<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Hi Tom</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="background-color:rgb(255, 255, 255);display:inline !important">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).</span><br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="background-color:rgb(255, 255, 255);display:inline !important"><br>
</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="background-color:rgb(255, 255, 255);display:inline !important"></span>The commands I used were: </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
>>> open 5gup; open 9539 from emdb</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
>>> <span style="background-color:rgb(255, 255, 255);display:inline !important">coulombic #1 surface #2</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="background-color:rgb(255, 255, 255);display:inline !important"><br>
</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="background-color:rgb(255, 255, 255);display:inline !important"><span style="background-color:rgb(255, 255, 255);display:inline !important">After this, I get this error (the residue list below is not complete, but I have left a few to help gauge
the error): </span><br>
</span></div>
<blockquote style="margin-top:0;margin-bottom:0">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="background-color:rgb(255, 255, 255);display:inline !important"><br>
</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-size: 8pt;">The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics:</span>
<div><span style="font-size: 8pt;">/2 SER 79...</span></div>
<div><span style="font-size: 8pt;">...</span></div>
<div><span style="font-size: 8pt;">/v GLU 452</span></div>
<div><span style="font-size: 8pt;">/x MET 289</span></div>
<div><br>
</div>
<div><span style="font-size: 8pt;">Using Amber 20 recommended default charges and atom types for standard residues</span></div>
<div><span style="font-size: 8pt;">Traceback (most recent call last):</span></div>
<div><span style="font-size: 8pt;"> 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</span></div>
<div><span style="font-size: 8pt;"> cmd.run(cmd_text)</span></div>
<div><span style="font-size: 8pt;"> 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</span></div>
<div><span style="font-size: 8pt;"> result = ci.function(session, **kw_args)</span></div>
<div><span style="font-size: 8pt;"> 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</span></div>
<div><span style="font-size: 8pt;"> assign_charges(session, needs_assignment, his_scheme, charge_method,</span></div>
<div><span style="font-size: 8pt;"> 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</span></div>
<div><span style="font-size: 8pt;"> add_charges(session, charged_residues, method=charge_method, status=status)</span></div>
<div><span style="font-size: 8pt;"> 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</span></div>
<div><span style="font-size: 8pt;"> uncharged_res_types = add_standard_charges(session, residues, status=status, query_user=query_user,</span></div>
<div><span style="font-size: 8pt;"> 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</span></div>
<div><span style="font-size: 8pt;"> for res_type, residues in uncharged_res_types.items():</span></div>
<div><span style="font-size: 8pt;">RuntimeError: dictionary changed size during iteration</span></div>
<div><br>
</div>
<div><span style="font-size: 8pt;">RuntimeError: dictionary changed size during iteration</span></div>
<div><br>
</div>
<div><span style="font-size: 8pt;">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</span></div>
<div><span style="font-size: 8pt;">for res_type, residues in uncharged_res_types.items():</span></div>
<div><br>
</div>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-size: 8pt;">See log for complete Python traceback.</span><br>
</div>
</blockquote>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-size: 8pt;"><br>
</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-size: 8pt;">Thanks</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-size: 8pt;">Yaikhomba</span></div>
<blockquote style="margin-top:0;margin-bottom:0">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
</div>
<blockquote style="margin-top:0;margin-bottom:0">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
</blockquote>
</blockquote>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Y. Mutum <ym337@cam.ac.uk><br>
<b>Sent:</b> 14 February 2021 11:02<br>
<b>To:</b> Tom Goddard <goddard@sonic.net><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>
<div> </div>
</div>
<div>
<div dir="auto" style="direction:ltr; margin:0; padding:0; font-family:sans-serif; font-size:11pt; color:black">
Hi Tom<span id="x_ms-outlook-android-cursor"></span><br>
<br>
</div>
<div dir="auto" style="direction:ltr; margin:0; padding:0; font-family:sans-serif; font-size:11pt; color:black">
Thanks for this.<br>
<br>
</div>
<div dir="auto" style="direction:ltr; margin:0; padding:0; font-family:sans-serif; font-size:11pt; color:black">
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>
<br>
</div>
<div dir="auto" style="direction:ltr; margin:0; padding:0; font-family:sans-serif; font-size:11pt; color:black">
Thanks<br>
</div>
<div dir="auto" style="direction:ltr; margin:0; padding:0; font-family:sans-serif; font-size:11pt; color:black">
Yaikhomba<br>
<br>
</div>
<div dir="auto" style="direction:ltr; margin:0; padding:0; font-family:sans-serif; font-size:11pt; color:black">
<span id="x_OutlookSignature">
<div dir="auto" style="direction:ltr; margin:0; padding:0; font-family:sans-serif; font-size:11pt; color:black">
Get <a href="https://aka.ms/ghei36">Outlook for Android</a></div>
</span><br>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><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>
<div> </div>
</div>
<div class="" style="word-wrap:break-word; line-break:after-white-space">You can color a cryoEM map surface #2 directly using
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>coulombic #1 surface #2</div>
<div class=""><br class="">
</div>
<div class="">and also mlp should work</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>mlp #1 surface #2</div>
<div class=""><br class="">
</div>
<div class="">but the mlp command has a bug that prevents that from working -- I will fix it next week.</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<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>
<br class="x_x_Apple-interchange-newline">
<div class="">
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
Hi</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<br class="">
</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
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>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<br class="">
</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
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>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<br class="">
</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
First, I tried to generate a 'mlp' using the command:</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
>>> mlp #1 map true color true</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<br class="">
</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
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_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>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<br class="">
</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
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_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>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<br class="">
</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
Any workaround suggestions would be helpful for electrostatic too.</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<br class="">
</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
Thanks</div>
<div class="" style="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; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
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
mailing list</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">
<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">
<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">Manage
subscription:</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">
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" 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">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</body>
</html>