<div dir="ltr">Hi Elaine, <div><br></div><div>Thanks for your detailed instructions. My apologies for the confusion but your guess about the different models is correct. After following your instructions, I compared the first residue of the original PDB file with the first residue of 'model 2 (residues missing in chain A)' and following is what I got. Note, the x, y, z coordinates of the atoms have changed and the sequence of atoms has changed. I am not sure why this happens. Can you help me understand? Note, the missing residues where added in model 2 but I am not showing here as there is nothing to compare against.</div><div><br></div><div><div class="gmail-">The coordinates for chain A of the first residue in original PDB file:</div><div class="gmail-"><div class="gmail-" style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><div class="gmail-" style="margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 1 N CYS A 1 32.449 -7.381 50.051 1.00 18.85 N</span></div><div class="gmail-" style="margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 2 CA CYS A 1 31.974 -7.012 48.720 1.00 17.01 C</span></div><div class="gmail-" style="margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 3 C CYS A 1 33.101 -6.917 47.728 1.00 15.67 C</span></div><div class="gmail-" style="margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 4 O CYS A 1 34.254 -6.671 48.116 1.00 16.39 O</span></div><div class="gmail-" style="margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 5 CB CYS A 1 31.253 -5.658 48.764 1.00 17.77 C</span></div><div class="gmail-" style="margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 6 SG CYS A 1 32.167 -4.263 49.459 1.00 19.16 S</span></div><div class="gmail-"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures"><br class="gmail-"></span></div></div></div><div class="gmail-" style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures"><br class="gmail-"></span></div><div class="gmail-" style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-" style="font-family:Arial;font-size:12px">The coordinates for chain A of the first residue in PDB file after adding missing residues using Chimera-Modeller:</span></span></div><div class="gmail-" style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures"><div class="gmail-" style="margin:0px;line-height:normal"><div class="gmail-" style="color:rgb(0,0,0);margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 1 N CYS 1 32.426 -7.418 50.092 1.00 0.00 N</span></div><div class="gmail-" style="color:rgb(0,0,0);margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 2 CA CYS 1 31.954 -7.042 48.762 1.00 0.00 C</span></div><div class="gmail-" style="color:rgb(0,0,0);margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 3 CB CYS 1 31.233 -5.687 48.812 1.00 0.00 C</span></div><div class="gmail-" style="color:rgb(0,0,0);margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 4 SG CYS 1 32.146 -4.297 49.517 1.00 0.00 S</span></div><div class="gmail-" style="color:rgb(0,0,0);margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 5 C CYS 1 33.082 -6.942 47.773 1.00 0.00 C</span></div><div class="gmail-" style="color:rgb(0,0,0);margin:0px;line-height:normal"><span class="gmail-" style="font-variant-ligatures:no-common-ligatures">ATOM 6 O CYS 1 34.235 -6.698 48.164 1.00 0.00 O</span></div><div><span class="gmail-" style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><br></div></div></span></div></div><div class="gmail_extra"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div><div><div><div><div>Regards,</div><div>Daipayan<br></div></div></div></div></div></div><br></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Nov 14, 2017 at 12:00 PM, Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Forgot to finish this one thought, sorry...<br>
<span class=""><br>
> On Nov 14, 2017, at 9:47 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br>
><br>
> An important point is that the Chimera-Modeller interface will only model one chain at a time. It does not care that other chains are there, so any added residues/loops might end up clashing with the other chains. In this case it didn’t seem<br>
<br>
</span>… that bad since the added residues were on the outside of the complex. However, Find Clashes/Contacts (in menu under Tools… Structure Analysis) identified a few clashes between those chains and the other chains in the merged model in my test. I only made one Modeller model of each chain. One reason you might want to try making more than one model of each chain is that they may have different numbers of clashes with the other chains in the structure. However, whether you care about this depends on what you are going to do with this overall structure. If it’s just for a picture, it’s not important, or if you were going to run minimization or dynamics, the clashes would easily resolve themselves in this case because they involve peptide termini on the outside of the complex.<br>
<br>
Finally, if you want to use Modeller to model the multi-chain complex with awareness of the other chains, you would have to use it separately outside of Chimera.<br>
<span class="HOEnZb"><font color="#888888"><br>
Elaine</font></span></blockquote></div><br></div></div>