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Hi Tom<span id="ms-outlook-android-cursor"></span><br>
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Thanks for this.<br>
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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?<br>
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Thanks<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> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Saturday, February 13, 2021 9:06:59 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="" style="word-wrap:break-word; line-break:after-white-space">You can color a cryoEM map surface #2 directly using
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>coulombic #1 surface #2</div>
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<div class="">and also mlp should work</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>mlp #1 surface #2</div>
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<div class="">but the mlp command has a bug that prevents that from working -- I will fix it next week.</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div class="">On Feb 13, 2021, at 6:07 AM, Y. Mutum <<a href="mailto:ym337@cam.ac.uk" class="">ym337@cam.ac.uk</a>> wrote:</div>
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Hi</div>
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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.</div>
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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'.</div>
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First, I tried to generate a 'mlp' using the command:</div>
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>>> mlp #1 map true color true</div>
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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.<span class="x_Apple-converted-space"> </span><span class="" style="background-color:rgb(255,255,255); display:inline!important">I
also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.</span></div>
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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<span class="x_Apple-converted-space"> </span><a href="https://www.emdataresource.org/EMD-0667" target="_blank" rel="noopener" class="" style="box-sizing:border-box; color:rgb(51,122,183)">EMD-0667</a>.</div>
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Any workaround suggestions would be helpful for electrostatic too.</div>
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Thanks</div>
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Yaikhomba</div>
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">ChimeraX-users
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<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">ChimeraX-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
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