On 7/13/10 11:05 AM, Daniel Lietha wrote:
Does anyone know if the ZM-M215W and ZM-M240W Zalman monitors work in
3D with Coot and Pymol (would use them on Mac OS10.6)? If so, does the
increased resolution improve things compared to the ZM-M220W?
Thanks,
Daniel
Let me bring back to life the thre
Hi Matthew,
By now, you have received many posts telling you both how efficient and
inefficient TEVp is. You might be confused. This seeming contradiction
can be explained by a few events, among many others: Inaccessibility of
cleavage site, absence of reducing agents, and presence of deterge
I was surprised to get a few messages asking for our protocol for
reductive methylation of proteins for crystallization. We employ almost
exactly the protocol published by Walter et al, Structure, 2006. This is
a "Ways and Means" article that made us realize how easy it was to do
this regularl
ells rebuilt
models with a one-year warranty (I also heard one person mention that
they got their refurbished model from Alpha Biotech).
There was also one very favorable mention of the Cybi-Well robot from
Cy-Bio.
Thanks everyone again. This has been very helpful.
Engin
On 3/10/10 9:
Hi, everybody,
We recently recognized a problem with our Innovaplate SD-2 (a.k.a. MRC
2-Well) plates from Hampton. Our last batch of Innovaplates have an
inconsistent well height such that our crystallization robot (a
Mosquito) cannot put protein in all the wells. When tested with an older
In
1/18/10 2:03 PM, Ethan Merritt wrote:
On Monday 18 January 2010, Engin Ozkan wrote:
Hi everybody,
I have a question regarding glycosidic bonds. This relates to refmac,
phenix and cns, so I thought the best forum to pose this was here.
We have these very nifty link descriptions, such as BETA1
Hi everybody,
I have a question regarding glycosidic bonds. This relates to refmac,
phenix and cns, so I thought the best forum to pose this was here.
We have these very nifty link descriptions, such as BETA1-4, ALPHA1-6,
etc. that come with refmac and phenix. These essentially describe a
ch
There is no excuse for using MAN to mean both alpha and beta mannose.
It is easy to take a MAN-b-D.cif file and modify it to a BMA.cif. BMA
is already in the monomer library that comes with ccp4 (but I think it
does not have geometry descriptions), and the last time I checked, there
was not a
I have to agree with Ed Pozharski here. It has been shown that it can be
valid to use I/sigma levels as low as ~1 for refinement (Ling, Read, et
al, Biochemistry 1998; Delabarre, Brunger, Acta Cryst D, 2006). I am
bothered more when I see I/sigma cutoffs of >4, where Rsym is <30% in
the high re
at 08:14 -0700, Engin Ozkan wrote:
Does anyone already have the PDB-wide R/Rfree gap versus resolution data
(it does not seem that the PDB maintains one)?
Ed.
The friendly people in Uppsala has something here by the name Harry
Plotter: http://xray.bmc.uu.se/gerard/supmat/eds/plotter
Does anyone already have the PDB-wide R/Rfree gap versus resolution data
(it does not seem that the PDB maintains one)?
Ed.
The friendly people in Uppsala has something here by the name Harry
Plotter: http://xray.bmc.uu.se/gerard/supmat/eds/plotter.html
This might be somewhat dated now.
En
We tried that trick, which works amazingly well in insect cells, in
mammalian media, and it fails. It will depend on the exact media, obviously.
Engin
On 10/8/09 1:50 PM, Matthew Franklin wrote:
The trick we used at Genentech (which I'm still using) was for
secreted insect cell proteins, but i
That might be a sign of pseudo-translational symmetry. Check your native
patterson. phenix.xtriage will also tell you. In the presence of
pseudo-translational symmetry, twinning stats will be hard to interpret.
Engin
On 9/22/09 12:31 PM, Ben Flath wrote:
Hi all
when subjecting my data to th
Hi everybody,
I have a little weekend puzzle in my hands. I have (probably) two heavy
atom sites and pseudo-translation in P2(1) (i.e. an NCS 2-fold parallel
to the unique crystallographic axis). Doing a little algebra, I would
expect two self vectors and the pseudo-translation in the Harker s
Hi everybody,
Does anyone know a place to order heavy atom clusters, say with >=6
heavy atoms, in the US, preferably? Except for the Ta6Br14 cluster
(through Mitegen in the US), I don't know a good place to buy them (we
don't heavy any friends in an inorganic chemistry lab, and I already
have
ck in'?
Thank you,
Engin
On 8/22/09 12:22 PM, Anastassis Perrakis wrote:
Hi -
Maybe restarting ccp4i all together, re-reading the mtz (no re-run)
and so-on will solve this.
Tassos
On 22 Aug 2009, at 21:19, Engin Ozkan wrote:
Hi everybody,
I was messing around with Arp/warp in cc
Hi everybody,
I was messing around with Arp/warp in ccp4 recently, and got stuck with
the version that uses the new autotracing algorithm. The same run using
the "Classic" algorithm runs without a problem, but the "Expert System"
using flex-wARP 1.0 dies with "PHIB is not assigned to an mtz la
We have unsuccessfully used in the past (by that I mean less than
stellar incorporation) the Gibco/Invitrogen Sf900-SFM w/o Met/Cys media.
Then we saw Karin Reinisch's paper (Dong et al, Immunity, 2009) and they
used Expression Systems' ESF921. This protocol works for us.
Engin
On 8/18/09 2:4
Just checking my oxidized Se-Met experiments, I have 12658 to 12661 eV
for my peak energies, and 3 eV lower for the inflection.
As others have said, do the fluorescence scan. Use your experimentally
determined values.
Engin
On 7/16/09 11:54 AM, Phil Jeffrey wrote:
Always take the scan results
Your suspiciously low spread between R and Rfree might be because your
free flags might not have been chosen considering the twinning law.
Twin-related reflections should have the same flag value. You can get
phenix's reflection file utility to pick free flags for you while taking
the twinning
Here is a summary of responses to the thread I recently started on "phasing
with se-met at low resolution":
There were many suggestions. They can be grouped into two categories:
1. Aim for very high redundancy at one wavelength (peak) and watch out for
radiation damage. Sacrificing resolution is
The new OS X 10.5.7 update downgrades your X11 to 2.1.6. There is a new
X11 update, 2.3.3, only for 10.5.7 users.
It might be prudent to update to 10.5.7 and then xquartz 2.3.3, before
reporting that coot or something else is suddenly broken.
As usual, very annoying...
Engin
s loose a great deal of power
as the resolution of the map decreases (and the protein-solvent
contrast becomes less clear). IMHO it is ALWAYS better to collect MAD
data, because then the dichotomous phase ambiguity is resolved
experimentally. Two wavelengths are twice as good as one, even with
to death the "1 in 50" or "1 in 100" Methionine myths: it
depends on the quality of your data.
Engin
On 5/10/09 2:50 PM, Leiman Petr wrote:
Dear Engin Ozkan,
You have told us how bad your crystals are, but you did not mention how good
your anomalous signal is:
1. To what re
Hi everyone,
I thought I start a new thread while it is unusually quiet on the bb. I
am pondering over the practical limitations to MAD and SAD phasing with
Se-Met at low resolution. What is the lowest resolution at which people
have solved structures "only" using phases from selenium in a
"r
Have you tried M15[pREP4], which are the cells Qiagen would like you to
use? You can at least use pREP4 + your expression host, and have
repressor expression to prevent leaky expression. That can help you get
colonies of transformants.
Engin
On 5/4/09 7:04 AM, atul kumar wrote:
xl1-blue is
If you have found Bill Scott's pages on Macs useful, you may find his
Ubuntu pages similarly useful: another reason to go with linux over
windows. There are also people creating rpm packages to easily install
the likes of coot on Fedora/RHEL/Centos, another well supported option.
Also, phenix,
Hi everyone,
We just realized in the lab that the dimethyl-lysine in the ccp4 monomer
database (MLY) has planar tertiary amines, instead of trigonal pyramid
with ~109ยบ degree angles (which we have fixed for our purposes). Is
there a place to report such matters to, or is this a good enough pla
(510) 643 0164 (Fax: 2352)
On Apr 11, 2009, at 6:11 PM, Engin Ozkan wrote:
Hi,
The problem was the profile test failing as suggested by Wladek and
Lothar (thanks to both, for continuous teaching since grad school). I
was using a profile fitting radius of 25 (not the default 10), so
tha
Hi,
The problem was the profile test failing as suggested by Wladek and Lothar
(thanks to both, for continuous teaching since grad school). I was using a
profile fitting radius of 25 (not the default 10), so that's why I assumed
profile fitting was not the problem. But now, I have played with t
Hi everyone,
I have recently been plagued by incomplete data according to HKL2000. My last
dataset, which is 360 degrees of images, with < 0.1% rejected during scaling,
and no overlaps during indexing/integration, keeps on scaling in HKL2000 as
incomplete. It is reported incomplete only at high
27;ll forget to update the JRNL reference.
I believe that the lead time is unnecessarily long. Perhaps one day
might be more reasonable.
Phil Jeffrey
Engin Ozkan wrote:
I agree that the pdb deposition process has gotten better, but I
still regularly have issues with releasing of newly publ
Moving the subject further away from the original post...
I agree that the pdb deposition process has gotten better, but I still
regularly have issues with releasing of newly published structures.
There seem to be delays; just as you are reading this brand new,
interesting structure, you reali
:16 AM, Anastassis Perrakis wrote:
Hi Engin -
On Mar 27, 2009, at 15:57, Engin Ozkan wrote:
Dear Tassos,
Your assumptions are right, if (1) your dn/dc is accurate, or (2) your
machine is calibrated.
indeed!
We recently measured a protein of a similar size
to yours, and when a 700 Da ligand
Dear Tassos,
Your assumptions are right, if (1) your dn/dc is accurate, or (2) your
machine is calibrated. We recently measured a protein of a similar size
to yours, and when a 700 Da ligand was added to the buffer, the measured
protein mass was increased accordingly. So MALS can be pretty acc
Sang,
They are always different. But depending on your data/parameter ratio,
you may be better of assuming they are similar (with NCS restraints) or
even identical (with strict NCS). Ask to a friendly crystallographer
around you when employing NCS is good for you. Crystallographers with
high
Does this screensaver run on 10.5 intel Macs? It looks like it was
developed a while ago, and not updated since then.
Engin
Manish Chandra Pathak wrote:
For mac, a screen saver (structure) is already available. moreover
it's free and displays couple of structural information exactly the
wa
Hi, everyone,
Could there be an error in the ccp4-6.1.1 setup files
(ccp4-6.1.1/include/ccp4.setup) in the fink version? After the last
update, my CCP4_MASTER variable was defined as /sw/share/sw/share/xtal.
Obviously, that did not work.
Removing the extra /sw/share and updating fink solves
I have to second that.
I recently had crystals that will only grow after seeding and will live
for exactly five days. On the sixth day, the same drop will have tracks
of dissolved crystals left in every drop: they almost look like tire
tracks. The crystals frozen on the fifth day diffract to 2.
It does look like a conspiracy against Firefox to me. If you do a
search in google, I am getting the annoying "this site may harm your
computer" messages for every hit, but with safari, none of it is there.
This is on a Mac.
Engin
Pedro J. B. Pereira wrote:
Miguel Ortiz Lombardia wrote:
De
7 Dec 2008, at 22:54, William G. Scott wrote:
Please, we all need to mention this to the Apple people. This is
totally unacceptable.
On Dec 17, 2008, at 2:54 PM, Engin Ozkan wrote:
Yep, this happened because of the latest Mac OS 10.5.6 update. With
the update, my X11 version got downgraded
Now that everything with coot and imosflm has been settled, how about
sftools? I am getting errors when I try to open an sftools window with
ccp4i, with 6.1.0. I get the same error with a fink-installed mac
version, and a linux installation. Here is the error:
bad window path name ".main.ca
ariable
Bill
On Dec 17, 2008, at 1:53 PM, Engin Ozkan wrote:
By the way, is anyone experiencing the following problem with
fink-installed coot?
dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib
Referenced from: /sw/bin/coot
Reason: Incompatible library version: coot requires v
By the way, is anyone experiencing the following problem with
fink-installed coot?
dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib
Referenced from: /sw/bin/coot
Reason: Incompatible library version: coot requires version 3.0.0 or
later, but libXdamage.1.dylib provides version 2.0.0
As said, your Km is different in mother liquor than in your reaction
conditions, but even that is not the end of it: You ligand/substrate might be
inducing the slightest of all conformations in your protein that interferes
with crystallization, or might block crystal contacts. Then, you can eit
Another option is to use sbgrid's services to install every
crystallography/EM/NMR-related thing on your lab computers: linux, SGI,
powerpc or intel mac, and mixed labs are fine, so you are not restricted
to any OS. This has the advantage of never ever thinking about how to
compile anything eve
Hi everyone,
I was in the middle of creating a "Table 1" for a finished structure and
was puzzled by one number. It is the average B factor, especially in
the case of TLS-refined structures. In this case, the average reported
by refmac in the header is the average of the B factors in the pdb
Here is my two cents...
How strong zinc is captured by the protein is very protein dependent: I
always thought that a great case for this variability was the protection
of RING ubiquitin ligases against NEM. Cysteine-catalyzing HECT
ubiquitin ligase are killed by NEM; RING finger ligases, wher
From another member of the new generation...
I could not agree more with Scott. Stereo is not essential, my lab of
thirteen crystallographers does not even have the capability, and noone
has ever asked for it (including our older PI). And I have refined and
built in one year one 3.9 A and
I remember cuting and pasting on my little board in my cubicle Table I
from Randy Read, Acta Cryst (1986), when I was a graduate student
wondering about sigmaA. It is a table of definitions of terms and
formulas, and helps one conceptually understand the terminology. It is
from before the days
In this case, XDS-processed data is clearly twinned, if one were to
believe moments and the cumulative intensity distribution calculated
by truncate (and everyone should - channelling Dr. Dodson).
Why I'm worried about XDS separating relatively overlapped spots is
the funny intensity stats
Hi everyone,
I have been recently relying on XDS quite a bit, but at the same time
worrying about how XDS treats overlaps. We had one dataset that both
HKL2000 and Mosflm would show to have severe overlaps, as expected due
to unit cell parameters and the unfortunate crystal orientation in the
Hi, CCP4bb'ers,
I am having some trouble with Procheck. I am using two different
installations, one that came with CCP4-6.0.2 and the other is procheck
3.5.4 (I think they are the same versions).
Anyway, I can reproducibly get the .out file to correctly report many
bad contacts; however, th
Fellow crystallographers and biochemists,
This will be off topic. Does anyone have any experience with the new
ITC Microcal is selling (itc200)? They claim that itc200 requires one
seventh the sample volumes. We're especially interested in an
equipment that would require less sample withou
54 matches
Mail list logo
