[ccp4bb] Fwd: Position open in the HILIFE Instruct-FI cryoEM unit for a research technician - please distribute

[Kajander, Tommi A]

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
http://www.helsinki.fi/kajanderlab



From: "Butcher, Sarah" 
mailto:sarah.butc...@helsinki.fi>>
Subject: Position open in the HILIFE Instruct-FI cryoEM unit for a research 
technician - please distribute
Date: 16. June 2023 at 10.58.16 EEST
To: "Lak, Behnam" mailto:behnam@helsinki.fi>>, John 
Dolan mailto:j...@instruct-eric.org>>, 
"finstruct...@helsinki.fi" 
mailto:finstruct...@helsinki.fi>>, 
"tuesday-biophys...@helsinki.fi" 
mailto:tuesday-biophys...@helsinki.fi>>, 
"cryo...@scilifelab.se" 
mailto:cryo...@scilifelab.se>>, 
"michael.elb...@weizmann.ac.il" 
mailto:michael.elb...@weizmann.ac.il>>, 
"sharon.w...@weizmann.ac.il" 
mailto:sharon.w...@weizmann.ac.il>>, Celia Romao 
mailto:cmro...@itqb.unl.pt>>

Dear all,
we have an opening for a laboratory technician in the HILIFE Instruct-FI cryoEM 
unit, University of Helsinki, Finland. Deadline for applications 27.6.23. 
Please advertise further.
 
https://jobs.helsinki.fi/job/Laboratory-technician%2C-cryogenic-electron-microscopy-service/773176102/?feedId=350602_source=CareerSite_UniversityOfHelsinki

 Best regards

Sarah
_
Prof. Sarah Butcher, Ph.D.
Molecular & Integrative Biosciences Research Programme
Faculty of Biological and Environmental Sciences
&
Helsinki Life Science Institute-Institute of Biotechnology
room 2405
P.O. Box 56 (Viikinkaari 9)
FIN-00014 University of Helsinki
Finland
office: +358 2941 59563
cell: +358 50 4155492

https://researchportal.helsinki.fi/en/persons/sarah-butcher
https://blogs.helsinki.fi/butcher/
https://www.helsinki.fi/en/infrastructures/integrated-structural-cell-biology/cryoem
https://www.vibrant-itn.eu/
https://www.itqb.unl.pt/impact







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[ccp4bb] Post doctoral position in structural biology of ER protein complexes

[Kajander, Tommi A]

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 to continuation, if you or 
your colleagues know someone (or are someone) with right skill set might be 
interested please apply/ let them know / feel free to circulate.

Know-how in protein expression and purification/characterisation and preferably 
some experience structural biology is required,
but it will also be an opportunity to learn and utilise multiple techniques in 
biochemical and biophysical characterisation.

We have a very friendly vibrant and interactive scientific community in the 
research program and on campus overall.

The advertisement is available here (applications only via the web site):

https://www2.helsinki.fi/en/open-positions/postdoctoral-researcher-in-structural-biology


Best regards,

Tommi



Tommi Kajander, Ph.D. Adj. Prof.
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014 Helsinki, Finland
p. +358-2-941-58904
http://www.helsinki.fi/kajanderlab








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[ccp4bb] experiences with cross-polarisers / black-white imaging vs color

[Kajander, Tommi A]

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 Helsinki, Finland
p. +358-2-941-58904 / +358-050-4480991
tommi.kajan...@helsinki.fi
http://www.biocenter.helsinki.fi/bi/kajander/






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Re: [ccp4bb] coiled coil molecular replacement

[Kajander, Tommi A]

Hi all,
Just to conclude on this - ARCIMBOLDO via CCP4 in coiled coil mode worked quite 
nicely in the end now that I finally had time to work through it - took a few 
days with 8 x 20 aa peptides as the search set
on my old iMac but the end result was fine :). So didn't have to try other 
options really in the end. The pipe line worked quite nicely given there are 
400 residues in the asymmetric unit.

Thanks for everyone for the suggestions and advice!

Best,
Tommi


On Oct 8, 2019, at 12:00 PM, IRACEMA CABALLERO MUÑOZ 
mailto:icm...@ibmb.csic.es>> wrote:

Hi Tommi, as sent by Kay ARCIMBOLDO has a specific mode to solve coiled coils 
(http://scripts.iucr.org/cgi-bin/paper?cb5097).

Here you can find the tutorial: http://chango.ibmb.csic.es/tutorial_coiled, it 
explains how to launch it through the command line and a summary explaining the 
improvements of the mode.

It can also be launched through CCP4i, here you only need to activate "run 
coiled-coil mode" and put the search strategy (number of helices and helix 
length). In this supplementary table, you have examples of the search strategy 
for 150 cases  https://doi.org//10.1107/S2059798317017582/cb5097sup2.xlsx

[coiled_coil_mode_ccp4i.png]

And please if you have any questions just let me know.

Best wishes,
Iracema

El mar., 8 oct. 2019 a las 9:33, Daniel Rigden 
(mailto:drig...@liverpool.ac.uk>>) escribió:
Hi Tommi

Yes, AMPLE does well with coiled-coils. The QUARK route is the easiest
to try. In your position I would simply trim a bit of sequence off
either end. Maybe you can see homologs that are a bit shorter at one
terminus? In any case, that's unlikely to affect the modelling and we've
seen QUARK make good models of coiled-coil proteins.

For Rosetta modelling we simply recommend you use the Robetta server
http://robetta.bakerlab.org/fragmentsubmit.jsp for fragment libraries.
Unless you're processing large numbers of sequences it's not worth
getting to grips with local fragment library generation. At the moment
CCP4online takes a file of ready-made models, not carrying out the
actual modelling for you. Doing local Rosetta modelling via AMPLE is as
described here
https://ample.readthedocs.io/en/latest/examples/rst/abinitio.html#example-abinitio

Recently, in collaboration with Owen Davies in Newcastle, we've made
some big improvements to AMPLE's abilities with coiled-coils, involving
more bespoke modelling protocols, both of a single chain and, where the
information is known, of a parallel oligomer. I gather Owen has been in
touch with you about these. The code is available but is not in the
current CCP4 distribution. We're also planning to improve the AMPLE
documentation 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 (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 usage for generation of fragments for AMPLE would be 
> of help, not completely on top of that… (running the QUARK server, the real 
> sequence is bit over 200 aa so not sure what is the best approach here? 
> Rosetta? any how-to for that.. well i am running Robetta fragments too).
>
> with AMPLE can I do this with the online server or better run locally (need 
> Rosetta installed I take it?)
>
> Suppose I could try Rosetta-MR also, but to my recollection that requires 
> some kind of a phaser hit first to be improved, and i dont think I am there.
>
> Thanks for any comments,
>
> Best,
> Tommi
>
>
>
>
> 
>
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--
Prof Daniel Rigden
Institute of Integrative Biology
Room 101, Biosciences Building
University of Liverpool
Crown St., Liverpool, L69 7ZB

(+44) 151 795 4467
pcwww.liverpool.ac.uk/~drigden/<http://pcwww.liverpool.ac.uk/~drigden/>



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Tommi Kajander, PhD
Principal investigator
Structural Biology and Biophysics
Institute of Biotechnology
Biocenter 3, Viikinkaari 1 (PO Box 65)
University of Helsinki
tommi.kajan...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi>
+358 294158904








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[ccp4bb] Rigaku Minstrel and Windows10

[Kajander, Tommi A]

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
Structural Biology Program
Institute of Biotechnology
Biocenter 3, Viikinkaari 1 (PO Box 65)
University of Helsinki
tommi.kajan...@helsinki.fi
+358 294158904







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[ccp4bb] coiled coil molecular replacement

[Kajander, Tommi A]

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 usage for generation of fragments for AMPLE would be of 
help, not completely on top of that… (running the QUARK server, the real 
sequence is bit over 200 aa so not sure what is the best approach here? 
Rosetta? any how-to for that.. well i am running Robetta fragments too). 

with AMPLE can I do this with the online server or better run locally (need 
Rosetta installed I take it?)

Suppose I could try Rosetta-MR also, but to my recollection that requires some 
kind of a phaser hit first to be improved, and i dont think I am there.

Thanks for any comments,

Best,
Tommi 






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[ccp4bb] Group Leader position - Institute of Biotechnology, University of Helsinki

[Kajander, Tommi A]

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 are a good 
candidate please do apply - in particularly internationally high level 
macromolecular
crystallography applications needed,  while the call is open to all fields of 
research in biosciences as specified in the call text. Selection is solely 
based on excellence.
Early career stage researchers are especially encouraged to apply, but please 
read the advertisement.

Salary is competitive and Institute of Biotechnology was ranked as one the 
flagships of research at UH in the recent evaluations.

From the advertisement text:

We offer an international, inspiring, and supportive research environment, 
along with excellent research facilities including in-house state-of-the art 
technologies in imaging, genomics, proteomics, CryoEM, crystallography, and 
NMR. The successful candidate will also enjoy access to all HiLIFE 
infrastructure platforms 
(https://www.helsinki.fi/en/helsinki-institute-of-life-science/hilife-res...).
 The salary is based on the salary system of the Finnish universities for 
teaching and research personnel, depending on the appointees’ qualifications, 
career stage and experience. The position also comes with an attractive 
negotiable 3-5 year startup package.

The University of Helsinki offers comprehensive services to its employees, 
including occupational health care, health insurance, sports facilities, and 
opportunities for professional development.

Finland is a member of the EU, has high quality free schooling (also in 
English), generous family benefits, and excellent healthcare.

Finland was recently ranked as the best country in the world for expat families 
and Helsinki in the world’s top ten most livable cities.

For more information about working at the University of Helsinki and living in 
Finland, please see 
https://www.helsinki.fi/en/university/working-at-the-university.


Best regards,
Tommi


Tommi Kajander, PhD
Principal investigator
Structural Biology Program
Institute of Biotechnology
Biocenter 3, Viikinkaari 1 (PO Box 65)
University of Helsinki
tommi.kajan...@helsinki.fi
+358 294158904







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Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

[Kajander, Tommi A]

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 situ. So 
fishing, no cryo. But potentially high radiation damage. Can be considered if 
you have enough crystals, and if your crystallization plate makes it possible.

Regards

JL

On 14/08/2018 20:58, Thomas Krey wrote:
Dear crystallization experts,

We have 3D protein crystals grown from a microseed matrix screening vapor 
diffusion experiment in either

15% (v/v) Reagent alcohol
HEPES Na pH 7.5
0.2 M MgCl2

or in

27% Isopropanol
0.18 M MgCl2
90 mM HEPES Na pH 7.5
10% Glycerol

Upon opening the corresponding wells these crystals move quite a bit – 
presumably due to the volatility of the alcohols. Does anyone have a good 
suggestion to stabilize the swirling movements? Does anyone have experience, 
whether these conditions alone can serve as cryo-protectant (i.e., do we really 
have to fish, move into cryo solution and fish again)?
Any suggestion or input would be highly welcome.

Thank you very much in advance.

Thomas


Prof. Dr. Thomas Krey
Hannover Medical School
Institute of Virology
Structural Virology Group
Carl-Neuberg-Str. 1
D-30625 Hannover
phone: +49 (0) 511 - 532 4308
email: krey.tho...@mh-hannover.de


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--  Jean-Luc Ferrer Institut de Biologie 
Structurale 71 Avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 - FRANCE Ph.: 
+33 (0)4 57 42 85 22 Cell: +33 (0)6 89 45 13 57 email: 
jean-luc.fer...@ibs.fr 

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Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

[Kajander, Tommi A]

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% dilution of the reservoir 
to the drop. The larger volume of the drop appears to slow down the whizzing of 
the crystals and allows you to get a few crystals. Though it still occurs. You 
could also cool the area down or move into the cold room if your crystals 
survive the transfer as evaporation should be less at 4oC.

You can also spot several 1-2uL of neat reservoir solution around the drop to 
create a local vapor barrier to prevent evaporation of the drop. It can 
completely stop the movement of crystals for a few minutes.

Dan

Daniel A Bonsor PhD.
Sundberg Lab
Institute of Human Virology
University of Maryland, Baltimore
725 W Lombard Street N370
Baltimore
Maryland
MD 21201
Tel: (410) 706-7457


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas 
Krey
Sent: Tuesday, August 14, 2018 2:59 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fishing crystals from volatile solvent as precipitant

CAUTION: This message originated from a non UMB, UMSOM, FPI, or UMMS email 
system. Whether the sender is known or not known, hover over any links before 
clicking and use caution opening attachments.

Dear crystallization experts,

We have 3D protein crystals grown from a microseed matrix screening vapor 
diffusion experiment in either

15% (v/v) Reagent alcohol
HEPES Na pH 7.5
0.2 M MgCl2

or in

27% Isopropanol
0.18 M MgCl2
90 mM HEPES Na pH 7.5
10% Glycerol

Upon opening the corresponding wells these crystals move quite a bit – 
presumably due to the volatility of the alcohols. Does anyone have a good 
suggestion to stabilize the swirling movements? Does anyone have experience, 
whether these conditions alone can serve as cryo-protectant (i.e., do we really 
have to fish, move into cryo solution and fish again)?
Any suggestion or input would be highly welcome.

Thank you very much in advance.

Thomas


Prof. Dr. Thomas Krey
Hannover Medical School
Institute of Virology
Structural Virology Group
Carl-Neuberg-Str. 1
D-30625 Hannover
phone: +49 (0) 511 - 532 4308
email: krey.tho...@mh-hannover.de




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Tommi Kajander, Ph.D., PI
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014 Helsinki, Finland
p. +358-2-941-58904 / +358-050-4480991
tommi.kajan...@helsinki.fi
http://www.biocenter.helsinki.fi/bi/kajander/






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Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

[Kajander, Tommi A]

Hi Tim - There are reflections in all directions and only one clearly has 
systematic absenses. Although only few seem to be present in one direction (But 
thats the h00 direction here
+ all are present though) -phaser finds with same data P22121 as the strongest 
solution (few reflections are weak in that direction from below… but most not). 
 TZ-score diffrence is not
hure 13 vs 15.

P 2 2 21
  (   0,0,5): i/sigi =   20.8
  (   0,0,7): i/sigi =   19.6
  (   0,0,9): i/sigi =   21.0
  (   0,0,   11): i/sigi =1.9
  (   0,0,   13): i/sigi =   21.0
  (   0,0,   15): i/sigi =6.0
  (   0,0,   17): i/sigi =   20.8
  (   0,0,   19): i/sigi =0.9
  (   0,0,   21): i/sigi =9.0
  (   0,0,   23): i/sigi =1.0
  (   0,0,   25): i/sigi =4.9
  (   0,0,   27): i/sigi =   19.9
  (   0,0,   29): i/sigi =   20.9
  (   0,0,   31): i/sigi =   20.2
  (   0,0,   33): i/sigi =   19.1
  (   0,0,   35): i/sigi =   18.2
  (   0,0,   37): i/sigi =   13.1
  (   0,0,   39): i/sigi =   20.8
  (   0,0,   41): i/sigi =8.9
  (   0,0,   43): i/sigi =   12.7
  (   0,0,   45): i/sigi =2.5
  (   0,0,   47): i/sigi =0.8
P 21 2 2
  (   3,0,0): i/sigi =   31.2
  (   5,0,0): i/sigi =   25.2
  (   7,0,0): i/sigi =   21.0
  (   9,0,0): i/sigi =2.6
P 2 21 2
  (   0,5,0): i/sigi =0.7
  (   0,7,0): i/sigi =0.7
  (   0,9,0): i/sigi =0.7
  (   0,   11,0): i/sigi =1.1
  (   0,   13,0): i/sigi =1.0
  (   0,   15,0): i/sigi =1.5
  (   0,   17,0): i/sigi =0.7
  (   0,   19,0): i/sigi =0.7
  (   0,   21,0): i/sigi =0.7
  (   0,   23,0): i/sigi =0.8
  (   0,   25,0): i/sigi =0.7
  (   0,   29,0): i/sigi =0.7
  (   0,   31,0): i/sigi =0.8
  (   0,   33,0): i/sigi =0.7
  (   0,   35,0): i/sigi =0.7
  (   0,   37,0): i/sigi =0.9
  (   0,   39,0): i/sigi =0.7
  (   0,   41,0): i/sigi =0.7
  (   0,   43,0): i/sigi =0.7


Neither seem to refine now so have to work on it a bit more beyond this  - we 
see the same “conflict" with two different crystals - seems complicated - the 
other one processed much
better in P21  and seemed possibly twinned. Maybe the case here too.

Tommi





On Aug 9, 2018, at 10:29 AM, Tim Gruene 
mailto:tim.gru...@psi.ch>> wrote:

Dear Tommi,

did you check whether you collected any reflections at all that should
be absent for the second screw axis? If there are non - which could
easily happen with low resolution, incomplete data - pointless and 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 PM, Kajander, Tommi A wrote:
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 processes very 
well in P222.)

If i run the mtz after XDSCONV (ie F2MTZ) via pointless (instead of directly 
after XDS) it also suggests this - but i suppose i am not suppose to run merged 
data via pointless.

Thanks for comments,

Tommi



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--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OSUA/204
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


Tommi Kajander, PhD
Senior Scientist
Structural Biology Program
Institute of Biotechnology
Biocenter 3, Viikinkaari 1 (PO Box 65)
University of Helsinki







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Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

[Kajander, Tommi A]

Dear Eleanor, no tNCS is present here..(2 mols). I think its probably the 
somewhat incomplete low resolution (90% ish) that causes problems somewhere... 
which again follows from bit poir crystal quality in some directions - overall 
data is not great...

Best,
Tommi


Kohteesta: Eleanor Dodson
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 at 15:29, Kajander, Tommi A 
mailto:tommi.kajan...@helsinki.fi>> wrote:
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 processes very 
well in P222.)

If i run the mtz after XDSCONV (ie F2MTZ) via pointless (instead of directly 
after XDS) it also suggests this - but i suppose i am not suppose to run merged 
data via pointless.

Thanks for comments,

Tommi



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[ccp4bb] screw axes /system. absenses and phaser/MR solutions

[Kajander, Tommi A]

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 processes very 
well in P222.)

If i run the mtz after XDSCONV (ie F2MTZ) via pointless (instead of directly 
after XDS) it also suggests this - but i suppose i am not suppose to run merged 
data via pointless.

Thanks for comments,

Tommi 



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Re: [ccp4bb] data processing with split/bad crystals

[Kajander, Tommi A]

Thank you for the replies on this- i will report if we find a particular 
software to work better!

Best,
Tommi


On 17 Jul 2018, at 21:53, Murpholino Peligro 
mailto:murpholi...@gmail.com>> wrote:

Link provided not working. Need the http prefix, like this 
http://www.crystal.chem.uu.nl/distr/eval/

El mar., 17 de jul. de 2018 a la(s) 11:24, Kroon-Batenburg, L.M.J. (Louise) 
(l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl>) escribió:
Dear Tommi,
You may want to try EVAL: www. 
cryst.chem.uu.nl/distr/eval<http://cryst.chem.uu.nl/distr/eval>
EVAL can deconvolute reflections from multiple lattices.

Best wishes
Loes

___

Dr. Loes Kroon-Batenburg

Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands

E-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...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi>]
Sent: Monday, July 16, 2018 10:55 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] data processing with split/bad crystals

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 resolution (close to 7-8% depending on processing) - using 
XSCALE helps with the radiation damage correction some what.

Data looks like primitive orthorombic but not quite sure (also seems like it 
has one screw axis e.g. P2212 - but oddly phaser finds
solutions in P22121 also or even preferably…..). I am wondering a bit if it 
isn’t actually monoclinic.

Based on automated processing by Diamond pipeline XDS seems most robust - but 
any hints on such cases would
be welcome. Of course we will try to get better crystal but so far no luck.

Thanks for comments,

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





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Tommi Kajander, Ph.D., PI
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014 Helsinki, Finland
p. +358-2-941-58904 / +358-050-4480991
tommi.kajan...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi>
http://www.biocenter.helsinki.fi/bi/kajander/






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Re: [ccp4bb] data processing with split/bad crystals

[Kajander, Tommi A]

Thank you for the replies on this- i will report if we find a particular 
software to work better!

Best,
Tommi


On 17 Jul 2018, at 21:53, Murpholino Peligro 
mailto:murpholi...@gmail.com>> wrote:

Link provided not working. Need the http prefix, like this 
http://www.crystal.chem.uu.nl/distr/eval/

El mar., 17 de jul. de 2018 a la(s) 11:24, Kroon-Batenburg, L.M.J. (Louise) 
(l.m.j.kroon-batenb...@uu.nl<mailto:l.m.j.kroon-batenb...@uu.nl>) escribió:
Dear Tommi,
You may want to try EVAL: www. 
cryst.chem.uu.nl/distr/eval<http://cryst.chem.uu.nl/distr/eval>
EVAL can deconvolute reflections from multiple lattices.

Best wishes
Loes

___

Dr. Loes Kroon-Batenburg

Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands

E-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...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi>]
Sent: Monday, July 16, 2018 10:55 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] data processing with split/bad crystals

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 resolution (close to 7-8% depending on processing) - using 
XSCALE helps with the radiation damage correction some what.

Data looks like primitive orthorombic but not quite sure (also seems like it 
has one screw axis e.g. P2212 - but oddly phaser finds
solutions in P22121 also or even preferably…..). I am wondering a bit if it 
isn’t actually monoclinic.

Based on automated processing by Diamond pipeline XDS seems most robust - but 
any hints on such cases would
be welcome. Of course we will try to get better crystal but so far no luck.

Thanks for comments,

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





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Tommi Kajander, Ph.D., PI
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014 Helsinki, Finland
p. +358-2-941-58904 / +358-050-4480991
tommi.kajan...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi>
http://www.biocenter.helsinki.fi/bi/kajander/






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[ccp4bb] data processing with split/bad crystals

[Kajander, Tommi A]

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 resolution (close to 7-8% depending on processing) - using 
XSCALE helps with the radiation damage correction some what. 

Data looks like primitive orthorombic but not quite sure (also seems like it 
has one screw axis e.g. P2212 - but oddly phaser finds 
solutions in P22121 also or even preferably…..). I am wondering a bit if it 
isn’t actually monoclinic. 

Based on automated processing by Diamond pipeline XDS seems most robust - but 
any hints on such cases would
be welcome. Of course we will try to get better crystal but so far no luck.

Thanks for comments,

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





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Re: [ccp4bb] coordinate transformation

[Kajander, Tommi A]

On 12/14/17 6:38 PM, "Edward A. Berry" <ber...@upstate.edu> wrote:

>On 12/14/2017 04:34 AM, Tim Gruene wrote:
>> Dear Tommi,
>>
>1.
>> if you only need to consider translations, and not other symmetry
>>operations,
>> you can use moleman2, convert coordinates to fractional ones and add or
>> substract the integer that brings the centre of mass closest to 0.
>>
>2.
>> In case you want to take the symmetry operations into account, you
>>would have
>> to check for each operator, which one brings the centre of mass closest
>>to 0.
>> This could most likely be scripted with moleman2.
>>
>3. If you also want to consider origin shifts (in spacegroups where
>alternate origins exist) the achesym site does that. (If you can't bring
>the molecule to the origin, bring the origin to the molecule)
>
>4. If you also want to pack multiple chains that may have been built in
>various locations into a compact multimer, the achesym site does that.
>
>But no, it's not a simple script.
>And I believe the achesym site works not so much to put the center of
>mass near the origin, but to put as many atoms as possible in first unit
>cell (0<x,y,z<1; fractional). Moving closer to the origin within the unit
>cell is then a secondary priority.

Actually the case in hand is a monomer in AU with biomol dimer generated
by xtal symmetry. So 1) want to move close 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.
 

Thanks for the insights again,
Tommi

>
>> Best,
>> Tim
>>
>> On Thursday, December 14, 2017 8:39:48 AM CET Kajander, Tommi A wrote:
>>> Dear Paul,
>>>
>>>
>>> Yes thank you. This was the best answer i think. Someone else already
>>>also
>>> suggested that also.  Coot is very handy indeed.
>>>
>>>
>>> (Would still be curious of knowing how to find the "closest to origin"
>>>copy
>>> otherwise - but this solves my problem)
>>>
>>>
>>> Thanks to all who responded.
>>>
>>>
>>> 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 13/12/2017 13:50, Kajander, Tommi A wrote:
>>>> 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.
>>> At the risk of not answering the question because it's not a simple
>>>script,
>>> my I recommend Coot?
>>>
>>> File -> Open -> yourcoords.cif
>>> Draw -> Cell & Symm -> Master Switch -> Yes
>>> Show Unit Cells -> Yes
>>> OK
>>> Drag the View to the Origin # it's marked with an "O"
>>> Middle-mouse click on an Symmetry-related Atom # that's close to the
>>>origin
>>> Extensions -> Modelling -> Symm Shift Reference Chain Here
>>
>> --
>> --
>> Paul Scherrer Institut
>> Tim Gruene
>> - persoenlich -
>> OFLC/104
>> CH-5232 Villigen PSI
>> phone: +41 (0)56 310 5297
>>
>> GPG Key ID = A46BEE1A
>>

Re: [ccp4bb] coordinate transformation

[Kajander, Tommi A]

Dear Paul,


Yes thank you. This was the best answer i think. Someone else already also 
suggested that also.  Coot is very handy indeed.


(Would still be curious of knowing how to find the "closest to origin" copy 
otherwise - but this solves my problem)


Thanks to all who responded.


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 13/12/2017 13:50, Kajander, Tommi A wrote:
> 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.
>

At the risk of not answering the question because it's not a simple script, my 
I recommend Coot?

File -> Open -> yourcoords.cif
Draw -> Cell & Symm -> Master Switch -> Yes
Show Unit Cells -> Yes
OK
Drag the View to the Origin # it's marked with an "O"
Middle-mouse click on an Symmetry-related Atom # that's close to the origin
Extensions -> Modelling -> Symm Shift Reference Chain Here

[ccp4bb] coordinate transformation

[Kajander, Tommi A]

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

[ccp4bb] VS: [ccp4bb] Se-Met and Se-Cys double labelling

[Kajander, Tommi A]

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" 
Päivämäärä: 21.06.2017 19.51 (GMT+02:00)
Saaja: CCP4BB@JISCMAIL.AC.UK
Aihe: Re: [ccp4bb] Se-Met and Se-Cys double labelling

Halide soaks anyone? Cs or NaI?

Jacob

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J 
van Raaij
Sent: Wednesday, June 21, 2017 12:08 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Se-Met and Se-Cys double labelling

If your data is good enough, your SeMets alone might well be enough.
Soaking native crystals in Hg compounds may also work, avoiding SeMet 
altogether. We have had a lot of success with methylmercury chloride binding to 
free Cys. You may have to experiment with different soaking times and protocols.
Finally, don't give up on MR too early, what matters is the structural 
similarity, not directly the sequence identity. We've had success once with 19% 
identity.
Native protein may be much easier to produce than the SeMet and SeMet/SeCys 
versions (and may differ a lot between proteins).

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
http://wwwuser.cnb.csic.es/~mjvanraaij

On 21 Jun 2017, at 17:46, Vito Calderone 
> wrote:

I am working on a protein having 360 residues. In its sequence there are 3
Met and 5 free Cys.
I will need MAD to solve the structure since based on the sequence the
closest homologue has 20% identity匢 suppose MR would be very unlikely to
work卻o I would like to express a selenium derivative to exploit MAD.
Looking in the literature 1 Se-Met every 120 residues seems not to comply
the threshold to get a good anomalous signal. For this reason I would like
to exploit both Met and Cys so I would have 8 seleniums per 360 residues.
Could somenone suggest a reference to a protocol to express the double
mutant protein in NON auxotrophic strains of E. coli which you have
experienced working efficiently?
Thanks

[ccp4bb] rapper

[Kajander, Tommi A]

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 
missing? the PDB is OK by other programs - i can’t quite see what would be 
problem with it, error looks like this:



ERROR [General Error]:
  in file 
/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/checkout/rapper_ccp4-1.0a/LOOP/analyze.cpp
 at line 529
  No models could be generated under the provided restraints.  This means that 
either (1) the restraints are too specific or there is something wrong with the 
input PDB file.
***


#CCP4I TERMINATION STATUS 0 " 
--- 
ERROR [General Error]:   in file 
/Users/buildbot/Buildslaves/ccp4-slave/release-7_0-mac10_6/build/devtools/checkout/rapper_ccp4-1.0a/LOOP/analyze.cpp
 at line 529   No models could be generated under the provided restraints.  
This means that either (1) the restraints are too specific or there is 
something wrong with the input PDB file."
#CCP4I TERMINATION TIME 03 Apr 2017  14:19:03
#CCP4I MESSAGE Task failed

Thanks,
Tommi

[ccp4bb] refinement / modeling of partly mobile domain

[Kajander, Tommi A]

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 crystal - and not at the other end,
causing maybe kind of swinging of it/positional disorder) - any good ideas how 
to model this welcome...

including the _whole domain model_  seems to drop R-factors but cant see much 
additional density - maybe we just model the
missing part then for this structure if nothing else..

Thanks,
Tommi

[ccp4bb] solvent masks

[Kajander, Tommi A]

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 was wondering if the bulk solvent 
masking is just wiping it out. (basicly something like half a domain, e.g. half 
of
individual beta-strands, are missing.) resolution is bit limited (at best 3 Å) 
so automated building and refinement doesnt work terribly well.

I could just place a model there and make a mask somewhere and include in map 
calculation?

Thanks for suggestions,
tommi

[ccp4bb] MOLREP phased translation function

[Kajander, Tommi A]

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 coordinates).

-

I just get eg something like :


--- convert "molrep.crd" to "molrep.pdb" ---
  Time:15h 57m 14s  Elapsed: 0h 27m 19s

 OPENED INPUT MTZ FILE
 Logical Name: /Users/tkajande/….../overall_best_refine_data.mtz   Filename: 
/Users/tkajande/…../overall_best_refine_data.mtz

 Data line--- LABIN F=FP SIGF=SIGFP

 OPENED INPUT MTZ FILE
 Logical Name: /Users/tkajande/……./overall_best_refine_data.mtz   Filename: 
/Users/tkajande/…../overall_best_refine_data.mtz

 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib
 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib

#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 18 Jan 2017  15:57:50
#CCP4I TERMINATION OUTPUT_FILES  XXX_42_molrep.doc XXX_42_molrep.xml 
XXX_42_rf.molrep_rf XXX_42_align.pdb
#CCP4I MESSAGE Task completed successfully



(probably not a good solution but also output file name does not match the one 
suggested..  starting to get bit tired of it...)

Thanks,
Tommi

Re: [ccp4bb] completeness drops from conversion from XDS to Fs

[Kajander, Tommi A]

Problem solved, or well, circumvented - for the record: This seems to happen 
during XDSCONV indeed (F2MTZ seems to dump half the reflections?)
and running via aimless seems to work. Either there is a bug with the 
conversion in the SG or I made  some mistake (which i cant quite figure out 
now).

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 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 XDSCONV to truncate for a check, or to phenix - I get a 
completeness of ca. 50% for the Fs…

… cant quite figure out where this is coming  from…? Never happened before. Too 
tired now. Any suggestions?

Tommi

[ccp4bb] completeness drops from conversion from XDS to Fs

[Kajander, Tommi A]

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 XDSCONV to truncate for a check, or to phenix - I get a 
completeness of ca. 50% for the Fs…

… cant quite figure out where this is coming  from…? Never happened before. Too 
tired now. Any suggestions?

Tommi