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CP4 page is down, and I don't know where to look.
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Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
http://voices.uchicago.edu/ozkanlab
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On 7/23/19 3:35 AM, melanie.voll...@diamond.ac.uk wrote:
> No longer those 20 odd names for ammonium sulphate
You mean ammonium *sulfate*. As it is called across the pond. :)
On a related note on common nomenclature for recording crystallization
experiments that Janet brought up:
I find it odd
Engin
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Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu
To unsubscribe from the CCP4BB list, click the following link:
Do it the same way we used to do all glycans last year, before the new
Coot interface for adding glycans:
* "Get monomer" to get the monomer you want to add roughly where it goes.
* Remove hydrogens from it.
* Position the O1 atom roughly where you have the O-gamma of Ser/Thr,
rotate and tran
Just to make the point that you are not alone, I have observed the same
issue on Mac with CCP4-installed Coot 0.8.9.1 using latest OS and
Xquartz. This started happening with a recent update.
Interestingly, the 'Edit Chi Angles' dialogue now allows us to modify
non-chi angles as well (not sur
Dear all,
I have to agree with all sentiments stated, and I have definitely seen
the value of restraining distance values in weak and anisotropic data,
which is great for those of us who deal with such data on a regular
basis. However, I also just went through a search of all refined
DISTANCE
Hi,
I have been using Xquartz 2.7.11 (the latest release) perfectly fine on
High Sierra. We did not have to downgrade to 2.7.8. CCP4i and Coot works
perfectly fine with XQuartz 2.7.11 on multiple iMacs and MacBook Pros we
have in the lab.
Best,
Engin
On 12/4/17 4:49 AM, Martin Montgomery
parameters did you give (or what was your script)? (often the
FORMAT statement is the problem).
And in what way the output mtz file is not working? maybe use mtzdump
to show what you got.
Hope that will lead to a speedy resolution!
--
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry
Hi,
I am unable to reach the CCP4 website and the CCP4 online services
regularly. The websites appear to be down (for everyone) on and off.
Could we alert someone responsible to look into this?
Thank you,
Engin
Not observing a complex on a gel filtration run for a week complex
(micromolar) is not necessarily unexpected. It all depends on your
protein concentrations, the dissociation kinetics (remember, a gel
filtration run is not an equilibrium experiment - it dilutes and
separates your sample), etc.
Dear Scott and the board,
Sorry for the email not intended for all. This is a really useful
protocol for S2s; we so use slightly different ways of making protein in
S2. My students will takes notice of this!
Best,
Engin
On 12/23/16 5:56 AM, Engin Özkan wrote:
Hi guys,
Here is a
email:wal...@ibbr.umd <mailto:wal...@ibbr.umd>.edu
phone: (240) 314-6478
fax: (240) 314-6255
On Dec 22, 2016, at 7:52 PM, Engin Özkan <mailto:eoz...@uchicago.edu>> wrote:
Nothing specific about S2 cells to contribute... However, S2s usually
grow fine in other insect media, su
Nothing specific about S2 cells to contribute... However, S2s usually
grow fine in other insect media, such as those intended for lepidopteran
cell lines like the Sf9 and High Five. Protocols established for those
cell lines, for example, check out those using the medium ESF-921, would
probably
As was reported before many times, the solution to the error you're
getting is reinstalling Xquartz.
Engin
On 5/28/15 7:33 AM, saleem raza wrote:
Hi,
I recently updated the OSX on my IMAC to OSX Yosemite version 10.10.3.
Since then I am unable to open CCP4. I have tried to reinstall the
CCP
Magnesium phosphate crystals? I've definitely seen salt crystals with
that morphology before. Check out the Ksp for Mg3(PO4)2.
Engin
On 5/17/15 6:45 PM, Bishwa Subedi wrote:
Hi All,
I know that its hard to say if the crystal is protein crystal just by looking
at its morphology, however I was
Source (APS) of the Argonne
National Laboratory.
Those interested should send a CV, including a list of three references,
with a cover letter describing your personal interests, experience and
your interest in our laboratory. Below is the contact information:
Engin Özkan, Ph.D.
eoz
this or other models in
this category.
Thanks,
Engin
On 11/12/14 11:40 AM, Engin Özkan wrote:
Hi,
Our experience was the opposite. Ours did not work well and completely
broke soon after. This incubator quickly turned into the largest door
stop in the lab. I'm sure ours was just a le
Hi,
Our experience was the opposite. Ours did not work well and completely
broke soon after. This incubator quickly turned into the largest door
stop in the lab. I'm sure ours was just a lemon, but I thought I'd still
mention it to warn others.
I am still interested in hearing what models of
in advance.
Have a good day
Anita
--
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu
Do those fixes also make it to the phenix version of the library? Yes,
this is the CCP4bb, but the monomer library is also used by Phenix, and
a good number of structures (almost half of those deposited this year?)
in the PDB now come from phenix.refine. Or in other words, is there a
central, h
I doubt it is ferritin sucking up metals; although the problem of
crystallizing ferritin is an issue in secreted preps. See this paper,
where they made lemonade (a PNAS paper) from this lemon (High Five
ferritin crystals): " Secreted ferritin was isolated from the
supernatants of baculovirus-in
On 4/23/14, 1:53 PM, Francis Reyes wrote:
Office 365 is $10 a month, Adobe Creative Cloud (what used to be their Creative
Suite) is $50 a month with an annual commitment.
Licensing the use of software on a time-limited basis as a business model seems
like it's going to stick around.
And that's
On 2/6/14, 10:32 AM, Thomas, Leonard M. wrote:
Finally as an observation over the years the art of mounting a crystal for a
room temperature or 4 C shot is a dying art. I am not firmly convince the
Mitogen mounts work really well, I have always had better luck with a
capillary. That just may
UNL is for unknown ligand, while UNX is for unknown atom/ion.
And as Robbie said, UNK implies an amino acid of unknown identity.
http://www.wwpdb.org/documentation/format32/sect4.html
On 2/5/14, 1:38 PM, Robbie Joosten wrote:
Just to add to Matthew's good advice, UNK is the standard residue name
There is quite a bit of literature on this, but my favorite paper is this:
http://www.ncbi.nlm.nih.gov/pubmed/18391402
Towards a rational approach for heavy-atom derivative screening in
protein crystallography.
Spoiler: The overall winner is ethyl mercury phosphate (Figure 7). Of
course, chem
On 1/15/14, 9:34 AM, Matthew Franklin wrote:
- I usually approximate the peak as a triangle, so that the total peak
area is 1/2 height (absorbance maximum) x base (the number of ml in
your pool)
GE's UNICORN for AKTAs (and probably the new Biorad FPLC software)
integrates and tells you the are
Hi,
On 11/20/13, 4:17 PM, Zhijie Li wrote:
If you need to refine the structure with phenix.refine then you need
to make an edit file to specify that the mannose C1 is linked to the
ser OG by a covalent bond.
I am not sure if this is what was meant, but you don't need to define
bonds explicitl
To add one more nugget, in your pdb you might see a
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.36
or some such thing. Ignore it (I am not sure why this isn't closer to
zero, but that must be a result of French/Wilson). This is *not* your
observed criterion for sigma for F's, although I
On 7/23/13 9:01 AM, Edward A. Berry wrote:
Here we need some clarification on which I/s(I) is meant - sigma(I)
for the
individual measurements, or sigma(I) from error propagation to the final
which as Engin notes will be lower.
Isn't the reported Mean(I/sigI) in the reported Aimless table fo
On 7/22/13 11:20 PM, Ethan Merritt wrote:
Which brings up the point that something seems to have
gone wrong in one of your processing runs.
Both runs claim mean (I/sigI) in the outer shell is 2.0,
but in one case this is for the 2.4A shell and in the other case
it's for the 2.2A shell. That is
Unfortunately, not all is ever that easy. If we were to follow Mark's
rules, glycoproteins would end up losing their asparagines (and others
residues depending on the type of glycosylation) to numerous
underdefined new residue types. And consider the confusion caused by the
different versions o
Please direct your inquiries to Dr Garcia:
Dear Colleagues, I have an opening for a senior post-doc or staff level
crystallographer in my group. This is an ideal transitional position for
someone at later stages of a post-doc who is looking to bolster
experience and/or publication record
1st stable assembly,
navigate to that assembly in the result tree on the left (that means, open Assemblies/Stable and
highlight 1st assembly), and then choose "File/Export plain text" from windows' menu.
I hope that this helps,
Eugene
On 4 Mar 2013, at 07:13, Engin Özkan wrote:
copy and paste from a browser
when using the webserver. I must clearly be missing something using the
new and beautiful Qt interface (otherwise why produce these tables?).
Could someone please direct me to how to do this?
Cheers,
Engin
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K
To add another datapoint, a couple of weeks ago, I saw a friend's
MacBook Pro (probably 2007) had a battery case open up just like that.
My 17-inch MacBook Pro (2008) case is also bent in a million different
ways, and I have already had to change the bottom case once (for $130,
and at no labor
he money, over
the past few years. The only post I could find on the BB was from 2008. Have
His-Antibodies improved or are they still rubbish.
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
27
ps and was thinking of doing a rigid body or very restrained (
secondary structure | reference structure | etc ) refinement of the coordinates
for helping the fit.
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
--
E
s?
Kevin
p.s. I expect I'll have to spend at least a year working on the
problem before before I spell polysaccharide consistently.
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
De
in the XDS.INP file.
Cheers,
Florian
On Jul 25, 2011, at 1:14 PM, Engin Özkan wrote:
Hi all,
After about a year of not working with XDS, I was a little surprised
to see that adding a REMOVE.HKL file to the current directory and
running CORRECT does not remove outliers. I still see the same
Hi all,
After about a year of not working with XDS, I was a little surprised to see
that adding a REMOVE.HKL file to the current directory and running CORRECT does
not remove outliers. I still see the same reflections reported at the end of my
new CORRECT.LP file and I have grepped the XDS_ASCI
/ dislikes?
Many thanks,
Stephen
--
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
And as others have said shedding of dextran is a problem with GE columns
(this was confirmed to me by GE people), but after extensive system
equilibration, we do not see a problem significant enough to ever hurt
our light scattering measurements.
Engin
On 3/8/11 10:38 AM, Engin Özkan wrote
of the default 0.5 ml/min), since our
HPLC has a lot of back pressure for FPLC columns.
Best,
Engin
--
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ks in advance for any help!
Best Regards, Hailiang
--
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
mer of Coot in fact its stereoisomer known as
dithioerythritol? Should I import the correct DTT from elsewhere and
re-refine or is there something else behind this?
Thanks a lot for any suggestions!
Emmanuel
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Med
the tcl/tk supplied with OS X, and the latest
mosflm is in ccp4, so there is no need for any of that. Just use what is in
ccp4.
Sorry for this.
On Jul 5, 2010, at 4:34 PM, Engin Özkan wrote:
Hi everybody,
I was doing a regular fink update (OS X 10.6.4, 32-bit fink) when I encountered
a
ists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb
### execution of /sw/bin/dpkg-lockwait failed, exit code 1
Failed: can't install package imosflm-1.0.4-3
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Mole
ential and intended solely for
the addressee.
You must not disclose, forward, print or use it without the permission
of the sender.
______
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Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical
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