<div dir="ltr">Hello,<div><br></div><div><font face="arial, sans-serif">Yes, I did try to go off a couple of the examples. (i.e.Â
</font><span style="color:rgb(0,0,0)"><font face="arial, sans-serif" style="">atoms named N, CA, C, O in chain A) with the align command but I was missing certain classifiers I believe it said. The commands you used did help, as it gave a reference to go off of to start rotating bonds to create what I needed. Also, I used a text editor to fix the residue names. Thank you Elaine, I appreciate it.</font></span></div><div><font color="#000000" face="arial, sans-serif"><br></font></div><div><font color="#000000" face="arial, sans-serif"><br clear="all"></font><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div>Thank you,</div><div><br></div><div>Heather Noriega</div>PhD-Pharmaceutical Science student <div>Howard University<br><div><a href="mailto:heather.noriega@bison.howard.edu" target="_blank">heather.noriega@bison.howard.edu</a></div><div>520-203-1883</div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Mar 11, 2022 at 12:05 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;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Heather,<br>
You would specify the atoms directly in the command line. How to specify atoms in commands is explained here:d<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html</a>><br>
<br>
Actually if you would click the "matchatoms" or "refatoms" link in the help page for "align," it would show you that page anyway, which has several examples.  Did you try anything yourself?<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html</a>><br>
<br>
Issues I see are that <br>
<br>
(1) your model #1 has two copies of the PEG. Which one are you trying to align with #2?  By holding the mouse over some atom in each copy I can see that one is chain C (reported as #1/C in pop-up info balloon) and the other one is chain D. All three of them have the same residue name, UNL.<br>
<br>
(2) your model #2 has hydrogens but #1 does not. You need to have equal numbers of "matchatoms" and "refatoms" so you would either need to delete the hydrogens or a use a specification that excludes them<br>
<br>
Starting from your session I used these commands<br>
<br>
delete H<br>
align #2 to #1/C<br>
[.... or to do it for the other copy ...]<br>
align #2 to #1/D<br>
<br>
None of this cares what is selected, i.e. those commands don't use the concept of selection.<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 Mar 11, 2022, at 8:04 AM, Noriega, Heather via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hello,<br>
> I hope you are well Elaine. I am wondering if there is a way to align my combined model UNL to my model 2. In hopes this could be a reference model of my docking done in Chimera for future builds. I did figure out the bonding, thank you. :)<br>
> <br>
> I attached the session, and have read the align command. I am just unsure how to manipulate it to superimpose the ligand. <br>
> <br>
> align matchatoms (the whole model 2) toAtoms (UNL on model 1). <br>
> Thanks for your help. <br>
<br>
</blockquote></div>