If the I/sigI and CC1/2 that you quote are for the outer resolution shell
of your data, you can use data to a higher resolution limit. It may still
be tricky, and rebuilding will be worse; as Eleanor says you'll probably be
better off growing a better crystal.
Good luck!
--
Kevin Jude, Ph
DMSO is a good solvent for superglue and won't dissolve your loops.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
On Mon, N
eal anything and you don't
believe you have salt crystals, you probably need to do some mass spec to
figure out what species in your drop.
Best of luck
Kevin
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of M
x and
aimless masked that result for me. Thanks to those who responded for the
help and for the chance to dive into the International Tables.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177
rtment of Molecular Medicine
> Morsani College of Medicine
> *University** of South Florida*
> Schonbrunn lab, Moffitt Cancer Center
> Tampa, FL
> E-mail: reza...@yahoo.com, rez...@usf.edu
> Phone: +1-954-937-8487
> ORCID: https://orcid.org/-0002-0424-127X
> Linked
Hi all,
I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via
pointless and aimless. Everything looks good through pointless, as far as I
understand:
xds reports significant anomalous correlation in CORRECT.LP
Inspection of the mtz output from pointless shows that (+) and (-)
Thanks everybody for your replies. I am having another look at my data in
P1 and will post an update and summary to the list.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive
shes
Kevin
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
On Fri, May 31, 2019 at 1:35 PM Diana Tomchick <
diana.tomch...@utsou
Since I believe that my model is good (or at least the correct shape, based
on SAXS), I wonder if I'm misinterpreting my crystallographic data. Any
insights into how to approach this problem would be much appreciated.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard H
biological unit, as well as what
you know from biochemical studies (not to mention the position of CDRH3,
etc).
The easiest way to make the change, IMHO, is to open your molecule in Coot,
center on the appropriate symmetry mate, and use Extensions>Modelling>Symm
Shift Reference Chain Here.
--
Kevi
next time I use
STARaniso.
Best wishes
Kevin
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
On Wed, Sep 26, 2018 at 11:34 AM Kevin
th
mmcif before and am not sure what column names are permissible, nor what
would be recognizable to other users or software. I'm interested to hear
the thoughts and experiences of the community on this.
Best wishes
Kevin
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
H
Hi Charles, a couple of years ago a colleague and I put together a perl
script based on this paper. It worked pretty well in our hands. I'd be
happy to share it with you if you'd like.
Best wishes
Kevin
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hugh
described in Goodno CC. Myosin
active-site trapping with vanadate ion. Meth Enzymol. 1982;85 Pt B:116–23.
Best wishes
Kevin
On Tue, May 2, 2017 at 9:04 AM, Adriana Sene
wrote:
> Hi
> What are good ATP non hydrolyzable analog for crystallization?
>
> best
>
> Adriana
>
--
Kev
HKL2000
> program to meet requirements for data completeness, but the problem is the
> Rmerge value was too high to go on every time.
> Did anyone have met the same problem and how to solve it? or some tips for
> solve this problem？
>
> All comments will be appreciated!
>
you please share
> your experience with us?
>
> Thanks for your help.
>
> Joseph Ho
>
--
Kevin Jude, PhD
Research Specialist, Garcia Lab
Departments of Molecular & Cellular Physiology and Structural Biology
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
I am actually a big fan of using KGlu solutions for protein purification
and have found it to be compatible with both IEX and DNA binding (for
replication proteins) at concentrations that NaCl does not support.
On Thu, Jan 12, 2017 at 2:14 AM, Jon R Sayers
wrote:
> Following on I read somewhere
In this case, calculating Matthews coefficients / solvent fractions for
different possible complexes will be helpful.
http://www.ccp4.ac.uk/html/matthews_coef.html
In the general case, without solving the structure I would dissolve the
crystals and run them on an SDS-PAGE gel, then silver stain t
t work normally
> now?
>
> Best regards
> Andrey
>
>
> On 26 May 2015, at 18:36, Kevin Jude wrote:
>
> Dear colleagues,
> I'm having an issue with a particular ligand in JLigand 1.0.40. When I
> load NRQ, the topology is correct but the bond lengths and angles
suite: patch level 6.5.008
Program: refmac5; version 5.8.0107
--- LIBCHECK --- /Vers 5.2.00 ; 12.12.2011/
dictionary version 5.44
Best wishes
Kevin Jude
ot;quality", but that is perhaps opening
> too large a can of worms.
> Basically though, beauty and truth are not synonymous, whether or not we
> regard protein
> crystallography as a video game where the person with the lowest R-factor
> wins.
>
> best wishes to all!
&g
I think the Ramachandranplot should be used in the refinement and
rebuilding process - a Ramachandran outlier is a flag that that region of
the model needs a closer look, and the fix may be more complicated than
simply rotating a peptide. Maybe a C-beta is pointing the wrong way, maybe
there is a r
In coot:
Extensions>Modelling>Symm Shift Reference Chain Here
Quick, but not automatic.
On Wed, Feb 11, 2015 at 7:07 PM, Keller, Jacob
wrote:
> Dear Crystallographers,
>
> I've encountered this many times, and fixed it a different way each time,
> but my molecules are all spread out into differ
Thanks to Jason Busby and Bernhard Rupp for pointing out that the
scattering type should be in columns 77-78, not 78-79. Thanks to others
for tips that may well prove useful!
kmj
On Wed, Jun 26, 2013 at 3:15 PM, Kevin Jude wrote:
> We are trying to get SAD phases using a Ta6Br12 clus
at of the
input pdb file with the HA sites to bypass this error.
We're using phaser from ccp4-6.3.0 distributed by sbgrid.
Any help will be much appreciated,
Kevin Jude
Note that you'll need a crossover rather than a straight through serial
cable and probably a DB25 to DS9 adaptor, but once you get your hands on
the cable this is a straightforward solution.
kmj
On Wed, Jan 23, 2013 at 5:49 PM, Johan Hattne wrote:
> On 23 Jan 2013, at 16:07, Dave Roberts wrote
I would bring up the DNA in TM buffer (10 mM Tris, 5 mM MgCl2) or similar
and anneal under dilute conditions to favor hairpin formation over dsDNA.
Fast cooling will also favor hairpin formation, so you may try heating to
95° and then cooling on ice, or using a short gradient on a thermocycler.
Yo
Probably, you have built water molecules that are associated with
symmetry-related macromolecules rather than the host molecule. Turn
symmetry on, check the nearest neighbors of the offending waters, and move
the waters close to the host molecule if appropriate. I believe you can do
this with the
I haven't had the good fortune of using SHELXL in a few years, but I seem to
recall that you need to make sure that you don't have an END statement
preceding your newly added waters. Check this after each cycle of SHELXWAT.
best wishes
kmj
On Fri, Feb 12, 2010 at 1:45 PM, Ajit Datta wrote:
> H
Note that, despite the claim otherwise in Kettenberger and Cramer, SYBR Gold
does stain at least some proteins, so be sure to run the appropriate
controls.
kmj
On Tue, Jun 23, 2009 at 11:52 AM, Allyn Schoeffler wrote:
> Dear Nick,
>
> If you have access to a fluorescent microscope, you can try
As an undergrad late in the last century, I used a micromanipulator,
quartz capillaries, and a device similar to a patch pipet (manually
operated via a screw) to do just this. It was just about the time that
nylon loops were coming into wide use, though, and I gladly abandoned he
capillary method
I'm not sure what name phenix or ccp4 like, but looking in
$CNS_TOPPAR/dna-rna.top, I see this line:
ATOM C5A TYPE=CC3E CHARGE=0.00END
so CNS likes C5A. If you want CNS to play well with other programs,
just change that line in your topology file to
ATOM C7TYPE=CC3E CHARGE=0
I've seen haunted crystals before - the culprit was indeed with the
mounting of the pins in their bases (I was re-using some pins and
apparently the adhesive had cracked or otherwise failed). Fortunately I
never leave home without a tube of Duco cement and was able to correct
the problem in si
PEG 3350 can also provide some cryoprotection; 22% PEG 3350 with 5%
glycerol has proved a good cryoprotectant in my hands.
kmj
Phoebe Rice wrote:
If you have high [DTT] in your buffer, you might be
catalyzing the addition of dimethyl arsenic (from the
cacodylate) to some of your cysteines?
Al
If your protein is autolyzing, you may need to crystallize it in the
presence of an inhibitor. In the case of trypsin, I have crystallized
in the presence of benzamidine, then removed the inhibitor by dialysis
after crystallization.
kmj
Ngo Duc Tri wrote:
Dear CCP4 experts,
I'm working on a
You could stain your crystals directly with Sybr Gold, which will
fluoresce upon binding nucleic acids, or you can visualize both protein
and RNA on a silver-stained SDS-PAGE gel.
Kevin
Rongjin Guan wrote:
> Dear All
>
> I am trying to co-crystallize a protein and dsRNA complex, and
> looking f
I have seen similar ripples with S-methylmercury cysteine - and an 80
sigma peak for Hg is not that surprising! Anisotropic refinement was
not helpful in reducing the ripples, as it is indeed a summation
problem. It's a good idea to refine occupancy of the Hg, though, and to
look for dual con
changes to the input file
provided, and it looks fine to me. Permissions on all relevant
directories are 755. I'm not sure what else to check. I'm running this
on a G5, OS X version 10.4.8. I'd appreciate any help from someone
who's gotten this to work.
Best wishes,
Kevin Jude
I use a multimeter from Radioshack (catalog number 22-812) that can
record this data on a PC via a serial connection. Presumably by now
there is a similar device with a USB connection. Publishing the
resulting text file on the web would be effortless on a *nix
machine, but I'm not sure how to do
Jacob, lsqman from USF will be happy without B and Q, and you can pick
the set of atoms that you want to align. I think that you can run it in
script mode, as well.
Kevin
Jacob Corn wrote:
Dear everyone,
I'm attempting to do a large scripted pairwise alignment of theoretical
models to calcu
There was a brief discussion of this on the board last year. See:
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg18757.html
Good luck
kmj
shivesh kumar wrote:
Dear all,
Can u suggest me about the peptide crystallization,some
references.Should I try it with PEG or MPD.It is 10-15 residues
We have an RAxis IIC that has been idle for a couple of years and will
clearly not be used in our lab again. We are still using the goniometer
and 2-theta stage, but the detector and controller are available to
anyone who can pay the shipping costs or preferably pick it up in
Philadelphia. Ri
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