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Thank you Elaine, Tom and Eric.<span id="ms-outlook-android-cursor"></span><br>
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Very helpful indeed!!<br>
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Yaikhomba<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, February 16, 2021 10:04:14 PM<br>
<b>To:</b> Y. Mutum <ym337@cam.ac.uk><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential</font>
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<div class="PlainText">Hi Yaikhomba et al.<br>
<br>
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.<br>
<br>
So if #1 includes nonprotein atoms, instead of <br>
<br>
coulombic #1 surface #2<br>
<br>
it would be safer to give <br>
<br>
coulombic protein surface #2<br>
<br>
...to use all protein atoms, or you could also be more specific about the model and/or chain ID:<br>
<br>
coulombic #1 & protein surface #2<br>
<br>
coulombic #1/A & protein surface #2<br>
<br>
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!<br>
Best,<br>
Elaine<br>
<br>
> On Feb 16, 2021, at 12:00 PM, Tom Goddard <goddard@sonic.net> wrote:<br>
> <br>
> I have fixed the mlp command so it can directly color volume surfaces -- will be in tonight's ChimeraX builds.<br>
> <br>
> Tom<br>
> <br>
> <br>
>> On Feb 13, 2021, at 1:06 PM, Tom Goddard <goddard@sonic.net> wrote:<br>
>> <br>
>> You can color a cryoEM map surface #2 directly using<br>
>> <br>
>> coulombic #1 surface #2<br>
>> <br>
>> and also mlp should work<br>
>> <br>
>> mlp #1 surface #2<br>
>> <br>
>> but the mlp command has a bug that prevents that from working -- I will fix it next week.<br>
>> <br>
>> Tom<br>
>> <br>
>> <br>
>>> On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk> wrote:<br>
>>> <br>
>>> Hi<br>
>>> <br>
>>> 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.<br>
>>> <br>
>>> 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'.<br>
>>> <br>
>>> First, I tried to generate a 'mlp' using the command:<br>
>>> >>> mlp #1 map true color true<br>
>>> <br>
>>> 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.<br>
>>> <br>
>>> 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.<br>
>>> <br>
>>> Any workaround suggestions would be helpful for electrostatic too.<br>
>>> <br>
>>> Thanks<br>
>>> Yaikhomba<br>
>>> _______________________________________________<br>
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>> <br>
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> <br>
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