Mark,
On Tue, 2010-09-14 at 13:34 -0400, Dr. Mark Mayer wrote:
> Where does the crystallographic community stand
> on deposition of coordinates with riding
> hydrogens?
Surely community is divided on this. There could be arguments made both
ways. Personally, I think that riding hydrogens can
Reply to myself:
The author changed his program so that only the
2 first columns are needed now, and they are obvious enough.
Regards,
F.
Francois Berenger wrote:
Hello,
First, sorry for this not directly CCP4-related question.
I have some software here that requires a seq.data file as one
o
Hello,
First, sorry for this not directly CCP4-related question.
I have some software here that requires a seq.data file as one
of its inputs: any idea on how to create such a file from a FASTA file?
Here is how the expected file looks like for protein 101M (it is named
seq.dat):
---
1
Two questions.
What is the resolution of your data? what is the percentage sequence
identity?
even if you are confident of C2, try using PHASER with all space groups and
searching for 2-4 monomers.
Ivan
On Mon, Sep 13, 2010 at 7:52 AM, Paul Holland wrote:
> Hello fellow crystallographers,
>
>
Dear Users,
The deadline for Nov/Dec 2010 Collaborative
Crystallography proposals will be *Sep 15, 2010. *
Through the Collaborative Crystallography Program (CC) at the
Advanced Light Source (ALS), scie
Hi Ethan,
yes, you are absolutely right, you would need to define somehow where
your model is... But you could, at least hypothetically, use non-atomic
models for this! Like cylinders (*), spheres and similar shapes. This is
what the density looks like at those "super-low" resolutions.
(*)
On Tuesday 14 September 2010 12:44:37 pm Pavel Afonine wrote:
> Hi Ethan,
>
> > I do not favor depositing riding hydrogen coordinates for
> > the same reason that I do not like the recent PDB preference
> > for depositing ANISOU records for structures that have been
> > refined with TLS.
> >
> >
Hi Ethan,
I do not favor depositing riding hydrogen coordinates for
the same reason that I do not like the recent PDB preference
for depositing ANISOU records for structures that have been
refined with TLS.
In both cases the enumeration of these many thousands of
parameter values gives the str
Even though SHELXL refinements often involve resolutions of 1.5A or
better, I discourage SHELXL users from depositing their hydrogen
coordinates. There are three reasons:
1. The C-H, N-H and O-H distances required to give the best fit to
the electron density are significantly shorter than thos
On Tuesday 14 September 2010 10:34:00 am Dr. Mark Mayer wrote:
> Here's one for the community, which I'll post to both Phenix and CCP4 BBs.
>
> Where does the crystallographic community stand
> on deposition of coordinates with riding
> hydrogens?
I do not favor depositing riding hydrogen coord
Here's one for the community, which I'll post to both Phenix and CCP4 BBs.
Where does the crystallographic community stand
on deposition of coordinates with riding
hydrogens?
Explicit H are required for calculating all atom
clash scores with Molprobity, and their use
frequently gives better g
Dear CCP4 List Members,
We are pleased to announce that a more uniform set of 3DEM map files is now
available through EMDataBank.org search services and ftp mirror sites.
Over this summer, our team carried out a comprehensive remediation project
involving every map file archived in the EMDB. Pa
Yuan,
On Mon, Sep 13, 2010 at 6:12 PM, 商元 wrote:
> Thanks, lan.
>
> For quaternions, it needs w^2+x^2+y^2+z^2=1, thus reduces variables to 3.
The number of degrees of freedom is of course reduced to 3 but the
number of variables is still to all intents and purposes 4, since no
useful simplificat
Dear Xingliang,
This is vaguely reminiscent to a pattern that was observed by Zora
Markovic-Housley on precession picture of crystals of ornithine
aminotransferase: the even layer (l=2n) had a nice pattern diffracting
to high resolution while the odd layer (l=2n+1) had a honeycomb stuctur
Dear Paul Holland,
I would spend some time in improving the search model, first. If there
are more than one possible search molecules in the PDB, I usually do a
structural alignment (ssm superposition) to get an idea about the
flexibility of the search molecules. Then I remove all parts that
Xingliangzhang
These are Kikuchi lines that usually are observed in the electron diffraction
from thick
specimen. For X-ray they are called Kossel lines. Well, if you are so called
high throughput structural biologist, you
can forget about that, It is hard core diffraction physics. But if you t
Interesting! it appears to be some kind of "secondary order"...I hope
someone wise/experienced can shed more light on this.
the diffraction spots appear to fall consistently in the middle of the
hexagonal(ish) grid lines, so it must be some partial order effect
related to the unit cell.
do yo
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