I am refining a 1.71A X-ray structure with phenix refine. I have everything
modelled in - ~150 residues in the ASU and a heme - and my R-work/R-free is
0.17/0.22. But when I went to deposit it, PDB pointed out that two of my
sidechains have distorted geometries. One is a His, and looking at it in
Igor
There is a Phenix BB for your Phenix related questions. You can subscribe
here.
http://www.phenix-online.org/mailman/listinfo/phenixbb
In the meantime, please send the Phenix version and OS to myself and Pavel
privately and I'm sure we can help. We may also need the inputs (privately,
of
Dear Igor
There's a phenix bulletin board for question like this, which is where you
should post the question. ( I crosspost here)
I would choose to not do the real space refinement in phenix.refine during
the last rounds of refinement of a model, when sidechain positions are
essentially
Hi Keitaro
Perfect!
Thanks, that's great.
Cheers
-- Ian
On Wed, 2 Dec 2020 at 22:31, Keitaro Yamashita
wrote:
> Dear Ian,
>
> For the moment in Refmac5 we need to use insertion codes to handle
> microheterogeneity. LINKR records are also needed in the header. So
> 7a5v.pdb should be
Dear Ian,
For the moment in Refmac5 we need to use insertion codes to handle
microheterogeneity. LINKR records are also needed in the header. So
7a5v.pdb should be changed like this:
954a955,957
LINKRTHR A 279 LYS A 279A gap
LINKRC VAL A
Hi Folmer,
I would choose to not do the real space refinement in phenix.refine during
> the last rounds of refinement of a model, when sidechain positions are
> essentially correct.
>
by design it is supposed to place and fit side chains as good as possible,
satisfying both map fit and geometry
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Only a hunch but this works:
ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O
ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O
And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50 27.65
N
ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C
ATOM
Dear All
I just downloaded a PDB file (7A5V) from the EBI server, tried to run
Refmac on it and got the error:
ERROR: in chain A residue: 279 different residues have the same number
There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
===>
Hi Ian,
AFAIK there is no clean solution for this and I imagine this problem goes very
deep into the internal representation of the model in REFMAC. That said, 1 in 6
missing PDB-REDO entries is caused by this problem, so a solution would be very
welcome.
Cheers,
Robbie
> -Original
Sorry Eleanor, same problem in 'interleaved' order (except for 2 extra
atoms in LYS).
Strangely the error message is now repeated 91 times, even though there are
only 16 atoms (7+9) in the 2 residues: previously I only got the message
once !
Guess I must have imagined that it worked - it's
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