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
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