[Chimera-users] Chimera/Modeller to add missing residues
sdaipayan at gmail.com
Wed Nov 15 19:27:04 PST 2017
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.
The coordinates for chain A of the first residue in original PDB file:
ATOM 1 N CYS A 1 32.449 -7.381 50.051 1.00 18.85
ATOM 2 CA CYS A 1 31.974 -7.012 48.720 1.00 17.01
ATOM 3 C CYS A 1 33.101 -6.917 47.728 1.00 15.67
ATOM 4 O CYS A 1 34.254 -6.671 48.116 1.00 16.39
ATOM 5 CB CYS A 1 31.253 -5.658 48.764 1.00 17.77
ATOM 6 SG CYS A 1 32.167 -4.263 49.459 1.00 19.16
The coordinates for chain A of the first residue in PDB file after adding
missing residues using Chimera-Modeller:
ATOM 1 N CYS 1 32.426 -7.418 50.092 1.00 0.00
ATOM 2 CA CYS 1 31.954 -7.042 48.762 1.00 0.00
ATOM 3 CB CYS 1 31.233 -5.687 48.812 1.00 0.00
ATOM 4 SG CYS 1 32.146 -4.297 49.517 1.00 0.00
ATOM 5 C CYS 1 33.082 -6.942 47.773 1.00 0.00
ATOM 6 O CYS 1 34.235 -6.698 48.164 1.00 0.00
On Tue, Nov 14, 2017 at 12:00 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Forgot to finish this one thought, sorry...
> > On Nov 14, 2017, at 9:47 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > 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
> … 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.
> 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.
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