<div dir="ltr"><div dir="ltr"><div>Hello Elaine,</div><div><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">Here is a little bit more detail about what we’re trying to
do. We are trying to use Chimera to model a fusion that we constructed in the
lab. The structure we’re working with (pdb: 3pgf) is a complex of a Fab and Maltose
binding protein (MBP). In the lab, we fused the C-terminus of the Fab heavy
chain to the N-termius of MBP with a short linker. In chimera, we would like to
duplicate the structure of the complex, and connect the C-temrinus of one to
the N-terminus of the other. Precisely, we would like to connect the C-terminus
of the heavy chain (Chain H), to the N-terminus of the MBP (chain A) of the duplicated
structure with the short linker. </p><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">

</span><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal"> </p><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">

</span><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">We have a couple of issues to overcome:</p><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">

</span><p style="margin:0in 0in 0pt 0.5in;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">1.<span style="line-height:normal;font-size:7pt;font-stretch:normal">    
</span>There are a few amino acids missing from the structure
at the C-terminus of chain H, and we would like to add those before connecting
to the N-terminal amino acid (first Lysine) of MBP.</p><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">

</span><p style="margin:0in 0in 0pt 0.5in;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">2.<span style="line-height:normal;font-size:7pt;font-stretch:normal">    
</span>When we try to use the Adda command we can only add a couple of residues until we get to the following command (adda ser,222 :221.h) at this point we start getting the message "can't add amino acid, model already contains residue with sequence '222'".</p><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">

</span><p style="margin:0in 0in 0pt 0.5in;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">3.<span style="line-height:normal;font-size:7pt;font-stretch:normal">    
</span>It would be very helpful we are able to
duplicate the entire structure, and connect the C-terminal of chain H in one structure
to the N-terminal of the MBP (chain A) with the following linker sequence in
between them: DKTHTSGSGA</p><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">

</span><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal"> </p><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">

</span><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">Thank you again and please let us know if you have any questions
or need additional information.</p><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal"><br></p><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">Thank you,</p><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">Brody</p><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal"><br></p><p class="MsoNormal" style="margin:0in 0in 0pt;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Calibri,sans-serif;font-size:12pt;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal">Attached is a photo of what we are trying to accomplish using Chimera.</p><b></b><i></i><u></u><strike></strike><br></div></div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Wed, Jun 3, 2020 at 12:10 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid">This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.<br>
-------<br>
<br>
Hi Brody,<br>
To say much of anything, we would generally need more details, such as: what exactly you are trying to do (e.g. what kind of residue on which end of what structure), the specific commands or tool steps that you used, and what you mean by "having trouble,."<br>
<br>
In case you didn't already know, there is a command "addaa" described here, including an example:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html" target="_blank" rel="noreferrer">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.                       <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Jun 2, 2020, at 6:19 PM, brody deming <<a href="mailto:demingb@iu.edu" target="_blank">demingb@iu.edu</a>> wrote:<br>
> <br>
> Hello,<br>
>  <br>
> I am a Student at Indian University South Bend and I am doing some modeling using Chimera. I am having trouble trying to add residues to an existing protein I am working with. I am wondering if you had any advice for how to do this.<br>
>  <br>
> Thank you,<br>
> Brody<br>
<br>
<br>
</blockquote></div>