Thank you Pavel for the clarification!
What I was really trying to point out is that a missing atom, occ=0.00
and occ=0.01 are not as similar as one might naiively think. Also, if
you put a ligand into a pocket and the occupancy refines to 0, that
does not necessarily mean the ligand is
Dear all
I am getting this error while running arp/warp to build DNA/RNA:
PHIB is not assigned to an mtz label
Input was merged data (.mtz)
However no such problem while using arp/warp classic as i chose for
automated model building from existing model and not experimental phases.
Kindly help how
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Hi All,
I had an interesting case recently where a Cl atom of a chlorophenyl moiety
went missing in a structure (primary X-ray damage was the suspected culprit).
Small molecule Mass Spec suggested the atom was there to start with but it was
quite obviously missing in the maps (1.9Ang) and the
Dear all
i have a small query to ask and seek your suggestions:
I have collected a data for a protein with 324 residues and processed at
its best in P212121. So Matthews suggest 1 mol in ASU with expected Mol.
weight of 43 kDa with sovent content of 58% and 2 mol./ASU with 18% solvent
content.
Dear Monica,
On Jun 16, 2014, at 10:39 AM, Monica Mittal wrote:
Dear all
I am getting this error while running arp/warp to build DNA/RNA:
PHIB is not assigned to an mtz label
Input was merged data (.mtz)
However no such problem while using arp/warp classic as i chose for automated
model
Dear James
You seem to be discounting the possibility of a true vacuum inside a
structure, which is obviously not the same thing as 'something' (bulk
solvent or whatever). I accept that this is unlikely in the case of ligand
binding sites exposed to solvent, or indeed any site on the outer
That is puzzling.
18% solvent is not common and you would expect very strong diffraction with
such a low solvent content.
one possibility is that the NC symmetry is parallel to a crystal axis and
is making monoclinic data appear to have an extra 2-fold axis. (There is a
case I have heard of
Dear CCP4bb,
I'm refining an antibody structure which requires Kabat residue numbering with
insertion codes. My setup of Refmac5 and Buster both break peptide bonds
between some (not all) of the residues with insertion codes. I was wondering
whether there is a special way of handling these
Dear Ian,
This has been discussed in a review and related articles by Brian
Matthews and Liljun Liu:
Matthews BW, Liu L. A review about nothing: are apolar cavities in proteins
really empty? Protein Sci. 2009 Mar;18(3):494-502. doi: 10.1002/pro.61. Review.
PubMed PMID: 19241368; PubMed
Dear Daniel
Thanks for the info. I knew that Brian Matthews' group had done some work
in this area.
Cheers
-- Ian
On 16 June 2014 11:16, Daniel Picot daniel.pi...@ibpc.fr wrote:
Dear Ian,
This has been discussed in a review and related articles by Brian
Matthews and Liljun Liu:
Dear Jeff,
I would assume that clashing hydrogen atoms beome less and less an issue
with current refinement programs, since those I am familiar with
(refmac5 and phenix) both genereate constrained hydrogen atoms by
default now, and it has been like this for quite some time - so the
situation
There is no actual requirement to use Kabat numbering, you can avoid it
alrogether. Some argue that L27A is actually 28th amino acid in the protein
sequence, and labeling it as L27A is simply incorrect. I would suggest doing
refinement with plain numbering (no insertion codes) and changing it
If your translational NCS is defined by a vector that does not correspond
to lattice centering, i.e. has numbers different from 0 or 0.5, this is
likely a case of order-disorder. Most such cases can be easily diagnosed
by abnormal patterns in spot shape, e.g. every second reflection has a
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Hi David -
Your input files for Refmac (I’m not sure about Buster) should have LINKR
records of the form:
LINKRGLY L 95 THR L 95A gap
This has worked fine for me in the past. The file I happened to excerpt here
was refined with Refmac 5.6.0117
...
On 13/06/14 00:19, Ethan A Merritt wrote:
Earlier this year for the first time I got back a validation report
from the PDB for a deposited structure that included wwPDB validation
of a ligand. This is great stuff. I approve. I am happy.
Unfortunately the validation check reported
Hi Tim,
just to spice your words up with some numbers
You may also want to note that constrained hydrogen positions are a
crude approximation and only work with X-ray data where hydrogen atoms
have little impact on the data.
This contribution can be as large as 1.5% difference in
Dear all
Would anyone have nice images of lysozyme crystals in different space groups
(monoclinic, triclinic and tetragonal)? Google wasn't particularly helpful...
Thanks.
Mohamed
The Stuckey Lab in the Life Sciences Institute at the University of
Michigan, Ann Arbor campus
has two jobs available. Please redistribute these postings however you see
fit. Visit umjobs.org for additional information and to apply.
Research Lab Specialist Intermediate\Associate
Insertion codes are a commonly used part of the PDB specification. It's odd
that they wouldn't be supported correctly. To take another similar case, what
would you say of a program that couldn't handle negative residue numbers as is
commonly done with N-terminal purification tags? All
Hi, Tim,
When we were working on our paper in 2011, refmac had a bug that always
indicated in depostions that riding hydrogens were used, whether they were or
not. Published methods did not always clarify this issue. Since we could not be
definitive, we refrained from saying too much about it.
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