and saw band for my protein
> all
> > throughout.
> >
> > Judging peaks on chromatogram is not useful as it doesn't have any
> aromatic
> > rings.
> >
> > Cheers,
> >
> > Allan
> >
> > --
> > Allan Pang
> >
> > P
ins and removing 2, 3 or 5 residues on each/both sides. I also tried
> other search models. Maybe some "magic" combination of parameters on Phaser
> or other programs can help me.
>
>What is your advice regarding how to proceed with MR? Is there some
> program, procedure, p
Laboratory Manager
> University of Oklahoma
> Department of Chemistry and Biochemistry
> Stephenson Life Sciences Research Center
> 101 Stephenson Parkway
> Norman, OK 73019-5251
>
> lmtho...@ou.edu
> http://barlywine.chem.ou.edu
> Office: (405)325-1126
> Lab: (
is signifcant? This type of question of course also applies to
other methods such as cryo-EM. Is a 7A movement of an entire domain
'significant' in a 10A map? If it is, how do we quantify the significance?
If anybody has a great reference or just an individual opinion, I'd like to
hea
for all
> atoms to be skewed in the same direction?
>
> Jacob
>
>
>
> On Mon, Nov 21, 2011 at 4:04 PM, Filip Van Petegem
> wrote:
> > Dear crystallographers,
> > I have a general question concerning the comparison of different
> > structures. Suppose you have a
his problem?
>
> Thanks in advance!
>
> Eric
>
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/
soluble?
Cheers
Filip Van Petegem
On Tue, Nov 16, 2010 at 6:15 PM, Jim Pflugrath wrote:
> With Izit or other dyes, you might wish to do a positive control with
> bona fide protein crystals and a negative control with bona fide salt
> crystals.
>
> --
12) 626-5226
> "If you never did you should. These things are fun and fun is good" Dr.
> Seuss
>
>
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/
?
- What are the usual reasons?
Cheers
Filip Van Petegem
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http
aconescu <
> deac...@brandeis.edu> wrote:
>
>> Dear ccp4bb enthusiasts:
>>
>> A question unrelated to ccp4: can anyone recommend a good 250 kDa standard
>> for gel filtration that is commercially available? It could be a single
>> polypeptide or an oligomer too...
>
among
crystallographers... (from what we can gather from this set of emails...).
On the other hand, this discussion has flared up many times in the past, and
maybe it's time for a powerful dictator at the PDB to create the law...
Filip Van Petegem
On Wed, Mar 30, 2011 at 8:37 AM, Mark J
CCP4-style map,
which you can read in with your favorite molecular graphics package.
Filip Van Petegem
On Thu, Jun 2, 2011 at 2:24 PM, Hailiang Zhang wrote:
> Hi,
>
> I am trying to compare a published EM map with X-ray map in hand, and have
> several questions:
>
> 1. EM ma
between two consecutive measurement) that we didn't consider this instrument
at all. So unless you just want a 'rough' estimate, I wouldn't recommend it
at all. But most respectable spectrophotometers will take cuvettes with 50ul
volumes - a big step up from 1ml volumes...
will give a better accuracy provided you clean them properly. Just
some water or EtOH is *not* enough...
Filip Van Petegem
On Thu, Jun 16, 2011 at 12:52 PM, aaleshin wrote:
> I also like our Nanodrop, but I do not recommend using it for Bradford
> measurements.
>
> The 25% accuracy
that requires mixing, the error will
be larger for smaller volumes.
cheers
Filip Van Petegem
On Thu, Jun 16, 2011 at 2:08 PM, Justin Hall wrote:
> Hi Alex,
>
> I read Filip's comment about volume not as a path length argument, but
> about concentration uncertainty in mixing s
with Biuret or
>
> Kjeldahl nitrogen, or solution made up by weight?
>
>
> ---
> Mischa Machius, PhD
> Director, Center for Structural Biology
> Assoc. Professor, Dept. of Pharmacology
> Member, L
Just another example of where it would have been good for the reviewers to
get access to the data during the review process... and where at least one
of the reviewers *should* be a protein crystallographer...
Filip Van Petegem
On Wed, Aug 10, 2011 at 2:01 PM, David Schuller wrote:
> Time
in the cryoEM world?
(My apologies to the cryoEM people on this bulletin board: if you have been
making your maps available, you'll agree that clearly not everybody does...)
Filip Van Petegem
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of B
, but the 2 year hold is currently a big loophole. Many more journals,
however, don't require the deposition of maps at all. Of course it would
help if the EMDB didn't allow for these loopholes...
Sincerely,
Filip Van Petegem
On Thu, May 20, 2010 at 7:16 AM, Cathy Lawson wrote:
>
your colleagues. More
signatures = more pressure.
http://www.petitiononline.com/cryoEM/petition.html
Sincerely,
Filip Van Petegem
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm
represent
the sodium channel family.
(Science.<http://www.ncbi.nlm.nih.gov/pubmed/11743207> 2001
;294,2372-2375)
There are structures of small cytoplasmic loop segments (PDB ID 2KAV, 1BYY,
1QG9), but these won't tell you anything about sodium selectivity.
cheers
Filip Van Petegem
On
#x27;d appreciate if you could send me the reference
to the primary paper that described the cryoEM structure, as well as the
specific issue and outcome (e.g. were the journal editors contacted and
could they resolve the issue).
Thanks
Filip Van Petegem
--
Filip Van Petegem, PhD
Assistant Profe
Hello James,
You can try the map2map from the SITUS package (
http://situs.biomachina.org/fguide.html) or em2em (
http://www.imagescience.de/em2em/)
Cheers
Filip Van Petegem
On Tue, Jul 13, 2010 at 5:32 AM, James Whittle
wrote:
> Hi all-
>
> I'm trying to convert a cryoEM map
was complexing bME or DTT
in your sample: Ni-bME forms a tight brown complex.
Filip Van Petegem
, so it's not necessary to search through all possible
> orientations. However, we do feel that it can be worthwhile to try a
> reasonably large number of orientations in difficult cases.
>
> Best regards,
>
> Randy Read
>
> P.S. When we generate our list of orientations, we use
27;m especially interested in
comments from people who have used both instruments before.
Cheers
Filip
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604
Thanks to all those who responded. Here is a summary of the
responses. Overall,
there are mixed feelings, but there is a clear bias towards Akta, with a
better service and durability – individual experiences with service might be
due to geographical distributions?
Filip
_
raded as
> efficiently as with Dnase I from Sigma.
>
> I am looking for ways to show that my preparation does not have any
> Dnase contamination. I would appreciate it very much if someone points
> me in the right direction.
> Thanks a lot
> Subbu
>
--
Filip Van Petegem
wever, the crystallization conditions themselves
(PEGs, non-neutral pH) are likely to affect the binding as well.
Cheers
Filip Van Petegem
On Mon, Jun 30, 2008 at 10:42 AM, Philippe DUMAS <[EMAIL PROTECTED]>
wrote:
> Hello
>
> We have had an interesting example where the crystal p
) for 100nM and
weaker binders, but not for 10nM and stronger binders. What you were saying
is the other way around (tight binders not binding).
Cheers
Filip Van Petegem
On Mon, Jun 30, 2008 at 2:22 PM, Jens T. Kaiser <[EMAIL PROTECTED]> wrote:
> Dear Filip and others,
> To pla
could be tested directly in an ITC
experiment - the effect of 10% PEG4000 would be harder to assess due to
insolubility (crystallizability) of the protein...
Cheers
Filip Van Petegem
On Mon, Jun 30, 2008 at 4:47 PM, John A. Newitt <[EMAIL PROTECTED]>
wrote:
> At 3:28 PM -0700 6/30/08,
A postdoctoral position is available for a highly motivated individual in
the laboratory of Filip Van Petegem, University of British Columbia (UBC),
Department of Biochemistry and Molecular Biology (http://www.biochem.ubc.ca ;
http://crg.ubc.ca/VanPetegem/).
The postdoctoral fellow will be
o put in time to do multiple HPLC runs, reagent, cost for Mass
> Spec verification... Does anyone have suggestion about which one will be
> more efficient? Thanks.
>
> Best,
> Chen
>
>
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Bio
kinetics of binding
and unbinding. SPR could answer if that's the case.
Other things to consider: temperature difference between ITC and pull-down?
Cheers
Filip Van Petegem
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Bi
protein or how I could analyze possible bound metals or
> > prosthetic groups using only a small amount of protein would be helpful.
> >
> > Matt
> >
>
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: [EMAIL PROTECTED]
http://crg.ubc.ca/VanPetegem/
t;
> Director, Biochemistry Graduate Program
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA 19102-1192 USA
>
>
> (215) 762-7706
>
> [EMAIL PROTECTED]
>
>
s you would do for
flash-cooling the crystal in paratone. And a major advantage: you can use
the same crystal to collect under cryo-conditions and directly compare the
impact of cooling the crystal...
Cheers
Filip Van Petegem
--
Filip Van Petegem, PhD
Assistant Professor
The University of Br
A postdoctoral position is available in the lab of Filip Van Petegem at the
University of British Columbia.
Our lab focusses on calcium channels in both the plasma membrane and
intracellular compartments. Calcium is an important 2nd messenger and
channels allowing influx of calcium into the
reaction was finished (the protein even
crystallized at pH 4).
This of course only has a small chance of working in your case, but it's
quick to test various different mini-deglycosylation experiments using an
array of conditions.
Cheers
Filip Van Petegem
On Mon, Mar 16, 2009 at 9:29 AM, Y
cells; if these
now do: you definitely have phages.
Cheers
Filip Van Petegem
On Thu, Jul 2, 2009 at 9:42 AM, Jacob Keller
wrote:
> Dear crystallographers,
>
> I recently expressed some new constructs, and found after my usual
> expression protocol that the cell pellets were not com
stribution. What you describe happens
a lot to us with proteins that don't precipitate and that crystallize
afterwards.
Cheers
Filip Van Petegem
On Thu, Jul 2, 2009 at 8:53 AM, peter hudson
wrote:
> Hello all
>
> I am working with a small protein-protein complex. This complex ex
don't know a
priori by how much the EM map would have to be inflated. I'm using the
SITUS package for docking - converting from ccp4 to situs, spider or any
other common map format all deliver maps with the wrong size.
Sincerely,
Filip Van Petegem
--
Filip Van Petegem, PhD
Assi
:
filip.vanpete...@gmail.com
--
Filip Van Petegem, PhD
Professor, Dept. of Biochemistry and Molecular Biology
The University of British Columbia
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/
ead and re-adjust everything.
best regards,
Filip Van Petegem
--
Filip Van Petegem, PhD
Professor, Dept. of Biochemistry and Molecular Biology
The University of British Columbia
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: filip.vanpete...@gma
freedom into account.
If anybody has any pointers to some reference text or paper that has
performed such an analysis, I would be very interested.
Regards,
Filip
--
Filip Van Petegem, PhD
Associate Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Healt
into separate pdb files for each rigid body. No need to do any
conversion. All you need is the pdb and the EM map downloaded from the
EMDB. All are very simple to run and the documentation is very good.
Regards,
Filip
--
Filip Van Petegem, PhD
Associate Professor
The University of British
ung
> Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches
> Ministerium für Wissenschaft und Kultur
> Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA
> Gesellschaft mit beschränkter Haftung (GmbH)
> Sitz der Gesellschaft: Braunschweig
> Handelsregister: Am
f the same condition should give the answer as
to which B-factor normalization is the most appropriate.
Filip Van Petegem
On Mon, Mar 4, 2013 at 11:16 AM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:
> You only entertain addition+subtraction--why not use
> multiplication/divis
of Prof. Harry Brumer and
Prof. Filip Van Petegem.
The successful applicant must have a Ph.D. in structural biology. Excellent
theoretical knowledge and practical skills in X-ray crystallography are
required. Experience with cryogenic electron microscopy is advantageous.
Likewise, familiarity
(UBC), under the co-supervision of Dr. David Fedida and Dr. Filip Van
Petegem.
The successful applicant must have a Ph.D. in structural biology. Excellent
theoretical knowledge and practical skills in either X-ray crystallography
or cryogenic electron microscopy are required. Likewise, familiarity
heart.
The position will be held within the Life Sciences Centre and Departments
of APT and Biochemistry and Molecular Biology at the University of British
Columbia (UBC), under the co-supervision of Dr. David Fedida and Dr. Filip
Van Petegem.
The successful applicant must have a Ph.D. in structural
Dear community,
a postdoctoral position is available in the lab of Filip Van Petegem at the
University of British Columbia. The project involves the structural and
functional investigation of ion channels using cryo-EM and X-ray
crystallography, supplemented with various functional assays. For a
Dear colleagues,
Two postdoctoral positions are available at The University of British
Columbia in Vancouver, Canada:
*Position 1:*
A postdoctoral position is available immediately to work on ion channel
structural biology in the lab of Filip Van Petegem, Department of
Biochemistry and
contact
details for 3 references to *filip.vanpete...@gmail.com
*.
--
Filip Van Petegem, PhD
Professor, Dept. of Biochemistry and Molecular Biology
The University of British Columbia
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
names and contact details for 3 references
to filip.vanpete...@gmail.com.
--
Filip Van Petegem, PhD
Professor, Dept. of Biochemistry and Molecular Biology
The University of British Columbia
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: filip.vanpete
*Postdoctoral opportunity in Protein Design and Structural Biology*
A postdoctoral position is available in the laboratory of Prof. Filip Van
Petegem at the University of British Columbia. The goal is to apply state
of the art computational protein design methods to create novel protein
nd
contact details for 3 references, and describe your motivation to join the
team. This is an excellent opportunity for structural biologists to learn
complementary methods, or for electrophysiologists to get exposed to
structural biology methods.
Filip Van Petegem
--
Filip Van Petegem, PhD
Dear community,
A joint postdoc position is available in the labs of Drs. David Fedida and
Filip Van Petegem at the University of British Columbia (UBC) in Vancouver,
Canada.
The project involves cryo-EM investigation of voltage-gated potassium
channel structure and pharmacology. The successful
> tool to swing a monomer or hexamer into the cryoEM density?
> Thank you, Gloria
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
--
Filip
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