[Chimera-users] Chimera/Modeller to add missing residues

Daipayan Sarkar sdaipayan at gmail.com
Wed Nov 15 19:27:04 PST 2017


Hi Elaine,

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
  N
ATOM      2  CA  CYS A   1      31.974  -7.012  48.720  1.00 17.01
  C
ATOM      3  C   CYS A   1      33.101  -6.917  47.728  1.00 15.67
  C
ATOM      4  O   CYS A   1      34.254  -6.671  48.116  1.00 16.39
  O
ATOM      5  CB  CYS A   1      31.253  -5.658  48.764  1.00 17.77
  C
ATOM      6  SG  CYS A   1      32.167  -4.263  49.459  1.00 19.16
  S


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
  N
ATOM      2  CA  CYS     1      31.954  -7.042  48.762  1.00  0.00
  C
ATOM      3  CB  CYS     1      31.233  -5.687  48.812  1.00  0.00
  C
ATOM      4  SG  CYS     1      32.146  -4.297  49.517  1.00  0.00
  S
ATOM      5  C   CYS     1      33.082  -6.942  47.773  1.00  0.00
  C
ATOM      6  O   CYS     1      34.235  -6.698  48.164  1.00  0.00
  O


Regards,
Daipayan


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.
>
> Elaine
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