[Chimera-users] alignment of identical sequences

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 28 16:02:51 PST 2015

On second thought, the unaligned parts might make the process harder, because when you align the sequence of your target with those templates, you would have to make sure the target residues are aligned with the template with 3D structure, instead of the one lacking those residues.

Thus, in this case I recommend just using the MatchMaker alignment and skipping the Match->Align step.  Turn on the option on the MatchMaker dialog to “Show pairwise alignment(s)”, or if you are using the matchmaker command, use the “show” option.  The command could be something like:

mm #0 #1 show true

I hope this helps,

On Jan 28, 2015, at 3:55 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Monete,
> The short answer is that it does not matter for modeling, because all of the residues that are the same but not aligned in the sequence alignment are missing from the 3D structure of one or both of your two structures.  Only the residues in the 3D structure(s) will be used for templating.  The residues in the sequence are read from the SEQRES section of the PDB file, but some of those residues are often not visible in the 3D crystal structure, so they are not included in the atomic coordinates section of the PDB file.  The residues missing from the 3D structure are shown in the red outlines.  (Not the light orange boxes, only the red outline boxes.)
> The longer answer is to explain why they are missing:
> I am guessing you first used MatchMaker but then created the alignment with the next step mentioned in that earlier e-mail, Match->Align.  Match->Align uses only 3D structure, not the sequence to create the alignment, and thus it will not align sequences that are not in both 3D structures.  If you instead use the sequence alignment from the MatchMaker step, it will have all the identical residues aligned correctly.  However, as mentioned above, this does not matter for any 3D comparative (homology) modeling you might do later that uses those 2 structures as templates.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jan 28, 2015, at 1:38 PM, Monete Rajão Gomes <moneterg at gmail.com> wrote:
>> Hi,
>> I have some problem these days about superimpose templates with matchmaker. I followed this tutorial http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006686.html.
>> There are regions on aminoacids sequences which are identical. So, when I superimpose them, they stay separated. I am sending a screenshot attached. It would be great if you could help me.
>> Best,
>> Monete
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