If you have not edited the file, the WebCSD file will contain the contents of
the asymmetric unit of a small molecule structure, with reported geometry and
esds, but no restraints, not least of all because small molecule refinements
are (nearly always) unrestrained. This would be CIF format.
C
An NIH-funded postdoctoral research position is available immediately in the
Hughson lab at Princeton University. Our group’s research focuses on the
remarkable protein machinery that generates the interior architecture of
eukaryotic cells by orchestrating the formation and fusion of cargo-carry
Paul was a little too terse, perhaps.
In script form
peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx
keywords in here
EOF-pmx
at least that's what works for me in Csh. Bash proselytizers will correct me
as necessary...
Phil Jeffrey
Princeton
R1 of 17% is bad for small molecule.
0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs
then these might be too aggressive for small molecule-type refinement stats -
try a more conservative cutoff lie 0.9 and see how that changes R1. However I
suspect it's more to do w
You're casting yourself in the Emma Thompson role for the remake of "I Am
Legend" ?
Phil
From: CCP4 bulletin board on behalf of Jacob Keller
Sent: Wednesday, February 17, 2021 2:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Contagious, Self-Distributi
K-containing
structures, I haven't found a counter-example yet - apart from those where the
UNK residues are a single contiguous stretch and given their own chain ID. So a
recent problem?
From: Philip D. Jeffrey mailto:pjeff...@princeton.edu>>
Sent: 12
Doesn't seem to be the case for all instances: that table isn't present in 5BV0
despite the N-terminal residues of Nyv1 being modeled as UNK in the
Vps16:Vps33:Nyv1 complex due to a symmetry overlap. Nyv1, C165-179 are UNK
with partial occupancy, which is the N-terminal part of the model for th
As Paul observes, there's a bona fide email list for phenix, but in fact
comparing REFMAC to phenix.refine might be useful to see if this really is a
program bug or if it's a bug in the model. Sometimes one is better than the
other.
For phenix.refine:
Put the Tyr in the "right" place and scou
:: which indicates the 6 molecules are far away from each other.
Those are just the symmetry operators for space group P321. It tells you
nothing about how far apart the molecules are, although the cell dimensions do
in fact impose some constraints.
However look at REMARK 350 in the PDB format
Sanity check:
Please check that the number of the reflections in the .mtz file is the same as
in the .sca file.
Please check that the cell dimensions in the MTZ file are the same as in the
header of the .sca file
If that's true, and it probably is, then this is a general issue with SCALEPACK
-
Hello Abhik
In coot use: Calculate>Merge Molecules to append one structure to another.
Coot will change the chain labels for you, which might work out OK in this case.
Alternatively, I've done a lot of this in my time:
Make a copy of the reference PDB file
Open it in a simple text edit (emacs,
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