and detailed contacts, please visit
www.biocenter.helsinki.fi/bi/recruit or contact bi‐direc...@helsinki.fi.
www.biocenter.helsinki.fi/bi
Tommi Kajander, Ph.D.
Team Leader
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014
FYI, on behalf of the search committee (see links below):
The Institute of Biotechnology is a leading European research institute within
the University of Helsinki with a mission to increase knowledge in
cross‐disciplinary biology and biotechnology. The Institute has state‐ofthe‐art
don't show
interpretable density in that region.
I would call everything else 'tabloid science'.
Cheers,
Tim
On 10/24/2014 04:11 PM, Michal Jamroz wrote:
Dnia 2014-10-22, o godz. 15:43:18
Tommi Kajander tommi.kajan...@helsinki.fi napisał(a):
Would anyone know a software to model
Hi All,
Would anyone know a software to model (just with some kind of random coil) the
amino acid chain for
the assumed flexible disorderd regions between domains, or at one end of
protein? just for illustrative purposes.
Thanks!
Tommi
Dear All,
Can someone sugegst what would be the best options for stereo viewing for macs
currently?
Any good experiences with Stereo-TVs? Other? I would like know the specific
combination (at least
which mac computer etc) if possible to find out something that works.
Thanks,
Tommi
Tommi
A postdoctoral position is available in the Biocenter Finland Crystallization
Core Facility, in the research group of
Dr. Tommi Kajander at the institute of Biotechnology at University of Helsinki,
Finland.
The position is funded for two years starting from September 2014.
The position
A postdoctoral position in structural biology is available from Sept 2014
earliest in the research group lead by
Tommi Kajander at Institute of Biotechnology, University of Helsinki, Finland.
The position is funded by the Academy of Finland at the Finnish university
salary scale 5
Dear all,
I would be interested in comments/opinions about what is your experience on
which
would be the best mammalian cell culture vector/cell line/medium combination
for transient
expression to get the best yields. Depends, of course, but anyway obviously
there are
differences, HEKs are
Ok. you filled my mailbox the second time today - please do stop sending junk
to the list.
-tommi
On Mar 23, 2013, at 3:59 PM, Wei Feng wrote:
Dear Steffi,
Thank you very much for you patient reply!
I have tried to use your script to convert the map format, but no
***omit_map.coeff can
/3ix2ln69wZz74LWwaPMdBhFQCfS9C6
nvrZMfMmeekAauJ26jy6jbE=
=nbV+
-END PGP SIGNATURE-
Tommi Kajander, Ph.D., Docent
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
http
Hi all,
Does anyone a program/paper that would give some quantitative estimate for
protein solubility based on surface property analysis?
(excluding obvious things such as integral membrane / TM regions)
Best
Tommi
://scratch.proteomics.ics.uci.edu/
Or
http://mips.helmholtz-muenchen.de/proso/proso.seam
http://www.biotech.ou.edu/
Thanks,
Debanu
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tommi
Kajander
Sent: Friday, October 12, 2012 10:23 AM
well, actually i recommend having a look at the old but good scalepack manual
for why Rmerge is inferior..
(i thought this was clear long ago.. so i am bit amazed that this discussio is
still alive and kicking..)
question of where to cut, is a different one and thats where the recent papers
if you have peek surface or titanium parts (if i recall right) there are no
problems with salt solutions.
tommi
On May 30, 2012, at 3:39 AM, aaleshin wrote:
Back in Iowa State University we used Waters HPLC for protein purification
during many years without noticeable damage to the
, but i havent done a systemic test.
(which now seems like a good idea.. as the samples are _quite
precious_ and i certainly want to keep a track of them all the way through)
--Observations?
(and yes we do 2 ul samples with nanodrop.)
Thanks in advance,
Best,
T.
Tommi Kajander, Ph.D
if you use oil do direct dry Paratone-N, with paraffin oil is not as good.
Li-salts should
work also - i would almos imgaine you can freeze directly from so high
(NH4)2SO4 conc.
but perhaps not. little bit (10%) glycerol probably does it also..
Tommi
On Feb 6, 2012, at 12:55 AM, Vineet Gaur
.)
--would like to be able to correct this.
Thanks for comments.
Cheers,
Tommi
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
would need to get the averaging
to work first... )
Tommi Kajander, Ph.D., Docent
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
On Dec 21, 2011, at 12:56 PM
...)
favorite programs for NCS averiging?? DM obviously, and solomon doesnt do it.
Others that do it
(with out a PDB or atoms to derive it from, but rather operators)
Thanks,
Tommi
Tommi Kajander, Ph.D., Docent
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Training Program
email: j-kell...@northwestern.edu
***
Tommi Kajander, Ph.D., Docent
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan
Hi, anybody have a script to to find a translation for 2-fold NCS (rotaion)
axis based on the center of NCS symmetry..?? (ie to the midpoint of line
between to heavy atoms)
This search option doenst seem to be endoed anywhere (why??) ...stupid me...
Thanks,
tommi
Hi, if you change crystal infro (SG P2 -- P21) and column labels at the same
time F col label (like FP) cant be changed to anything else
at the same time for whatever reason... at least i had this prob. ccp4 vs 6.2
tommi
broadening when using these small
columns with a regular fplc (rather than Akta's microFPLC)?
I would greatly appreciate your comments! Many thanks...
Bests,
Alex
.
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O
with SYBR Safe?
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
Tommi Kajander, Ph.D.
Junior Group Leader
Structural
-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
:36:59PM +0300, tommi kajander wrote:
Dear all,
Does anyone have suggestions for 6 Å resolution phasing with large
number (40-50) Se sites (SAD so far)??
Thanks a bunch,
Tommi
Tommi Kajander, Ph.D., Docent
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
I would add that there are some issues with air, you have to be careful with
nanodrop that the path is ok, and also if concentrations are low, 1 mg/ml for
instance, i am not sure one can trust it - compare 50 ul 1 cm path results with
nano at 0.5-1 mg/ml... i get inconsistency there.. its good
Dear all,
Does anyone have suggestions for 6 Å resolution phasing with large
number (40-50) Se sites (SAD so far)??
Thanks a bunch,
Tommi
Tommi Kajander, Ph.D., Docent
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O
of the thread.
Best regards
Savvas et al.
Savvas Savvides
Unit for Structural Biology @ L-ProBE
Ghent University
K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
Tel/SMS/texting +32 (0)472 928 519
Skype: savvas.savvides_skype
http://www.LProBE.ugent.be/xray.html
Tommi Kajander, Ph.D.
Structural
...@northwestern.edumailto:j-kell...@northwestern.edu
***
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p
The Netherlands
Tel. +31-30-253-2383
--
Xiaoguang Xue, PhD student
Utrecht University
Crystal Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
be happy to hear if anyone had similar problems
Thanks!
tommi
Tommi Kajander, Ph.D., Docent
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014
,
Tommi Kajander, Ph.D., Docent
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax +358-9-191 59940
I think the likely reason here are the points where you did the
mutations having adverse effects
- how do the mutants behave without labeling? this would be of course
an important control...
-Tommi
On 25.1.2011, at 12.52, Paula Salgado wrote:
Dear Abhilash
You could try an alternative
will be appreciated!!
Best wishes,
Xiaopeng Hu
Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Hello all,
Would anyone happen to have a met auxotroph S. cerevisaea strain at
hand that you
could send some of to us for testing Semet labelling?
Thanks very much!
Regards,
Tommi
Tommi Kajander, Ph.D.,
Macromolecular X-ray Crystallography
Research Program in Structural Biology
overall of the different manufacturers equipments
accuracy, etc...
e.g. viscometer seems rather unnessary to me, as does online DLs..
Thanks for comments,
Tommi
--
Tommi Kajander, Ph.D., Docent
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute
and filters. So it all pays off only
of you need large scale cultures long-term.
If you are aware of a dry serum-free insect cells medium, please
let me know - I'd love to try it.
Dima
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
be as a toolbox of Matlab software.
Thank you in advance,
Azadeh
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN
Would the exact analysis of how each of these things were wrong and
fabricated be somewhere
available Would be fair (apart from the known case of C3b) to have
the whole analysis available
instead of just this kind of news feed. I suspect its not obvious by
five minute check in all cases.
very much for comments,
Tommi
Tommi Kajander, Ph.D., Docent
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Apologies, i know this is not phenix bb but since i am here (and not
subscr. there), does anyone
know how to control rigid body ref positions in phenix.refine, i am
trying to do very low res check
(6 Å) with quite many molecules, and they start landing on each other
while the MR solution
for the rigid body refinement
because at 6A you only have so many reflections)
Best
Jacques
Le Nov 26, 2009 à 8:32 PM, Tommi Kajander a écrit :
Apologies, i know this is not phenix bb but since i am here (and
not subscr. there), does anyone
know how to control rigid body ref positions
Hi, the latest arpwarp via ccp4 6.1.2 GUI on Mac OS X 10.5 something
does
not work, it wants a sequence file which isnt an option in the GUI...
(you put in the coordinates and update them thats all right?) i just
want to improve
the maps if possible. also the model if possible.. flex-warp
Dear all
I was wondering if anyone knows a simple way to generate a missing
loop (strech of amino acids)
really in just some simple manner (no fancy minization necessary, of
course some constraints probably dont
hurt), just for visualization purposes of further simulations etc
thanks!
cannot find how to fix this.
It have also one more warning message - * Missing value set to NaN
in input
mtz file
but as I read it is not a problem - mtz is still readable.
I would be glad for any help or advice.
Thanks.
Sergii
P.S. Please, find attached mtz and logs.
Tommi Kajander
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax +358-9-191 59940
Hi,
I have been using a dimer as a search model in MOLREP (there will be
several in AU),
for some reason the program tends to break the dimer into monomers
wihtout asking me..
how is this determined in the program... a more detailed manual would
be nice, also on the output
as the different
a bit easier.
Tim
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax +358-9-191 59940
is simply combining lines which start with same set of
characters (ID) but removing the IDs
codes from everyelse but the beginning. i am not much of a script
writer obivously
Thanks a bunch!
Tommi
Tommi Kajander
Structural Biology and Biophysics
Institute of Biotechnology
University
..
tommi
On Sep 13, 2009, at 3:52 PM, Tommi Kajander wrote:
Hi,
off-crystal topic: i was wondering if anyone has a simple solution to
combining e.g. CLUSTAL etc ouput files to format (ie idcodes then 60
residues strech and start again below the same...) ...that has only
one line per sequence
with decent data.
BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tommi
Kajander
Sent: Friday, March 20, 2009 3:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problems with phasing a protein (1300aa)
this cant be true,
in the idea case
(Space group I222
or
I212121). But we are having tough time phasing it.
...
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
For this discussion another relevant reference might be:
The 1.8 A crystal structure of a statically disordered 17 base-pair
RNA duplex: principles of RNA crystal packing and its effect on
nucleic acid structure.
Shah SA, Brunger AT.
J Mol Biol. 1999 Jan 29;285(4):1577-88.
-tommi
On Jan
, where the protein is a monomer in
solution (as evident from light scattering, MW determination through
centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer?
Bernie Santarsiero
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural
with secondary structure assigned from DSSP.
Thanks!
Charu
Mayer lab/NIH
--
MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: [EMAIL PROTECTED]
Phone: + 44 208 816 2515
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
enough for demonstration
purposes, so we need more)
Thanks very much!
best,
Tommi
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
[EMAIL PROTECTED]
Also, i think that would be nice if this type of info could be put on
the web, part of the wiki for instance..
if there is some consensus to what works + the typical proteins easily
available.
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University
Answer:
8) Is there any software you would like to have available in the
computing environment to assist you in molecular model building
and/or
visualization that is not currently available?
Answer:
Thank you for your time.
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
system
for more efficient recombinant protein production in insect cells.
Protein Expr Purif. 2005 Jul;42(1):211-8
or if i can reach one of the authors is reachable this way and willing
to send some material i would be greatful.
thank you,
tommi
--
Tommi Kajander, Ph.D.
Macromolecular X-ray
://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
RNA is really nifty
DNA is over fifty
We have put them
both in one book
Please do take a
really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp
--
Tommi Kajander
,
--
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]
Tommi Kajander wrote:
couldnt agree more.. just
Ammonium Sulfate.
Thank you so much.
Ji
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
plunging.
The best way to freeze things is to put a small container of liquid
ethane
or propane into a liquid N2 bowl, and plunge into the ethane/propane
(this
methods was suggested earlier).
Petr
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program
___
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax
:
3163 Life Sciences Institute,
University of Michigan,
210 Washtenaw Avenue
Ann Arbor, MI, 48109-2216
Phone: 734-615-2078
==
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute
lt.Numerous xtals appears and but small is size.Do anyone can share
their
experience with Isopropanol as a precipitant and to improve the xtal
quality
with other precipitants.All suggestions are welcome.
Thanx in advance.
Shivesh
--
Tommi Kajander, Ph.D.
Macromolecular X-ray
for me? Thanks very much, -J.J.
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9
difference (getting xprep will cost some money so i would like to know
where the difference lies if there is any significant difference??)
Thanks for advice,
Tommi
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute
state of the
protein --suppose some neutron scattering studies on model systems might
give the answer --havent looked. just wondering..
-tommi
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
PO box 65
europe most relevant)
thanks very much,
tommi
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
PO box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel
Quoting Anastassis Perrakis [EMAIL PROTECTED]:
On Aug 9, 2007, at 15:02, Tommi Kajander wrote:
so, a) WHAT IS GAMMA??
gamma is possibly the letter of the greek alphabet that has had most
abuse from scientists.
thats what i thought...
http://en.wikipedia.org/wiki/Gamma_
success to go beyond it by any
meanstweaking parameters in arpwarp now suggestions??)
many thanks...,
tommi
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
PO box 65 (Street address
opinions though...)
cheers,
tommi
Quoting Anastassis Perrakis [EMAIL PROTECTED]:
On Jul 31, 2007, at 15:24, Tommi Kajander wrote:
Hi,
i would be interested in hearing about people's preferences on
programs
for doign auto-tracing of protein chains (with not so great maps),
I do like
Quoting Priyank Maindola [EMAIL PROTECTED]:
Hello all,
I am struggling with getting the phases out for my protein. Heavyatom
database shows that only mercury and samarium have the binding motifs in
it.
Sodium iodide soak is killing the crystal even as less as 0.2 Molar
concentration for
Get a FREE Web site, company branded e-mail and more from Microsoft
Office Live!
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
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