On behalf of Mar Pérez (Head of CNIO Training Office)
Dear colleague,
We would like to draw your attention to the calls for the International
Ph.D. and Postdoctoral Programmes at the Spanish National Cancer Research
Centre (CNIO) in Madrid. We would greatly appreciate if you could forward
the
The average atomic B factor in the PDB at a given resolution "d" is roughly:
B = 4*d^2+12
So, I am willing to bet your resolution is 3.1 A? If so, then you are
"normal" (whatever that means).
-James Holton
MAD Scientist
On Wed, Dec 15, 2010 at 8:38 PM, Pavel Afonine wrote:
> Hi Afshan,
>
> y
Hi Afshan,
you didn't mention the resolution, which is essential.
For ultra-high resolution structures the average B may be well less than 10,
and less than ~4-5 is the condition to see the bonding density (see
aldose reductase, 1uso, for instance). While a structure at 3.5A resolution
may have B
Dear all,
Recently, I have solved a low resolution structure (2.85 Å) by MR; an
alpha-beta mix. In this structure, one of the alpha helices (which is missing
in the model) has a tube of density where I can only trace the main chain. In
COOT, upon Map sharpening adjustments I could see density f
I don't know how many of these crystals you have, but if you can spare one try
freezing it straight out of the drop without cryoprotection. Certain salts can
act as cryoprotectants at high enough concentrations. I don't know about
phosphate salts, but I've had crystals that grew in 2.5M ammonium
Quickly passing the crystal through Paratone N has worked well for me
when I crystallize in ammonium sulfate or sodium citrate conditions.
Another trick is to dissolve sucrose (table sugar) in 10uL of the
reservoir solution until it is saturated. Then separate the
sucrose-reservoir mix into two 5ul
First Announcement:
Second Course on Neutron Scattering Applications in Structural Biology
Oak Ridge, TN. May 23 - May 27, 2011
Application deadline: March 11, 2011
The Course in Neutron Scattering Applications in Structural Biology aims at
educating and enabling a new generation of researcher
I've had good luck cryoprotecting high salt crystal conditions with sodium
malonate (2.0-2.5M). Start with a 5M sodium malonate solution and dilute to
40-50% with mother liquor.
good luck,
Rob
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of
Dear Yu
I cannot say about other programs. refmac uses equation in slides No 13-14 of
the presentation:
http://www.ysbl.york.ac.uk/refmac/Presentations/ Refmac_Erice_workshop.ppt
If your crystal is a perfect twin and you have processed data in true space
group then refmac will give map for a s
Mother liquor plus 30% glycerol or 30% glucose will cryoprotect pretty
much anything, if it does not cause crystal cracking. We have had very
good general luck with 25-30% glucose, and it's easy to prepare from
your well solution or crystallization master mix. Add 150 mg of glucose
to a microce
On Wed, Dec 15, 2010 at 6:10 AM, Kevin Cowtan wrote:
> Looks like you're missing
> -colin-fo '/*/*/[F,SIGF]'
that did it.
i gather the input is much like buccaneer then.
also - is 0.2 the latest version - and the only command line options
in v0.2 (15/04/05) that i see listed are:
Usage: cmake
We have a slightly different approach to this.
Local machines are laptops if you want to do model building you can do it
locally either 2d or connected to a Zalman in 3D.
I have one Mac mini hooked up to a Zalman as "permanent" 3D station. The dual
HexaCore MacPro (16 GB RAM) is connected also
By all means 50 is OK. The low end in the PDB is probably ~10,
whereas the high end is ~100
On Wed, 2010-12-15 at 10:24 -0800, Afshan Fayazi wrote:
>
>
> Actually i have sioved my structure of the protein but the B factor
> (temperature) overall is very high . it sis more than 50 so how can i
Actually i have sioved my structure of the protein but the B factor
(temperature) overall is very high . it sis more than 50 so how can i reduce
this or what is the acceptable B factor for the submission
Best Regards
AFSHAN
Ronnie
Just a few comments..
There are no 'true' virtual sessions for OS X Server. (Well there is,
but it's developed by a separate company and they charge per seat ==
expensive). What I define as a 'virtual session' is that you get a
login window and your own desktop all running over VNC.
That's my whole point, it's not an arbitrary threshold, it's
determined completely by what the data are capable of telling you
about the structure, depending on the resolution. Either you have
sufficient resolution to be able to say that the atom is disordered
off the s.p. or you don't and you hav
Dear Ian,
I think you are putting too much importance on the numerical
instability of an atom's position when refining with full matrix
refinement. When developing TNT's code for calculating second
derivatives I found that building into the calculation the effects
of such an atom overlapping i
Dear all,
I have a question about twin refinement of Refmac in CPP4. I was told that
the refmac (Phenix also?) will generate the detwined map after the
refinement with twin. My question is that If my crystal is a perfect
hemihedral twin, how can the refmac make a detwined map after the
refinement?
I agree with Herman. It is simply not acceptable to have a sudden
discontinuous change in "effective occupancy" at some arbitrary point
as a disordered atom approaches a special position. Anyway, whatever the
CIF people decide, I will not introduce an incompatibility between
different versions o
Dear all,
We are currently considering buying a computer which can be used by multiple
people, via our existing network, as a workstation for crystallography
purposes. My thoughts are currently going towards a 8-core Apple Pro (or
12-core) with a lot of RAM, with OS X Server, which in theory sh
Hi Herman
What makes an atom on a special position is that it is literally ON
the s.p.: it can't be 'almost on' the s.p. because then if you tried
to refine the co-ordinates perpendicular to the axis you would find
that the matrix would be singular or at least so badly conditioned
that the solutio
Thanks Claudio,
I have two versions of PyMol currently installed. One came with Phenix when
I installed it, that is version 1.3. The other PyMol installation was found
and installed by the Ubuntu update manager. Both of them have this same
problem.
MikeM
On Wed, Dec 15, 2010 at 11:21 AM, Claudio
Dear Michael,
we are running pymol on several ubuntu machines including laptops. I
simply installed the package pymol from synaptic. If you cannot find the
pymol package you might have to activate all software sources /
channels. There is no need to download any files from the pymol website.
Best
Ronnie,
The main rub is that any of the graphical software will have to be
run on the local CPU to take advantage of accelerated video
graphics. The approach I've taken is to have a central
server (which is actually my office workstation) that serves up a
Dear Ian,
In my view, the confusion arises by NOT including the multiplicity into the
occupancy. If we make the gedanken experiment and look at a range of crystal
structures with a rotationally disordered water molecule near a symmetry axis
(they do exist!) then as long as the water molecule is
I running Ubuntu on a laptop (Toshiba Satellite L505 ATI/AMD FGLRX graphics
driver). I downloaded and installed PyMol but it runs poorly. For some
reason, it runs fine the very first time I use it after I login, but every
time I launch it after that all of the buttons and text of the the PyMol
View
Dear George
I notice that the Oxford CRYSTALS program, which is what I used when I
did small-molecule crystallography and which is still quite popular
among the small-molecule people (maybe not as much as Shel-X!), uses
the CIF convention:
OCC= This parameter defines the site occupancy EXCLUDING
Dear Ian,
Yes. Once an atom has been identified as on a special position because it
is within a specied tolerance, SHELXL applies the appropriate contraints
to both the coordinates and the Uij so there is no danger of the atom
wandering off the special position. Usually, when an atom it very cl
On 14/12/10 20:01, Julian Nomme wrote:
I can easily convert my composite omit map from cns to ccp4 format and
open it into coot.
Very good, but no need to do that.
However, how can I make coot use this map to fit density to my structure ?
I can only use this map for visual support and for exa
Dear George
I would say that an atom has fractional occupancy (but unit
multiplicity) unless it's exactly on the special position (though I
can foresee problems with rounding of decimal places for an atom say
at x=1/3), so that effectively once the atom is fixed exactly on the
s.p. the symmetry co
Dear Ian,
Of course I could convert the occupancy on reading the atom in and convert
it back agains on reading it out. This is not quite so trivial as it
sounds because I need to set a threshold as to how close the atom has
to be to a special position to be treated as special, and take care
t
Dear George
Is applying the multiplicity factor to the occupancy internally in the
program such a issue anyway? It need only be done once per atom on
input (i.e. you multiply each input occupancy by the multiplicity to
get the combined multiplicity*occupancy value that you would have
reading in d
Bryan Lepore wrote:
does cmakereference v0.2 in ccp4 6.1.13 require 'project', 'dataset'
or 'crystal' to be in the .mtz? because i thought by default, these
were eponymous
I'm pretty sure it doesn't.
e.g my .mtz - that has labels F and sigF - :
* Dataset ID, project/crystal/dataset names, c
33 matches
Mail list logo
