... however, I am not convinced that the result would be meaningful, at least in part because of the different shapes of the two molecular surfaces.
For details of how to use these commands and their options, see their respective help pages:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 8, 2024, at 12:39 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
In the case of looking at SASA changes, you may also want to consider which atoms within the residue become more or less exposed. Hydrophobic vs. hydrophilic residues are classified based on their side chains, but if the only part of a hydrophobic residue that becomes more exposed is its backbone, it might not make the surface more hydrophobic. Elaine
On Jan 8, 2024, at 4:24 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, This also sounds good, I will try to make it, thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
On Jan 8, 2024, at 16:14, Tom Goddard <goddard@sonic.net> wrote:
This Message Is From an External Sender This message came from outside your organization. Hi MJ,
Maybe coloring residues by change in per-residue solvent exposed surface area would get at what you are trying to show. ChimeraX can compute the per-residue exposed surface area with the "measure sasa" command
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa
and if you subtracted the values for the two conformations you could see which residues are becoming more exposed and which less. You could focus on hydrophobic residues only if you are interested in hydrophobic patches becoming exposed.
Tom
On Jan 8, 2024, at 2:58 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Got your point! Thank a lot! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
On Jan 8, 2024, at 14:52, Elaine Meng <meng@cgl.ucsf.edu> wrote:
!-------------------------------------------------------------------| This Message Is From an External Sender This message came from outside your organization. |-------------------------------------------------------------------!
Hi MJ, There is a different value for each surface vertex (it is not per atom), and there is not a one-to-one relationship between surface vertices on two different structures. So it wouldn't be clear what to subtract from what, and also messy because there are a large number of surface vertices.
For properties that vary continuously on the molecular surface, my opinion is that they are best understood by side-by-side visual interpretation of coloring according to the surface values.
Maybe if the structures are superimposed, you could use the "map" option of the "mlp" to command to create a map model of the MLP values (values at points on a grid) for each one and then "volume subtract" to create a difference map from the two MLP maps, and then color one of their molecular surfaces by the difference map with "color sample" ... however, I am not convinced that the result would be meaningful, at least in part because of the different shapes of the two molecular surfaces.
For details of how to use these commands and their options, see their respective help pages:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 8, 2024, at 12:39 PM, M.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Elaine Meng -
M.J. -
Tom Goddard