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It worked!! Thank you so much again!</div>
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Matteo</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Monday, January 23, 2023 8:49 PM<br>
<b>To:</b> Citterico, Matteo <matteo.citterico@helsinki.fi><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] electrostatic surface of docking model</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Matteo,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>I guess my suggestion is to use a text editor to split the chains into two PDB files. Then open those files in ChimeraX and use the "combine" command to combine them into a single
model ("combine #1-2 close true"). That will rename one of the chains to 'B'. You could then save the combined model as a new PDB ("save some_folder/combined.pdb").</div>
<div class=""><br class="">
</div>
<div class="">--Eric<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 23, 2023, at 10:37 AM, Citterico, Matteo via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
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Thank you for the quick reply! I am not very experienced in modifying pdb files. <span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">The only option I can think of is changing to "B" the chain ID of every residue of the second
protein in the pdb text. Could you suggest me a faster way to do this? </span></div>
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<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Thank you very much for your help!</span></div>
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<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><br class="">
</span></div>
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<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Matteo</span></div>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Monday, January 23, 2023 7:44 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Citterico, Matteo <<a href="mailto:matteo.citterico@helsinki.fi" class="">matteo.citterico@helsinki.fi</a>><br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [chimerax-users] electrostatic surface of docking model</font>
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Hi Matteo,
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>The problem is that both your chains have chain ID A. They need to have different IDs.</div>
<div class=""><br class="">
</div>
<div class="">--Eric<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 23, 2023, at 9:29 AM, Citterico, Matteo via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; background-color:rgb(255,255,255)">Hi Eric,</span></div>
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<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; background-color:rgb(255,255,255)">Thanks for your reply and explanation! Attached here is my model. I already tried to directly delete residue 244, but then I get the same
error message for residue 243. I have no clue to understand why that is happening, so thank you very much for digging into it!</span></div>
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Have a nice day!</div>
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Matteo</div>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_x_Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class="">
<b class="">Sent:</b><span class="x_x_Apple-converted-space"> </span>Friday, January 20, 2023 6:50 PM<br class="">
<b class="">To:</b><span class="x_x_Apple-converted-space"> </span>Citterico, Matteo <<a href="mailto:matteo.citterico@helsinki.fi" class="">matteo.citterico@helsinki.fi</a>><br class="">
<b class="">Cc:</b><span class="x_x_Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a><span class="x_Apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class="">
<b class="">Subject:</b><span class="x_x_Apple-converted-space"> </span>Re: [chimerax-users] electrostatic surface of docking model</font>
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Hi Matteo,
<div class=""><span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>I guess you need to figure out why there is a hydrogen bonded to the backbone C of residue 244. The C of an amino acid shouldn't have any hydrogens bonded to it. If you wanted,
you<span class="x_x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> </span>could send the structure to me and I'd try to offer further insight as to what is happening (I don't have permission to access your job via the link you included).</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">--Eric</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
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<blockquote type="cite" class="">
<div class="">On Jan 20, 2023, at 4:01 AM, Citterico, Matteo via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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<span class="x_x_x_elementToProof" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; background-color:rgb(255,255,255)">Hello everyone,</span></div>
<div class="x_x_x_elementToProof" 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="x_x_x_elementToProof x_x_x_ContentPasted0" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; background-color:rgb(255,255,255)">I am trying to visualize the electrostatic potential surface of a docking model generated with
ClusPro2.0 (job: <a href="https://cluspro.bu.edu/models.php?job=898454" id="LPlnk568970" class="">https://cluspro.bu.edu/models.php?job=898454</a>).</span></div>
<div class="x_x_x_elementToProof" 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="x_x_x_elementToProof x_x_x_ContentPasted0 x_x_x_ContentPasted1 x_x_x_ContentPasted2" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; background-color:rgb(255,255,255)">When I click on the electrostatic button on ChimeraX
1.3 to visualize<span class="x_x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> </span>the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb
#/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)."</span></div>
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<span class="x_x_x_elementToProof x_x_x_ContentPasted0 x_x_x_ContentPasted1 x_x_x_ContentPasted2" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; background-color:rgb(255,255,255)">How can I solve this problem? </span></div>
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Thank you for the help and always a big up to the Chimera staff!</div>
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Matteo</div>
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<span id="x_x_cid:AE77EDE6-6A5A-4345-B8C7-9BDBDD01E998" class=""><model.000.01.pdb></span><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">
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<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>
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