/
Kristof
On 31 Jul 2008, at 16:55, Jacob Keller wrote:
Dear crystallographers,
is there a program around, ccp4 or otherwise, into which one can input a
sequence and get a .pdb of an ideal helix of the input sequence?
Thanks,
Jacob Keller
Dear crystallographers,
is there a program around, ccp4 or otherwise, into which one can input a
sequence and get a .pdb of an ideal helix of the input sequence?
Thanks,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist
Doesn't the technique in that paper seem like just a fancy way to elevate
the temperature briefly? What else could zapping with a 780 nm laser do?
Also, it seems that since N = 1, the technique is way too nascent (and it
might be stillborn) to be applied.
Jacob K
a of "the truth,"
as if taking many snapshots of the same object, and putting them together to
form a three-dimensional object. In Hazes' language, don't all isomorphous
crystals "draw from the same [underlying] distribution?"
Jacob Keller
ps admittedly if there is rad
s
another reason I ask for the sources of the numbers quoted in a couple of
the responses.
Thanks for all of the helpful responses so far,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Se
assume that the affinity is weak, but at the
concentrations at which we are wont to use it in our elutions (~100-500 mM),
does it not seem likely that other metal ions are being competed away from our
proteins as well?
Jacob Keller
***
Jacob Pearson Keller
Wouldn't it make sense to do MIRAS with both the Se and Hg derivatives, and add
in some multi-crystal averaging from the native set? You seem like you are
almost there, though. I assume you have already tried DM and NCS averaging (if
there is any)?
Jacob
***
I have been interested in this topic as well, so could any responses that are
not also addressed to the BB be sent to me as well?
Thanks very much,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos
background very clean, and one could see easily the degree of
mono/polydispersity of the SEC peak(s). It was not, however, inexpensive.
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F
Dear Crystallogrphers,
does anybody here know a protocol to get consistently well-diffracting but
smaller, ~50um, cryoprotect(ed/able) lysozyme crystals?
Thanks,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training
Dear Crystallographers,
is there a list somewhere of spacegroups which can and cannot be
birefringent? Upon what feature of the spacegroup does this depend?
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training
about for more conventional,
known crystallization conditions? It seems that this would be a spectacular
way to decrease damages/stresses caused by handling...
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
between
salt, temp, cmc, and cloud points, but nothing on precisely this topic
(detergent-related crystallization artifacts).
Best Regards,
Jacob Keller
ps. in passing, it seems like it would be a great idea to get together an
excel database of all false-positive results (e.g. phosphate salt
Perhaps it should also be noted here that the long crystal axis should be
oriented close to parallel to phi, in order to minimize overlaps. I have
heard anecdotal evidence (anyone else?) that this long axis, in plate
crystals, is usually normal to the surface of the plates.
Perpendicularly-bent
Dear Crystallographers,
does anybody have an nicely-formatted excel file with all or several of the
commonly-used crystal screens in it? That would be quite helpful for me.
Thanks,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical
Has anybody heard about what happened in the end with the Ajees et al
debacle which raised so much dander?
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus
Dear crystallographers,
has anybody here ever heard of a protein structure with coomassie dye bound?
Seems like it would be easy enough to do, but a search of the PDB did not
yield anything. Surely somebody must have done this...?
Jacob
***
Jacob Pear
Dear Crystallographers,
does anybody know the extent to which the outer membranes of e. coli and/or
the cell walls of s. cerevisiae are permeable to various solutes? In
particular, I was thinking of small, hydrophilic molecules. References would
be great as well--I am not sure where to look...
ECTED]
***
- Original Message -
From: "Artem Evdokimov" <[EMAIL PROTECTED]>
To: "'Jacob Keller'" <[EMAIL PROTECTED]>;
Sent: Monday, March 03, 2008 6:31 PM
Subject: RE: [ccp4bb] Copper Staining
There's an even faster reagen
Dear Crystallographers:
just to share something I found out recently, that is really helpful to
know:
5 min Copper Stain protocol
Normal SDS-PAGE gels can be stained in 5 min with 300mM CuCl2. Simply remove
the gel, rinse ~10s in water, place 5 min in CuCl2, and the gel is
negatively staine
There was once a fellow named Zeno who made a similar argument.
Aristotle was not convinced.
Dr. Merritt,
are you bringing a proof from Aristotle? But he believed in intelligent
design (see below for his argument), and therefore would be shunned and
blacklisted these days from any scientific
Dear Crystallographers,
I am looking for a way to modify any specific set of sidechains in my
protein (e.g., all K's, or all D's and E's, etc.). A few requirements:
1. Relatively cheap
2. Definitely non-cell-membrane-crossing
3. Specific
4. Any reasonable amount of change in mass (+ 5-5000 Da?
other, because there are about twenty times the number of reflections to
describe the same underlying structure, all other things (e.g., solvent
content) being equal. Is there a indication of this in the statistical measures
usually reported in Tables I*, or anywhere else?
Regards,
Jacob
Hi Jerry,
I believe that if you make your cuvette and sample buffers exactly the same,
you would really cut down on noise, and get an accurate reading. Did you do
that, or is it possible?
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Sci
, and I was imagining a
"moleman" homolog for bioinformatics (perhaps seqman?).
Regards,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
E
Hi All,
Thanks for all of the great suggestions--it was actually Ethan Merritt's
suggestions and pointing to the right Gnuplot documentation that really
worked for me. Gnuplot is actually pretty powerful, and can make quite nice
images. Again, thanks a million for the help.
Jacob K
at I want is a ~1500 x 1500
grid with boxes color-coded by their z values. I cannot figure out how to do
this in gnuplot or anywhere, despite efforts to learn gnuplot and other
programs. Any suggestions?
Best regards,
Jacob Keller
***
Jacob Pearson
.
Enjoying the debate,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.467.4049
cel: 773.608.9185
email: [EMAIL PROTECTED
were given in one recent
BB posting, but I was looking for a more systematic tabulation...
Thanks,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston
Dear Crystallographers,
I have just found some crystals in a 1 year old screen, and, having been
repeatedly trained to be very skeptical, think that probably they are salt. So
the question: has anybody seen malonate crystals before? I was wondering
whether they could possibly be birefringent, g
Did you check the pH of your DTT and the protein solution before and after?
I have had some experience with DTT changing pH (as might well be
expected...).
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos L
Hi All,
Sorry for the non-ccp4 question, but it is of general crystallographic
interest, and I believe this list may be the best place to ask, as we all
need to know about solubilities almost all of the time, so...
Does anybody know of a good online database of solubilities of common
compoun
Does anyone here know what, if anything, happened with the whole Ajees et
al. debacle? Just swept under the carpet, lost in the mists of time?
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos
I solved a structure in the presence of SAM, which is the same as SAH but
with a donor methyl group, and saw clear density for SAH, and not SAM, so it
seems that the SAM was either spontaneously de-methylated in solution, or
the protein which bound the SAM spontaneously demethylated it. In any c
inding in the mortar, but for me, it is still
better than shivering in the cold room by the sonicator.
Regards,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Camp
Does anyone have or know of a program to calculate net charge of a protein
sequence in a user-defined sliding window? Somewhat like a hydropathy plot,
but with positive and negative values instead of absolutes. It should be out
there, I would think.
Jacob
*
Hello all,
does anybody know of a program which calculates net charge within a sliding
window of user-defined size? Hydropathy programs are almost this, but not
quite--they use absolute values rather than the signed ones (what is the
opposite of an absolute value called? the relative value?).
(517) 353-9125/
/FAX: (517) 353-9334Email: [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>/
/****/
On Oct 22, 2007, at 5:48 PM, Jacob Keller wrote:
Dear CCP4BB,
Although this is not exactly CCP4-related, I thought somebody here
might know whether there is somewhe
Dear CCP4BB,
Although this is not exactly CCP4-related, I thought somebody here might
know whether there is somewhere a definitive list or tabulation of detergent
properties which are not simply copied out of catalogs, but have been
traceably experimentally determined. In particular, it would
, was successfully purified. Of course this makes
complete biochemical
sense, but nevertheless I am very glad I checked the pH.
Jacob Keller
On Wed, 10 Oct 2007 8:12:46 pm CDT changrui lu wrote:
Dear all,
I am trying to express a 150 kd protein in E coli. I have it in two
constructs, one with
/ Monash University Senior Logan fellow
Department of Biochemistry and Molecular Biology
Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia
+613 9905 3747 (Phone)
+613 9905 4699 (Fax)
+61 418 170 585 (Mobile)
===End of original message text===
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)491-2438
[EMAIL PROTECTED]
***
en. BE A BETTER
WELTENBUMMLER!===End of
original message text===
*******
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)491-2438
[EMAIL PROTECTED]
***
unlabelled. Those bands with a shift would have been exposed to the reagent in
that experiment,
indicating that fragment/lysine's location with respect to the cell membrane.
I suspect that somebody must have thought of this previously...there is nothing
new under the sun.
Jacob Keller
program last, right before composing "Table I" for publication? That seems
suspicious...
Jacob Keller
==Original message text===
On Fri, 07 Sep 2007 3:39:27 am CDT Andreas Kohl wrote:
Dear all,
we have currently two open postdoctoral positions in our department
I second Dr. Loll's question, and would like to be CC'd in whatever MS tips,
including
service-providers, are sent. I have been having a bit of a debacle with a
certain MS service provider.
Jacob Keller
==Original message text===
On Wed, 05 Sep 2007 11:41
a ref about this? I always thought it was an anomaly, but
All the best,
Jacob Keller
u can check the paper
describing a single domain of this protein complex or contact one of its
authors.
Bart
J Mol Biol. 1998 May 15;278(4):855-70.
Crystal structure of a functional unit from Octopus hemocyanin.
Cuff ME, Miller KI, van Holde KE, Hendrickson WA.
Jacob Keller wrote:
> I am stil
rick FRS
>Dept. Structural Chemistry,
>University of Goettingen,
>Tammannstr. 4,
>D37077 Goettingen, Germany
>Tel. +49-551-39-3021 or -3068
>Fax. +49-551-39-2582
>
>
>On Mon, 27 Aug 2007, Jacob Keller wrote:
>
>> What a beautiful and interesting diffraction
s probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
> What a beautiful and interesting diffra
ou put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two interpenetrating,
non-commensurable
lattices in it. That would be pretty fantastic.
==Original message text===
On Mon,
omething which it seems would be necessary to produce
interference.
NB this issue came up in a crystallography class several years ago, and I have
been ruminating on
it, on and off, since then.
JPK
*******
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chica
el: +44-(0)1223-766 044 / 760 468,
fax: 766 002
___
===End of original message text=======
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
Hello All,
This debacle is actually quite reminiscent of a similar incident that Wayne
Hendrickson caught in
the 1970's concerning purported "tRNA crystals." Turned out to be completely
fabricated, and the
guy's career went down the drain, I think. A good example to tell y
I forgot to mention we also tried urea, at various concentrations.
JPK
==Original message text===
On Wed, 15 Aug 2007 11:39:14 am CDT Jacob Keller wrote:
Sorry about this not being exactly CCP4 related, but I think it is still of
general interest to the
structural
, and the subunits
do not exhibit
crosstalk, what on earth is the reason for their oligomerization?
All hypotheses and especially references would be greatly appreciated,
Jacob Keller
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
with two conformations. Therefore, if there is not an
easy way to do this
now, we should try to implement a good way to do this in the future.
All the best,
Jacob Keller
==Original message text===
On Fri, 06 Jul 2007 12:46:29 pm CDT Prasenjit Bhaumik wrote:
Hello,
W
ft which is little shifted from the Compton-scattered wave, although
it might be even a
few periods behind. I will try to look into this, and see if the observations
and equations agree
with what I am saying.
All the best,
Jacob Keller
ps perhaps "anomalous" is better than "resonant,&
==Original message text===
On Wed, 30 May 2007 6:51:09 pm CDT Ethan Merritt wrote:
On Wednesday 30 May 2007 16:24, Jacob Keller wrote:
> I have been wondering recently whether the anomalous component of a
> diffraction pattern is of a
> different wavelength
exactly the same.
Does anybody know here for sure, or at least where to look or whom to ask?
All the best,
Jacob Keller
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
Hi Oleg,
I solved a structure that uses a c-terminal beta hairpin to tetramerize the
protein. See 1F38.
All the best,
Jacob Keller
==Original message text===
On Wed, 30 May 2007 5:01:09 pm CDT olegchem wrote:
Dear all,
I am looking for examples of protein-protein
be the best way to implement this idea in the given software?
All the best,
Jacob Keller
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
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