Coloring Atoms by Hydrohpobicity and Electrostatic potential
Hi I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant. I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'. First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it. Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667<https://www.emdataresource.org/EMD-0667>. Any workaround suggestions would be helpful for electrostatic too. Thanks Yaikhomba
Hi Yaikhomba, It doesn't make any sense to color the atoms by MLP... the point of the MLP calculation is to combine all the atomic contributions into a potential that other molecules would "see" at the surface of the protein. I could say exactly the same thing about ESP (electrostatic potential). The values of ESP at the centers of same atoms used to compute the ESP are singularities (i.e. infinity if you ignored the effects of discretizing the calculation on a grid). In other words, the location is important and you definitely don't want the values from the atomic centers. However, it sounds like your ultimate goal is to apply the coloring to the isosurface of a cryoEM map instead of the atomic structure's molecular surface. To do that you first create a map file of the MLP (mlp command with map true), and then use that map to color the isosurface of the cryoEM map with the "color sample" command. In that command, surf-spec is the cryoEM map model, and then map map-model gives the MLP map. <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 Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.
I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.
First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.
Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667.
Any workaround suggestions would be helpful for electrostatic too.
Thanks Yaikhomba
The "coulombic" command to calculate ESP does not yet have an option to create a map model, sorry. Elaine
On Feb 13, 2021, at 9:09 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yaikhomba, It doesn't make any sense to color the atoms by MLP... the point of the MLP calculation is to combine all the atomic contributions into a potential that other molecules would "see" at the surface of the protein. I could say exactly the same thing about ESP (electrostatic potential). The values of ESP at the centers of same atoms used to compute the ESP are singularities (i.e. infinity if you ignored the effects of discretizing the calculation on a grid). In other words, the location is important and you definitely don't want the values from the atomic centers.
However, it sounds like your ultimate goal is to apply the coloring to the isosurface of a cryoEM map instead of the atomic structure's molecular surface.
To do that you first create a map file of the MLP (mlp command with map true), and then use that map to color the isosurface of the cryoEM map with the "color sample" command. In that command, surf-spec is the cryoEM map model, and then map map-model gives the MLP map. <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 Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.
I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.
First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.
Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667.
Any workaround suggestions would be helpful for electrostatic too.
Thanks Yaikhomba
Hi Elaine Thanks - both your suggestions on deleting surfaces to regain the speed, and this point about coloring the cryo-EM map works. Yaikhomba ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 13 February 2021 17:10 To: Y. Mutum <ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential The "coulombic" command to calculate ESP does not yet have an option to create a map model, sorry. Elaine
On Feb 13, 2021, at 9:09 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yaikhomba, It doesn't make any sense to color the atoms by MLP... the point of the MLP calculation is to combine all the atomic contributions into a potential that other molecules would "see" at the surface of the protein. I could say exactly the same thing about ESP (electrostatic potential). The values of ESP at the centers of same atoms used to compute the ESP are singularities (i.e. infinity if you ignored the effects of discretizing the calculation on a grid). In other words, the location is important and you definitely don't want the values from the atomic centers.
However, it sounds like your ultimate goal is to apply the coloring to the isosurface of a cryoEM map instead of the atomic structure's molecular surface.
To do that you first create a map file of the MLP (mlp command with map true), and then use that map to color the isosurface of the cryoEM map with the "color sample" command. In that command, surf-spec is the cryoEM map model, and then map map-model gives the MLP map. <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 Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.
I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.
First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.
Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667.
Any workaround suggestions would be helpful for electrostatic too.
Thanks Yaikhomba
You can color a cryoEM map surface #2 directly using coulombic #1 surface #2 and also mlp should work mlp #1 surface #2 but the mlp command has a bug that prevents that from working -- I will fix it next week. Tom
On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.
I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.
First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.
Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667 <https://www.emdataresource.org/EMD-0667>.
Any workaround suggestions would be helpful for electrostatic too.
Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Hi Tom Thanks for this. I've realised that the electrostatic calculation doesn't work, if there are posttranslationallymodified residues. In the case of pdb:6g2j for example, there's 2MR (dimethylated arginine). Could we please have a fix for this too? Thanks Yaikhomba Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Saturday, February 13, 2021 9:06:59 PM To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential You can color a cryoEM map surface #2 directly using coulombic #1 surface #2 and also mlp should work mlp #1 surface #2 but the mlp command has a bug that prevents that from working -- I will fix it next week. Tom On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk<mailto:ym337@cam.ac.uk>> wrote: Hi I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant. I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'. First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it. Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667<https://www.emdataresource.org/EMD-0667>. Any workaround suggestions would be helpful for electrostatic too. Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom I forgot to add, in addition to the non-standard protein residues, there are also a couple of errors, attributed to terminal OH group not added. The ChimeraX version here is: 1.2.dev202102050202 (2021-02-05). The commands I used were:
open 5gup; open 9539 from emdb coulombic #1 surface #2
After this, I get this error (the residue list below is not complete, but I have left a few to help gauge the error): The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /2 SER 79... ... /v GLU 452 /x MET 289 Using Amber 20 recommended default charges and atom types for standard residues Traceback (most recent call last): File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 275, in execute cmd.run(cmd_text) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/coulombic.py", line 86, in assign_charges add_charges(session, charged_residues, method=charge_method, status=status) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 19, in add_charges uncharged_res_types = add_standard_charges(session, residues, status=status, query_user=query_user, File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges for res_type, residues in uncharged_res_types.items(): RuntimeError: dictionary changed size during iteration RuntimeError: dictionary changed size during iteration File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges for res_type, residues in uncharged_res_types.items(): See log for complete Python traceback. Thanks Yaikhomba ________________________________ From: Y. Mutum <ym337@cam.ac.uk> Sent: 14 February 2021 11:02 To: Tom Goddard <goddard@sonic.net> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential Hi Tom Thanks for this. I've realised that the electrostatic calculation doesn't work, if there are posttranslationallymodified residues. In the case of pdb:6g2j for example, there's 2MR (dimethylated arginine). Could we please have a fix for this too? Thanks Yaikhomba Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Saturday, February 13, 2021 9:06:59 PM To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential You can color a cryoEM map surface #2 directly using coulombic #1 surface #2 and also mlp should work mlp #1 surface #2 but the mlp command has a bug that prevents that from working -- I will fix it next week. Tom On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk<mailto:ym337@cam.ac.uk>> wrote: Hi I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant. I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'. First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it. Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667<https://www.emdataresource.org/EMD-0667>. Any workaround suggestions would be helpful for electrostatic too. Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Yaikhomba, It is not simple to add charge calculations for nonstandard residues, and we have been working on it for months. In fact, an initial version of this capability is available in the "coulombic" command in the ChimeraX mac version current daily build, but is not documented yet, and needs to be better tested and probably improved before it is ready for wider use. *** More importantly: I do not think it is reasonable to do electrostatics calculations on this huge structure, not because of its size per se, but because as the Log messages are telling you, it is missing atoms from many dozens of STANDARD residues, i.e., their side chains were not built or were only partially built. Probably the atom positions could not be resolved by the authors from the density map at this resolution. *** Obviously if lots of charged residues are missing their side chains, their charges will not be represented and it will be fairly meaningless to calculate an electrostatic potential from the remaining atoms, or to try to draw any conclusions from what you get. It is important to pay attention to these Log messages telling you that there are atoms missing. Finally if you believe there is a bug causing a traceback, please use the "report a bug" dialog (e.g. from the Help menu, or sometimes the error dialog has a button to open it directly) rather than sending e-mail to this list. I hope this clarifies the situation, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2021, at 5:06 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi Tom
I forgot to add, in addition to the non-standard protein residues, there are also a couple of errors, attributed to terminal OH group not added. The ChimeraX version here is: 1.2.dev202102050202 (2021-02-05).
The commands I used were:
open 5gup; open 9539 from emdb coulombic #1 surface #2
After this, I get this error (the residue list below is not complete, but I have left a few to help gauge the error):
The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /2 SER 79... ... /v GLU 452 /x MET 289
Using Amber 20 recommended default charges and atom types for standard residues Traceback (most recent call last): File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 275, in execute cmd.run(cmd_text) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/coulombic.py", line 86, in assign_charges add_charges(session, charged_residues, method=charge_method, status=status) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 19, in add_charges uncharged_res_types = add_standard_charges(session, residues, status=status, query_user=query_user, File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges for res_type, residues in uncharged_res_types.items(): RuntimeError: dictionary changed size during iteration
RuntimeError: dictionary changed size during iteration
File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges for res_type, residues in uncharged_res_types.items():
See log for complete Python traceback.
Thanks Yaikhomba
From: Y. Mutum <ym337@cam.ac.uk> Sent: 14 February 2021 11:02 To: Tom Goddard <goddard@sonic.net> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential
Hi Tom
Thanks for this.
I've realised that the electrostatic calculation doesn't work, if there are posttranslationallymodified residues. In the case of pdb:6g2j for example, there's 2MR (dimethylated arginine). Could we please have a fix for this too?
Thanks Yaikhomba
Get Outlook for Android
From: Tom Goddard <goddard@sonic.net> Sent: Saturday, February 13, 2021 9:06:59 PM To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential
You can color a cryoEM map surface #2 directly using
coulombic #1 surface #2
and also mlp should work
mlp #1 surface #2
but the mlp command has a bug that prevents that from working -- I will fix it next week.
Tom
On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.
I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.
First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.
Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667.
Any workaround suggestions would be helpful for electrostatic too.
Thanks Yaikhomba
I have fixed the mlp command so it can directly color volume surfaces -- will be in tonight's ChimeraX builds. Tom
On Feb 13, 2021, at 1:06 PM, Tom Goddard <goddard@sonic.net> wrote:
You can color a cryoEM map surface #2 directly using
coulombic #1 surface #2
and also mlp should work
mlp #1 surface #2
but the mlp command has a bug that prevents that from working -- I will fix it next week.
Tom
On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk <mailto:ym337@cam.ac.uk>> wrote:
Hi
I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.
I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.
First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.
Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667 <https://www.emdataresource.org/EMD-0667>.
Any workaround suggestions would be helpful for electrostatic too.
Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Yaikhomba et al. A brief cautionary note that when using the "surfaces" option, you may need to be more specific about which atoms to use in the calculation. The "mlp" command automatically ignores non-protein atoms, so it's less likely to cause a problem, but "coulombic" does not, so bear in mind that if you give #1 it will try to include the charges of all atoms in #1, including solvent, ligands, etc. It may needlessly try to calculate charges for nonstandard ligands (and sometimes fail) when you really meant only to consider the protein atoms. So if #1 includes nonprotein atoms, instead of coulombic #1 surface #2 it would be safer to give coulombic protein surface #2 ...to use all protein atoms, or you could also be more specific about the model and/or chain ID: coulombic #1 & protein surface #2 coulombic #1/A & protein surface #2 I tend to forget this but then run into it when I'm actually trying to use the command, or put it in a tutorial! Best, Elaine
On Feb 16, 2021, at 12:00 PM, Tom Goddard <goddard@sonic.net> wrote:
I have fixed the mlp command so it can directly color volume surfaces -- will be in tonight's ChimeraX builds.
Tom
On Feb 13, 2021, at 1:06 PM, Tom Goddard <goddard@sonic.net> wrote:
You can color a cryoEM map surface #2 directly using
coulombic #1 surface #2
and also mlp should work
mlp #1 surface #2
but the mlp command has a bug that prevents that from working -- I will fix it next week.
Tom
On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.
I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.
First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.
Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667.
Any workaround suggestions would be helpful for electrostatic too.
Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Thank you Elaine, Tom and Eric. Very helpful indeed!! Yaikhomba Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, February 16, 2021 10:04:14 PM To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential Hi Yaikhomba et al. A brief cautionary note that when using the "surfaces" option, you may need to be more specific about which atoms to use in the calculation. The "mlp" command automatically ignores non-protein atoms, so it's less likely to cause a problem, but "coulombic" does not, so bear in mind that if you give #1 it will try to include the charges of all atoms in #1, including solvent, ligands, etc. It may needlessly try to calculate charges for nonstandard ligands (and sometimes fail) when you really meant only to consider the protein atoms. So if #1 includes nonprotein atoms, instead of coulombic #1 surface #2 it would be safer to give coulombic protein surface #2 ...to use all protein atoms, or you could also be more specific about the model and/or chain ID: coulombic #1 & protein surface #2 coulombic #1/A & protein surface #2 I tend to forget this but then run into it when I'm actually trying to use the command, or put it in a tutorial! Best, Elaine
On Feb 16, 2021, at 12:00 PM, Tom Goddard <goddard@sonic.net> wrote:
I have fixed the mlp command so it can directly color volume surfaces -- will be in tonight's ChimeraX builds.
Tom
On Feb 13, 2021, at 1:06 PM, Tom Goddard <goddard@sonic.net> wrote:
You can color a cryoEM map surface #2 directly using
coulombic #1 surface #2
and also mlp should work
mlp #1 surface #2
but the mlp command has a bug that prevents that from working -- I will fix it next week.
Tom
On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.
I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.
First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.
Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667.
Any workaround suggestions would be helpful for electrostatic too.
Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ 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 (3)
-
Elaine Meng -
Tom Goddard -
Y. Mutum