Hi All,
Was there a convenient way to make a solvent mask for a region with a model -
its been a while - and use that to generate maps
(i have a domain that is only partially visible, could not be found be
molecular replacement), its there though.
Could be that its not well ordered, but I
Hi,
is the phased translation function in MolRep still working under CCP4 - doenst
seem to go forward with the old CCP4 GUI (i cant get any coordinated out phased
or not)
and the new one (CCP4i2) doesnt seem to have that option? (in other words i
cant get any solution written out as
Hi,
This seems very stupid but I have some data sets processed with XDS with
apparently close to 100% completeness (high symmetry F4132)
only 50 (or 100) degrees of data, fine, but still looks complete overall, given
the high symmetry, though low res could be better.
After running it via
).
Thanks for comments!
Tommi
On Oct 21, 2016, at 6:11 PM, Kajander, Tommi A
<tommi.kajan...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi>> wrote:
Hi,
This seems very stupid but I have some data sets processed with XDS with
apparently close to 100% completeness (high symmetry F4
Dear all,
Has anyone tested RAPPER recently - doenst seem to work with me from the ccp4i
7.0.015 with a map (from buster-TNT). (either ca-trace option - with partial
region defined or the "rebuild badly fitting residues"
- complains and generates nothing. Is there something obvious I might be
Any hints on what might work for modeliing a domain that seems to be there
visible in part and parly not?
(half ofan Ig-domain) - presumably the other end of the domain has larger
ensemble of coordinate
postions (attached from one end to other part of the same molecule and
neighbors in the
Something like Balbes for MR is worth a shot? I wouldnt bother manually with MR
anymore unless really clear. Or try Hg and Pt for Cys, His and Met. I would try
the Pt chlorides. All depends on pH etc...
Tommi
Alkuperäinen viesti
Lähettäjä: "Keller, Jacob"
to origin then 2) get the
transformation for dimer (coot + PISA seems to do fineŠ I thinkŠ wil check
what happens in refinementŠ)
Achesym just gave an error and didn't find any transformations for some
reason - this is in F4132.
No idea why it happened - will try to remember to report it.
T
.
Cheers,
Tommi
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul Emsley
<pems...@mrc-lmb.cam.ac.uk>
Sent: Thursday, December 14, 2017 3:25:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coordinate transformation
On 13/1
Hello,
If someone could point this out would be very helpful... Wasnt there a simple
script somewhere that would transfer coordinates close to origin - if they for
some reason are not? Just cant find anything right away. Sure i have done this
before...
Thanks,
Tommi
Lähetetty: keskiviikko 8. elokuuta klo 17.46
Aihe: Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions
Vastaanottaja: Kajander, Tommi A
Kopio: CCP4BB@JISCMAIL.AC.UK
How many molecules in the asymmetric unit? and is there a non-crystallographic
translaton?
Eleanor
On 8 August 2018
d XDS
might be conservative and not estimate the likelihood for the second
screw-axis.
MR, however, will pick up the space group with all data, and thus be
able to tell between P2212 and P22121 whether or not you recorded
reflections that are expected to be absent.
Best,
Tim
On 08/08/2018 04:29 P
Hi,
Any clues why the followting happens: pointless (and just looking at the XDS
output) clearly tells there is one screw axis in P-ortorhombic (P2212)
yet phaser gives the best Z-scores in P22121. (...I suspect this may be to do
with twinning - might be monoclinic twiined still though now
Hi, One way is to cover the drop with e.g. paraffin oil (to prevent
evaporation) and fish it out in the oil. Have had luck with that in some cases.
Tommi
On 14 Aug 2018, at 22:09, Bonsor, Daniel
mailto:dbon...@som.umaryland.edu>> wrote:
I have had some luck with adding ~5-10ul of 60%-70%
Yes sorry, i meant paratone-N also.
Tommi
Kohteesta: ferrer
Lähetetty: keskiviikko 15. elokuuta klo 0.41
Aihe: Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant
Vastaanottaja: ccp4bb@jiscmail.ac.uk
Dear Thomas,
Alternatively you can try shooting on crystals in the drop, in
Dear All,
I was wondering what would be the best software nowadays to try to process data
from crystal that clearly is split or
has a secondary set of lattice points (close, poor data) in the raw data - data
can be processed with XDS (2.9-2.8 Å) but Rmerge tends to be
bit high at low
mail : l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl>
phone : +31-30-2532865
fax: +31-30-2533940
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>]
on behalf of Kajander, Tommi A
[tommi.kajan...@
mail : l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl>
phone : +31-30-2532865
fax: +31-30-2533940
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>]
on behalf of Kajander, Tommi A
[tommi.kajan...@
Dear All,
I would like to draw your attention to the open group leader position at
Institute of Biotechnology, University of Helsinki, Finland:
https://www.helsinki.fi/en/open-positions/a-group-leader-institute-of-biotechnology-hilife
Structural biology one of the main fields - if you feel you
Dear All,
Bit off-topic if allowed: I would like to ask has anyone had problems or
successes updating the Rigaku Minstrel computers to Windows 10?
Would like to hear about experiences if anyone can provide insight.
Thank you very much,
Tommi
Tommi Kajander, PhD
Principal investigator
Hello,
We have a bit tricky case of coiled coil protein with good data (2.05Å) for
dimeric coiled coil (dimer in AU) - looks like AMPLE might be a way
to solve such cases, if you know other good programs please suggest (Better yet
if there is a clear how-to manual)
Some technical tips on
umentation in the next few months and we'll include an example of use
of this new coiled-coil mode at that time.
Best wishes
Dan
On 07/10/2019 22:33, Kajander, Tommi A wrote:
> Hello,
>
> We have a bit tricky case of coiled coil protein with good data (2.05Å) for
> dimeric coiled coil
Hi all, can I get views on imagers with with cross-polarizers and how well that
works with black-and-white imaging vs color?
Thank you,
Tommi
Tommi Kajander, Ph.D., PI
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014
Dear All,
I’d like to draw your attention to open post doctoral position in our
laboratory in Helsinki in biochemical and biophysical characterisation and
structural biology of novel endoplasmic reticulum stress regulator protein
complexes.
Position is for one year initially with possibility
Daer All,
FYI, we have a job opening in CryoEM for research technician in Helsinki.
Best,
Tommi
Tommi Kajander, Ph.D.
Head of Unit, Protein crystallisation
INSTRUCT-HiLIFE
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014 Helsinki, Finland
p. +358-50-4480991
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