/expertise of a molecular
biology lab (except us :-).
We can and will make the His-tagged proteins of interest for them, but if there
is an economical and reliable commercial source, it might be worth using that
for initial tests.
Best wishes,
Mark
Mark J van Raaij
Dpto de Estructura de Macr
ey are happy to be named)
Best wishes,
Mark
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/
> On 2 Jul 2020, a
I think most of us are such "excellent" cryo-coolers that for every beamline
shift we have multiple crystals with ice ring diffraction :-)
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 9
), so the difference can be quite
large. You can determine the real pI by iso-electric focussing.
Best wishes,
Mark
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
Section Editor Acta
a monomer.
It will be interesting to see how well future iterations of the method can
assemble the complete protein chain and the complete protein chains into the
correct heteromer.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28
tallising peptides.
Greetings,
Mark
Mark J van Raaij
On 6 Sep 2011, at 18:51, Chaudhary, Ritcha wrote:
> Dear all
>
> I am interested in crystallizing a 5 residue peptide. I have no prior
> experience in this field although I have crystallized larger proteins (5--60
>
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij
On 27 Sep 2011, at 17:55, Browning Christopher wrote:
>
PS I would also try substituting imidazole for HEPES and zinc sulphate for zinc
chloride and sodium sulphate.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http
having experience with both, I find Akta and Biorad both do the job, with the
Akta equipment giving a sturdier impression.
Neither of them is cheap, and given similar price I would go for an Akta when
buying new - however, if a significant price advantage exists, I would have no
problem choosing
one
could be myself, and the images being stored safely and centrally would make it
easier also for me to recover them.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585
works, you can just harvest from the equilibrated drop and directly
flash-cool
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular
.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij
can not always count on the crystal orienting randomly in a loop, i.e. many
crystals have preferred orientations when mounted...and one tends to mount the
loop on the goniometer the same way each time. So one would have to use
"random" starting phis.
Mark J van Raaij
Laborato
selected.
greetings,
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij
e normally just put a water
in it if it can make reasonable hydrogen bonds.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecul
be available before summer 2012.
There are no nationality restrictions. Interested individuals should submit
their CVs and a specific motivation letter by January 2nd, 2012 to the e-mail
address indicated.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de
problem to send (sorry, link) even large files. The only
disadvantage I can think of is that they expire after some time.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http
B-factor refinement (if you are using it), works
better in REFMAC than PHENIX?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research
avoid pRSET would be my recommendation - my impression from a couple of
examples is pRSET gives badly folded protein.
Can you easily subclone it in a better expression vector?
(personally, even if it were not so easy, I would reclone it in another
expression vector).
Mark J van Raaij
So, with the combined votes of Hendrickson, Blundell, Tickle and Google, can we
safely call it "Multi-wavelength Anomalous Diffraction" from now on and call
all other names wrong?
Mark
On 19 Jan 2012, at 18:50, Ian Tickle wrote:
> Perhaps I could chime in with a bit of history as I understand
if your crystals are from 2 M AmSO4 without buffer, try to measure the pH in
the drop, if possible.
Or if you have plenty of crystals, transfer to 2 M AmSO4 buffered at a wide
range of different pHs to see where the crystals are stable, before adding
cryoprotectant.
In the end, you may need to g
Rationalising it completely may only be possible once you know the nature of
the crystal contacts, i.e. when you have solved the structure. Until then it is
mainly a matter of experimenting.
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>
are just proteolysing some surface
loops and can still purify and crystallise the protein. This was done on
purpose for the cap-binding complex, see:
Crystal structure of the human nuclear cap binding complex.
Mazza C, Ohno M, Segref A, Mattaj IW, Cusack S.
Mol Cell. 2001 Aug;8(2):383-96.
Mark J
ution is to ask the CCP4bb administrators to unsubscribe
the email address for her...
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 16
a
minikappa or the bendable loop mounts are very useful.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 7 Mar 2012, at 08:44, Frank v
still be a good
idea to collect ice- or wax-rings on purpose before or after data collections
for determining accurate beam centres.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585
or you can just give the TER card an arbitrary number higher than your highest
ATOM number - the PDB coordinate submission server will take care of
renumbering.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid
committing these
violations.
I have witnessed authors being hesitant to complain about possible violations
and journals not always taking complaints seriously enough.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid
I don't agree, if we know a referee is dishonest we should try and ruin his
whole career, not just prevent him from scooping us in this one case.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spai
In fact, I would put it even stronger, if we know a referee is being dishonest,
it is our duty to make sure he is removed from science, blacklisted from the
journal etc.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E
- please do not reply to me but to the email address mentioned.
www.biocenter.helsinki.fi/bi
RESEARCH DIRECTOR IN STRUCTURAL BIOLOGY/BIOPHYSICS
The lnstitute of Biotechnology is a leading European research institute with a
mission to increase knowledge in cross- disciplinary biology and biotec
just out of curiosity, was one Se enough in this case to solve the structure of
your 0.2 kD protein by MAD?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es
Phoebe, Jan, PDB,
is this something particular to the US portal of the PDB, or general?
We always use the European portal pdbe and have not had such "problems".
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin
have a look at this case, no danger of your coordinates going to anyone but
yourself if you do it this way:
http://publicationethics.org/case/author-creates-bogus-email-accounts-proposed-reviewers
On 26 Apr 2012, at 12:02, Jrh wrote:
> Dear Colleagues,
> I have followed this thread with great i
use the pdbe deposition tool AUTODEP - or
the Japanese one, if you like.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 27 Apr 2012, at 20
In different datasets of P321 crystals, when you index them separately, the
hand may be different and you may need to invert it for some. They
"prohibition" in reindex is really a warning, and can be overridden.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromolecu
look like tyrosines to me!
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.researcherid.com/rid/B-3678-2009
On 24 Nov 2010, at 13:10, Vinson LIANG wrote
Dear Hubing,
please don't discard a structure just because the Rfree > 30%, or approve a
structure just because the Rfree < 30%. Other quality parameters like relative
absence of clashes and Ramachandran outliers are much more important. Perhaps
even more important is whether the structure gives
is this DVD ok or available in Europe, i.e. with the correct regional DVD
digital rights format etc.?
Mark van Raaij
On 3 Dec 2010, at 19:25, Bernhard Rupp (Hofkristallrat a.D.) wrote:
> FYI, crystal fans. Really worth watching, and with X-mas approaching perfect
> gifts for the crystals in y
In Europe:
http://www.trianatech.com/
Mark van Raaij
On 3 Dec 2010, at 19:25, Bernhard Rupp (Hofkristallrat a.D.) wrote:
> FYI, crystal fans. Really worth watching, and with X-mas approaching perfect
> gifts for the crystals in your life. BR
>
> From: JuanMa GarciaRuiz [mailto:juanma.garciar..
clashes
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.researcherid.com/rid/B-3678-2009
On 18 Jan 2011, at 10:34, Careina Edgooms wrote:
> D
CHAINSAW retains conserved amino acids but prunes nonconserved residues to the
C-beta or C-gamma atom.
PDBSET can renumber I think
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
the old map in coot instead of the new map
but I guess you checked all this...
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content
4. Review.
PMID: 20206698 [PubMed - indexed for MEDLINE]
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research
J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1
exing from two images at 90 degrees from each other is simply an easy "good
practice" rule that often, but not absolutely always, works.
Many times a single image is more than enough, sometimes many images and a lot
of trying is necessary to get the right indexing matrix.
Mark J van Ra
- try limited proteolysis to see if you can chop off a disordered region
- consider the fact that, although it purifies nicely, your protein may not be
well-folded
do you have a biochemical activity test?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de
a quick google search turned up:
http://people.mbi.ucla.edu/sawaya/tutorials/Phasing/gel.pdf
Acta Cryst. (2000). D56, 161-168[ doi:10.1107/S0907444999015188 ]
Mass-spectrometry assisted heavy-atom derivative screening of human Fc<>RIII crystals
P. D. Sun and C. H. Hammer
Mark J van
perhaps the IUCr and/or PDB (Gerard K?) should issue some guidelines along
these lines?
And oblige us all to follow them?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34
27;t think we are talking about students or research novices here, but about
"savvy" end-users to quote Phoebe Rice.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+
I completely agree, although if the IUCr or PDB decides otherwise, I'd be happy
to oblige.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
The program appears a bit black-box to me, could you provide more details
(today of course).
Mark
Sent from my HTC
- Reply message -
From: "Robbie Joosten"
Date: Fri, Apr 1, 2011 11:04
Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
To:
Hi Ethan,
Awsome p
Greetings,
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1
On 5 Apr 2011
From the two images, it appears there are two short cell axes and one long axis
- it also looks like trigonal or hexagonal, then the long axis should be c. Of
course lower symmetry with a nearly hexagonal-shaped cell can not be ruled out.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de
[switch not too serious mode on]:
well, it is lysozyme, which, according to diffraction properties, should
perhaps be classified as a salt (LyCl7), not a protein... :-)
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
never know.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij
On 24 May 2011, at 19:19, weikai wrote
using that and the original processed dataset (i.e. before it has "seen"
refmac), do the peaks also show up?
(I guess you have checked the pdb-file output from refmac carefully in a text
editor?)
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Bio
s / spacegroup already occur in the pdb and if
that protein could come from your expression host).
Greetings,
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585
translation along b. is not
determined.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij
On 9 Jun
k, because I
can convert them correctly to .ps with "pltdev" and view them correctly.
I am using MacOSX 10.6.7, CCP4 6.1.3 (didn't try updating yet, because it is a
relatively small problem).
Greetings,
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacion
script Jan Pieter Abrahams wrote, I don't know if
refmac has this possibility).
greetings,
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
- I think the original poster was only calling attention to the fact
that some proteins want to be treated respectfully in order to
crystallise (and the fact that Rigaku Japan realises this). I find
that indeed the case.
Other proteins, however, prefer the attitude "I don't know why I am
se
Rajan,
Likely you have the habit, like me and I suspect most people, to
contour difference maps at +/- 3 sigma. In the beginning of
refinement, these difference map will have significant peaks at 3
sigma, i.e. positive peaks were there is nothing and there should be
atoms and negative pea
Dear Al,
Refmac by default divides reflexions in 20 shells ("bins") - this can
mean a few of them do not contain a thin Rfree shell.
When this happens I add "bins 10" to the refmac com-file, or, in
CCP4i, instead of "run", do "run and view com file" and add "bins 10"
to the file before conti
in my opinion one should always first check RT diffraction and we use
the Mitegen plastic cap over the loop. We find the solutions slowly
dry out (6-18 hours), which can be enough to get a useful RT dataset
on the rotating anode.
If you like, the crystal can also be recovered after RT diffrac
as it appears to bear near the guanidine group of an arginine, I would
suggest it is a partially occupied and disordered sulphate and/or
phosphate.
whether this is practically modellable is another matter, a sulphate
at occ. 0.5 is an option, or putting a water with a remark in the pdb
that
this - to check the possibility
something else crystallised than the target protein.
Greetings,
Mark
--
Mark J van Raaij
http://webspersoais.usc.es/mark.vanraaij
http://www.ibmb.csic.es
Dear All,
is there a convenient way to look in the pdb database for specific cell
parameters and space
group combinations?
There is a "space group" button in the advanced search function, but no cell
parameter
selection as far as I can see.
I guess you can guess why I would want to do this - to
apologies for that question - it IS there, two positions about space group
search ("X-ray cell
dimensions"). Can't figure out why I did not see this...looking with my ears I
guess...
Mark
ree set with the working set. Given an expression to
> > predict the effect of reducing number of parameters, seeing
> > how much of the actual drop in Rfree/R it accounts for
> > would let us see how severe the linkage problem is.
> >
> > Ed
> >
>
--
Mark J van Raaij
http://webspersoais.usc.es/mark.vanraaij
http://www.ibmb.csic.es
8
> Baltimore, MD 21205
> Phone: +1-410-614-4742
> Lab: +1-410-614-4894
> Fax: +1-410-955-3655
> http://web.mac.com/bosch_lab/ <http://web.me.com/bosch_lab/>
>
>
>
> *P** **please don't print this e-mail unless you really need to*
> Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
> Department of Biochemistry (B8)
> Netherlands Cancer Institute,
> Dept. B8, 1066 CX Amsterdam, The Netherlands
> Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
>
>
>
>
>
--
Mark J van Raaij
http://webspersoais.usc.es/mark.vanraaij
http://www.ibmb.csic.es
try JM109(DE3) instead of BL21(DE3), combined with low temperature induction -
for several proteins this has yielded us soluble protein instead of inclusion
bodies. I think this is because JM109(DE3) grows a bit slower.
Mark J van Raaij
mvr...@ibmb.csic.es
http://webspersoais.usc.es
Dear All,
Having just installed LIGPLOT under Windows, I find it rather convoluted to
run. It has to be run via de command line window, and I try to avoid Windows as
much as I can anyway.
I also tried to install the Unix version on MacOSX, but was not able to get it
running properly, probably a
.
Mark
On 25 Aug 2010, at 19:51, Mark J van Raaij wrote:
> Dear All,
>
> Having just installed LIGPLOT under Windows, I find it rather convoluted to
> run. It has to be run via de command line window, and I try to avoid Windows
> as much as I can anyway.
> I also tried t
Interesting! it appears to be some kind of "secondary order"...I hope
someone wise/experienced can shed more light on this.
the diffraction spots appear to fall consistently in the middle of the
hexagonal(ish) grid lines, so it must be some partial order effect
related to the unit cell.
do yo
we had a P1 case with 12 mols/au, about 30% sequence id, 2.4A
resolution, which was solved after a lot of trials with phaser. Other
problems of these crystals were that they took months to grow and
invariable presented multiple lattices (we did not try microbeam).
See:
Crystallization of t
significantly in the coming years.
Best regards,
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
1865 - 287547
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
of mentoring and checking them. I
hope the authors provide the raw diffraction images to dispel any
doubts and would be curious to learn about the other structures of
the same group - anyone has a comprehensive, annotated list of them?
Greetings,
Mark J. van Raaij
Unidad de Bioquímica
mages, both to
prevent misconduct and to help program developers.
Mark
Mark J. van Raaij
Unidad de Bioquímica Estructural
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
On 1
it is still very bad, but at least it would mean there was some
experimental
evidence for the model and it was not completely made up.
Mark
Mark J. van Raaij
Unidad de Bioquímica Estructural
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
mprovement in the density for
the tail.
Mark J. van Raaij
Unidad de Bioquímica Estructural
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
On 24 Aug 2007, at 03:01, Petr Leim
"vault" be implemented to be effective? If left to the
experimenter, it would be very tempting to check R-sleep once in a
while (or often) during refinement, rendering it useless as an
unbiased validator.
or am I being paranoid and too pessimistic?
Mark J. van Raaij
Unidad de Bioquím
pe is not resistant.
- no replies about solvent-resistant Terazaki plates, we are still
looking for suitable micro-batch plates.
Greetings,
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
Terazaki plates we are still
interested.
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
Dear All,
In the latest Nature (which for once arrived in a few days to our
office...) there are interesting structures of the influenza M2
proton channel.
One is by NMR, which resulted in a model of a closed state with four
inhibitor molecules bound to the outside. Another is by X-ray
cry
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
.
Another common "mistake" is to take too much resin - the minimal
amount to bind the protein should be used, any more will usually lead
to more impurities upon elution.
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Dear All,
Anyone have experience with the NovaGen Duet co-expression vectors? Or
can recommend others?
http://www.emdbiosciences.com/html/NVG/Duet_Spot.html
Greetings,
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
the validation program who first fix their problems
will most likely earn the citation in the paper we are writing...
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
when the next version is released).
But I guess you've found one of the downsides of using websites to
do data processing.
Pete
-Original Message-
From: CCP4 bulletin board on behalf of Mark J. van Raaij
Sent: Thu 4/10/2008 9:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] anti-V
part of the standard ccp4 package.
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
On 15 Apr 2008, at 11:49, Eva Kirchner wrote:
Dear ccp4bb readers,
when I'm trying to run Proch
part of the standard ccp4 package.
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
with Rfree of
0.4 which have been carefully refined and for which the new
information content warrants a good publication.
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
On 2 Jun 2008,
in ccp4, "baverage" does the job.
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
On 4 Jun 2008, at 21:40, xu zhen wrote:
Hi, everyone,
I am preparing the table of data coll
opinion (more) generally accepted?
On a related note, how to refine a structure with only 5000
reflections, which could happen when you have a small a.u. and modest
resolution? Could, exceptionally, a lower absolute amount of
reflections be used for Rfree, say 500?
Greetings,
Mark
Mark J
acceptable.
Fig. 1 of the paper cited below nicely illustrates how putting more
refs in Rfree makes de rms of the refined structure larger, i.e. leads
to a more inaccurate structure.
Greetings,
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de
, what correlation can be expected with
measured values?
Of course, a web server or inclusion into ccp4 would be ideal :-)
Greetings,
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
thors of
both programs, how about a MacOSX version?
another paper:
Müller JJ. Prediction of the rotational diffusion behavior of
biopolymers on the basis of their solution or crystal structure.
Biopolymers. 1991 Feb 5;31(2):149–160.
Greetings,
Mark
Mark J. van Raaij
Dpto de Bioquímica, Fac
Dear Bulletin Boarders,
We have a protein cloned NdeI-ClaI in pT7.7, which expresses
insoluble. Ideally, we would like to do a simple sub-cloning using
NdeI and ClaI into another vector with an N-terminal His-tag, to
produce large amounts of insoluble protein which can then be easily
puri
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