Dear Pavel,
Also worth mentioning the obvious that the mathematical functional form of an
occupancy and a B factor in its -ve exponential is very different BUT at lower
resolutions they behave similarly. Thus higher resolution refinement allows an
'easier' determination of each parameter.
Hi Robby and Grant,
Here I must second Pavel. As Grant just discovered, modern refinement
programs have improved so much, that they will no longer allow to fudge
a low occupancy (sharper but less density) with a high Bfactor (broader
and more density), especially at higher resolutions. In this
What of course also could have happened, is that the Bfactor restraints
are too tight, forcing, too low Bfactors for the flexible side chain.
Especially after rotatable bonds, Bfactors can increase much more
sharply than many of the older parameter files would allow. In this
case, reducing these
Dear CCP4 colleagues AMoRe's funs.
We are organizing a mini-symposium (two days long) in honor of the
retirement of Jorge Navaza. If you are interested on attending this
meeting, please go to the link indicated below and input the dates of your
preference.
Please, feel free to distribute this
To add to the general list (and future class action). I have just had the
battery expansion on one for the second time. Added to the number of them I
have bricked by letting the charge run down to low by unplugging them.
Interestingly apple agreed to replace the bricked batteries free of
Dear All,
A quick reminder to you all about this coming January's CCP4 Study Weekend
entitled Molecular Replacements (January 3rd-5th 2010). As the title
suggests, the meeting will be all about the latest developments in molecular
replacement with many leading crystallographers and software
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Dear Hari,
this is hard to tell without debugging, but I have two guesses:
1) did you untick 'use anomalous data' but the script only partially
picked this up? In that case, the 'colano'-columns would not be present
2) some column name is too long
As an adjunct to B-factor vs occupancy thread, i might expect the b-factor to
halve if the occupancy is set to 0.5 (but I'm only a molecular biologist),
if so how many
cycles of refmac would it take for the value to settle? My limited experience
is that it dosn't exactly halve but i do tend
Hi Jim,
The speed at which the B-factor converges depends on many factors. The B-factor
restraint weight that Herman and I mentioned (the one you should optimise
before changing occupancies!) is an important factor. Also the position of your
atomic coordinates WRT where they should end up is
Didn't have the latest version of Coot but can now make the LINKs.
Many thanks for your help.
As already mentioned by jrh, I again want to impress that B-factor and
occupancy are in principle two entirely different parameters.
They may appear as achieving the same thing upon refinement at the
resolution we deal with in most macromolecular structures.
The fact is that reduced
Hi CCP4bb,
I updated our CCP4 6.3.0 for x86_64 linux to the September 21 CCP4 update
when it came out. The release notes said it had a patched areaimol in it,
and it did update the binary, but we are still seeing segfaults and NaN
values, etc.
The all-in-one update also contains an areaimol
I have never understood why Macs are so popular, although in this part
of the world they are appreciably more expensive. My vintage 2005 Dell
laptop does not have the sex appeal of a MacBook, but it has survived a
fire (not its fault) as well as being under water (to put out the fire)
and then
PS: Partial occupancy is not the same as disorder. You can have
well-ordered different occupancies that manifest themselves then in
superstructure patterns. Common in small molecule/materials.
Hello Bernhard
Agree with everything you said up till this point, but I think the owners
of the
On Mon, 2012-11-12 at 13:47 -0500, Ed Pozharski wrote:
Does anyone know of a tool that would generate a protein molecule
backbone from a set of phi/psi angles?
For the record.
Thanks to all who responded. Here is what I found out:
1. MOLEMAN works best. The most cumbersome part is to
Presumably then it was running Linux?
On Nov 20, 2012, at 7:39 AM, George M. Sheldrick
gshe...@shelx.uni-ac.gwdg.de wrote:
I have never understood why Macs are so popular, although in this part
of the world they are appreciably more expensive. My vintage 2005 Dell
laptop does not have the
Nomenclature hazard warning:-
Ian, Thankyou for drawing attention to the nomenclature school:-
Partial occupancy disorder
Which I prefer to refer to as
Partial occupancy order.
Outside our MX field static disorder refers to what we call split occupancy
order. I like the latter and dislike the
Dear all - we have a synchrotron trip coming up and have crystals that
are likely to contain intrinsically bound zinc atoms. The crystals
diffract to 4A-ish so far. We're hoping to collect both native datasets
at higher dose, and phasing datasets at lower dose (on separate
crystals). Can we
John
Having begun my crystallographic life with small molecules (organic
semiconductors) and subsequently moved to PX, and having worked on SOD
crystals I stand in both camps (i.e. both meanings: site-occupancy disorder
and superoxide dismutase!). It seems to me that static disorder is the
You'll see the zinc also at the Semet peak edge already check out Ethan's edge
plot web server. If you used his-tag purification methods it would be wiser to
collect passed the edge of either Ni or Co so you can distinguish them from Zn
sites.
Jürgen
..
Jürgen Bosch
Johns
native datasets? And would a native dataset for refinement be
compromised by friedel pair differences collected at an edge?
If you've got anomalous data available, you may get better results by
using your friedel pair differences in refinement - especially if your
diffraction stays in the ~
It is dual bootable Linux/Windows
George
On 11/20/2012 05:56 PM, William Scott wrote:
Presumably then it was running Linux?
On Nov 20, 2012, at 7:39 AM, George M. Sheldrick
gshe...@shelx.uni-ac.gwdg.de wrote:
I have never understood why Macs are so popular, although in this part
of the
It probably had a functional Firewall under Linux that's why it survived :-)
Jürgen
P.S. note to myself, don't ever give George my laptop, as it might be
mistreated - just for test purposes :-)
On Nov 20, 2012, at 12:57 PM, George M. Sheldrick wrote:
It is dual bootable Linux/Windows
George
Something you want to be very careful with here that appears to have not
been mentioned yet is phase bias.
If you have built in a wrong side chain or other entity that is not
actually there, but still force it to have occupancy=1 and reasonable B
factors (B factor restraints might do that)
Ian, yes absolutely but your very description of where the unit cells are not
identical is NOT the situation where we see fractional occupancy moieties. In
such cases a large fraction of the unit cells ARE ordered. QED. John
Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair
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