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Dear ,
Can you clearify what you mean by the sentence
"when i tried to use the MR solution generated in phenix with the mtz
file from ccp4 the model shows a lot of clashes"?
I do not understand what you need the mtz file for in order the check
for
I am a bit puzzled - do you know the direction of the rotation axis
which can be converted to polar phi/psi angles, a mid point you want to
rotate about, and the distance of the centre of mass of your molecule
from that point, from which you could find the tranlation shift?
If so I could desig
Do you mean just any tetramer?
If so, Why not use an existing one - eg haemoglobin..
Eleanor
On 12/12/2011 09:42 PM, Fred wrote:
I only want to produce an artificial tetramer.
Em 12-12-2011 19:41, Jacob Keller escreveu:
Can you clarify your reason for doing this?
JPK
On Mon, Dec 12, 2011 a
PHIC wont do any harm - you may need it for various reasons - I use it
mostly as input for a DANO map to check out possible metal sites..
The reason for not using a refmac output mtz as input for the next run is
1) the refmac output Fobs has been scaled by the anisotropic scale so
all subsequ
csymmatch pdbin-ref my_favorite.pdb pdbin the-other.pdb -origin-hand
This should move the-other.pdb to overlay my-favorite.pdb
It WONT relabel the Chain IDs though..
Eleanor
On 12/13/2011 04:26 AM, intekhab alam wrote:
Hi All
I have a 3.0A dataset of a protein-protein complex. I used one of
Dear ccp4bb
on behalf of Ludvig Sollid, I would like to announce the following PhD
studentships.
"We are seeking to fill two fully funded PhD fellowships (Early Stage
Researcher, SKO 1017, stipendiat) in the biochemistry and immunology of
coeliac disease for the Marie Curie Initial Training Net
Experimental Postdoctoral Position in High Throughput Small Molecule Ligand
Screening
Outstanding postdoctoral applicants to work jointly with Drs. Julia Kubakek,
Mark Hay and Jeffrey Skolnick at the Georgia Institute of Technology are sought
with the following qualifications:
* Extensive exp
On Tue, 2011-12-13 at 02:31 +, Yuri Pompeu wrote:
> Hi Ed,
> I just had a chance of looking at your comment more closely.
> You are right it only uses PHIC if in refmacs set up you choose to refine
> "with prior phase information" -AFAIU.
> So what exactly is the info contained in the output
I was just contacted by a group looking for install disks for the Biosys
program used to run the old Biosys2000 FPLC from Beckman. I don't have the
install disks anymore (we eventually bludgeoned our Biosys to death, and then
set it on fire, if I recall--it was always very unreliable).
However
Dear BB readers,
at the University of Milan in the Dept. of Biomol. Sciences we are
currently looking for a motivated candidate for a 3-year Postdoctoral
position in the lab of Prof. Bolognesi, under my supervision. The contract
will start sometimes this spring (most likely March-April).
The proj
A small but potentially important correction:
FC_ALL PHIC_ALL from REFMAC are indeed the calculated structure factor
of the coordinates+bulk_solvent, but AFTER multiplying by the likelihood
coefficient "D" (as in 2*m*Fo-D*Fc ). So, if you subtract ( FC_ALL
PHIC_ALL ) from ( FC PHIC ) you will
Dear CCP4bb list,
Thank you very much all of you who have answered my post. I'm really
sorry if I was unclear. Such operation is so unusual that I could be
able to express myself appropriately. From quick reading some replies
(James Stroud and Guillaume Ponchel), it seems is possible do build
Hi all,
For those who teach xtallography - we found some plastic turtles that can be
snapped together in an amazing variety of space groups. Worked well in a
workshop for our students, so I thought I'd share the shopping tip. They're
called Reptangles, and we got them from Amazon.
http://ww
whoa - now that looks like fun! Amazon just made some money off of me.
Thanks for sharing!
Steve
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe
Rice
Sent: Tuesday, December 13, 2011 5:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] sy
reminds me of these symmetric 2D P3 lizards:
http://www.worldofescher.com/store/Z51.html
I bought the RGB-coloured set/puzzle after visiting an Escher
exhibition and sometimes use them in crystallography/symmetry teaching.
Nice to make the students assemble them and then decide on the
symmetry
Does anyone know where one can acquire some Penrose tiles? I think
they'd be great toys as well, and drive you a little bonkers. Maybe a
kitchen/bathroom floor made from them?
Jacob
On Tue, Dec 13, 2011 at 5:03 PM, VAN RAAIJ , MARK JOHAN
wrote:
> reminds me of these symmetric 2D P3 lizards:
> ht
(oops, previous mail got sent before I wanted)
the turtles would be really nice to extend things into 3D.
great find,
Mark
Quoting Phoebe Rice:
Hi all,
For those who teach xtallography - we found some plastic turtles
that can be snapped together in an amazing variety of space groups.
Wo
Thank you for the info. It looks great for teaching or for just having fun.
Carlos R. Escalante Ph.D
Assistant Professor
Department of Physiology and Biophysics
VCU School of Medicine
1220 East Broad Street
MMRB 2-040
Richmond, VA 23219
cescala...@vcu.edu
(804)628-1202
On 12/13/11 5:53 PM, Phoe
If you go to froogle.google.com you will find that you can
buy these at a noticeably lower price than at amazon.com,
at least for people in the USA - just search for Reptangles.
Frances
=
Bernstein + Son
we have a whole street made of them... welcome to Helsinki...
t.
On Dec 14, 2011, at 1:10 AM, Jacob Keller wrote:
> Does anyone know where one can acquire some Penrose tiles? I think
> they'd be great toys as well, and drive you a little bonkers. Maybe a
> kitchen/bathroom floor made from them?
I am looking at a highly unusual crystal lattice right now and can't figure out
what is going on, so I decided to ask the experts.
I recently got data on a oligomeric protein with many highly correlated NCS
units (4.0A resolution, linear R-sym is 0.16-0.21 in I4, I422, F222, C2 and
0.12 in P1)
Hi Stefan,
1)
just out of curiosity I wrote a tiny script using CCTBX that estimates
solvent content via bulk-solvent mask, and quickly run this script for all
PDB structures for which I could re-calculate the R-work within 5% from
published value. Also, this script extracted the solvent content v
If you have air in the packing that's worrysome. If symmetry mates don't make
crystal contacts you are in trouble.
Have you checked a simple selfrotation function in your currently favored space
group ?
Do you have sufficient data collected to start out in P1 or C2 ? Then I would
start there
Don't forget that if you have poorly resolved spots due to the long axis, the
intensity statistics may falsely seem to indicate twinning, since weak spots
may be contaminated by neighbouring strong ones
Phil
On 14 Dec 2011, at 04:47, Stefan Gajewski wrote:
> I am looking at a highly unusual cr
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