[ccp4bb] Group Leader position in Helsinki, Finland

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

[ccp4bb] GL position available/Finland

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 facilities

Re: [ccp4bb] "modeling" flexible ends on proteins

and that the data 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

[ccp4bb] "modeling" flexible ends on proteins

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

[ccp4bb] Stereo on macs revisited

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

[ccp4bb] Post doctoral position at the protein crystallization core facility / Institute of Biotechnology, University of Helsinki

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 will

[ccp4bb] Post doctoral position at Institute of Biotechnology, Univ. Helsinki

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. The

[ccp4bb] best transient mammalian expression systems..?

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 sup

Re: [ccp4bb] How to convert file format from CNS to CCP4

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 c

Re: [ccp4bb] Assemble Protein-DNA complex

urify with gel filtration column. However, >> the one I am currently working on seems to be very picky. If you >> have any suggestion regarding to my problems, I will be thankful. >> >> Best regards, >> > > - -- > - -- > Dr Tim Gruene > Institu

Re: [ccp4bb] solubility estimates for domains/structures?

us overexpression, you can try: > SOLpro in http://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:CCP4B

[ccp4bb] solubility estimates for domains/structures?

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

Re: [ccp4bb] @Ian:Death of Rmerge

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 an

Re: [ccp4bb] Akta vs HPLC

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 sta

[ccp4bb] nanodrop vs larger vol measurenment of absorbance?

, 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

Re: [ccp4bb] Freezing crystal

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 wr

[ccp4bb] mask effects in solvent flattening / NCS

looks like.) --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

Re: [ccp4bb] density mod., NSC and software..

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

[ccp4bb] density mod., NSC and software..

...) 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

Re: [ccp4bb] symmetry for ages 6 and up

rsc.org/shop/books/2008/9780854042722.asp >>> >> >> >> >> Mark J van Raaij >> Laboratorio M-4 >> Dpto de Estructura de Macromoléculas >> Centro Nacional de Biotecnología - CSIC >> c/Darwin 3, Campus Cantoblanco >> 28049 Madrid >> tel. 91 585 4616 >

Re: [ccp4bb] ncs axis...

this mid-point > plus other pairs (symmetry-equivalent) ... ? > > Cheers > > Clemens > > On Fri, Nov 25, 2011 at 10:55:49AM +0200, Tommi Kajander wrote: >> Hi, anybody have a script to to find a translation for 2-fold NCS (rotaion) >> axis based on the center of NCS

[ccp4bb] ncs axis translation

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

[ccp4bb] sftools bug

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

Re: [ccp4bb] small 3ml Superdex column performance

ificant band 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

Re: [ccp4bb] detect dsDNA

. Can you do the toothbrush test with SYBR Safe? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** Tommi Kajander, P

Re: [ccp4bb] question regarding secondary-structure restraints

f Biochemistry Ludwig-Maximilians-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,

[ccp4bb] xplot84

HI, looks like - at least for us on Mac OSX (both snow leopard and Lion), in the latest CCP4 (and already previous versions of CCP4) xplot84 is broken, the .plt plots dont work (ie programs that produce these are useless for that purpose...). ...worth fixing perhaps? Tommi Tommi Kajander

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

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

Re: [ccp4bb] low res. SAD phasing

at 04:36:59PM +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 Bioph

[ccp4bb] low res. SAD phasing

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

Re: [ccp4bb] off topic: problematic protein

. I will prompty post a summary 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/x

Re: [ccp4bb] what to do with disordered side chains

gram cel: 773.608.9185 email: j-kell...@northwestern.edu<mailto: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

Re: [ccp4bb] [OT] which column to use in SLS/MALS instruments

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. +358-9-19158903 tommi.kajan...@helsinki.fi

Re: [ccp4bb] CCP4 for iphones

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 Viikin

[ccp4bb] MALLS analysis question

would 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-

Re: [ccp4bb] very low R factor for twin refinement

of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Ave Bronx, NY 10461 phone 718-430-2745 yu...@medusa.vioc.aecom.yu.edu Tommi Kajander, Ph.D. Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland

[ccp4bb] The 2nd Advanced Protein Characterisation and Crystallisation Course in Helsinki, Finland

, 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

Re: [ccp4bb] Se-Met Protein Purification

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 la

Re: [ccp4bb] What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?

902-149 e-mail: fabio.dallanto...@embl-hamburg.de 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

Re: [ccp4bb] Space group and R/Rfree value

stupid, any help 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)

[ccp4bb]

300mM NaCl 3.Before making complex I spun the protein @14,000rpm 10min. the complex solution is clear. Regards Dilip 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

[ccp4bb] met auxotroph S.cerevisiae strain?

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 and

Re: [ccp4bb] Protein melting temperatures

mbus, OH 43210-1185 (614) 859-5743 phone (Google Voice) (614) 292-1685 fax magli...@chemistry.ohio-state.edu http://www.chemistry.ohio-state.edu/~magliery Tommi Kajander, Ph.D., Docent Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O.

Re: [ccp4bb] how to optimize crystallization of a membrane proteinf

-- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------ / Lao Tse /

[ccp4bb] LS / RI detector systems

think 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 Inst

Re: [ccp4bb] insect cell media

equipment 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 He

Re: [ccp4bb] Reg Protein purification

Padavattan 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

Re: [ccp4bb] SCA

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-00014 H

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....

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.

[ccp4bb] UV detection of crystals/survey

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

Re: [ccp4bb] phenix rigid body ref.

t; etc... (I suggest you take only one zone 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

[ccp4bb] phenix rigid body ref.

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 from

[ccp4bb] arpwarp improve maps

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 didn

[ccp4bb] loop modelling?

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! to

Re: [ccp4bb] How to compare the binding affinity between two domains structurally?

ce does not provide definitive answer, given that the interacting residues on the interface are also different. BTW, we were not able to purify individual domains, so we cannot measure the binding affinity by wet lab approaches (so far). Thank you in advance for your inputs. -- Best regards, Joe

Re: [ccp4bb] Anomalous map creating

ng data." And I 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.

[ccp4bb] MOLREP

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 c

Re: [ccp4bb] MSA formatting...

ion 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

Re: [ccp4bb] MSA formatting...

nks anyway.. 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 pe

[ccp4bb] MSA formatting

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 of

Re: [ccp4bb] Problems with phasing a protein (1300aa)

ble 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 (

Re: [ccp4bb] Problems with phasing a protein (1300aa)

on of 3.3A (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

Re: [ccp4bb] .phs file conversion

convert the file to either a ccp4 or cns map file, or a file format that pymol will recognize. I do not have an .mtz file with the same map coefficients included. Can anyone help me? Thanks, John Tommi Kajander, Ph.D. Macromolecular X-ray Crystallography Research Program in Structural

Re: [ccp4bb] Small lines in diffraction pattern (more info)

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 2

Re: [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer?

of the opposite case, 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 Res

Re: [ccp4bb] Protein folding pattern schematic

file 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 Biop

Re: [ccp4bb] Definition of salt bridge

--- >> Chavas Leonard, Ph.D. @ home >> Research Associate >> Marie Curie Actions Fellow >> >> Faculty of Life Sciences >> The University of Manchester >> The Michael Smith Buildi

[ccp4bb] test data sets part II...

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 of

[ccp4bb] recipees for prep of test derivatives

good 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]

Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard

ALWAYS OFTEN SOMETIMES RARELY NEVER 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

Re: [ccp4bb] peptide for co-crystallization

with regard to what is "guaranteed"--usually you get a mass spec / HPLC etc sheets telling you what the real purity is. checking that is certainly worthwhile. i would perhaps first try with 95% pure and then if not good enough purify further. this purity scale has worked ok for us. tommi

[ccp4bb] baculovirus GFP vectors

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

Re: [ccp4bb] Concentrating protein

re sample, of course. > > Cheers, > > -- > > 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)

Re: [ccp4bb] Concentrating protein

kindly help me to progress in my experiment. > Phoebe A. Rice > Assoc. Prof., Dept. of Biochemistry & Molecular Biology > The University of Chicago > phone 773 834 1723 > http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123

Re: [ccp4bb] about anisotrophic diffraction

prove my > diffraction data? > This crystal grew in 2.5M 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

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

liquid N2, which causes boiling around the crystal immediately after > 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 ea

Re: [ccp4bb] mosaicity,was:crystallisation

--- > > > > > ___ > > Dr. Christian Biertümpfel > Laboratory of Molecular Biology > > NIDDK/National Institutes of Health phone: +1 301 402 4647 >

Re: [ccp4bb] insect expression system

ey are secreted into the media. > > 1) Baculovirus system > 2) Drosophila system > > Which system would you recommend for high expression and convenience? > Has anyone ever compared those systems side by side? > > Any suggestions or references are greatly appreciated. >

Re: [ccp4bb] space group problem

t; >> > >> *** > >> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > >> * > >> * Global Phasing Ltd. > >> * Sheraton House, Castle Park > >> * Camb

Re: [ccp4bb] isopropanol as a precipitant

rop size is 3+1 with mother liquor 300 > micro > 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.

Re: [ccp4bb] rescuing crashing-out protein eluted from Nickel column

glycerol into one of the fractions but that made it even more cloudy > > (ohh no...). > > > > While the protein is dying in the tube, do you have some quick remedy > > for me? Thanks very much, -J.J. > > -- Tommi Kajander, Ph.D. Macromolecular X-ray Crystallograp

[ccp4bb] xprep vs shelxc

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 of

Re: [ccp4bb] His tag does not bind.

es > not bind amylose resin any better with majority flows right through. All > purification are carried out under standard conditions as mentioned in > the > manuals. The protein is soluble and does not precipitate in the columns. > I > appreciate and ideas or explanations. > &g

Re: [ccp4bb] Solvent content of membrane protein crystals

size/Mw? is this really so? --- of course this may further vary depending on the oligomeric 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 Crystallo

[ccp4bb] HT-thermal melts

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

[ccp4bb] combining various SAD phases

Hi, i would be interested in hints about what would be the best way to combine & improve SAD phases from two (or several) non-isomorphous crystals, i can only get reasonable phases from SHARP so far i think. (the other set is very poor but has some signal there) one back as HLs into sharp? or d

Re: [ccp4bb] refmac problem in running arp/warp

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:

[ccp4bb] refmac problem in running arp/warp

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

Re: [ccp4bb] auto-tracing programs

ed to hear 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

[ccp4bb] auto-tracing programs

cases where there was some difference to what you started with... ..of course one can always complete and correct by hand but when you are doing this with phasing iteratively it would be interesting to hear opinions.. thanks, tommi -- Tommi Kajander, Ph.D. Macromolecular X-ray Crystallog

Re: [ccp4bb] heavyatom soaking problem

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 > concentra

Re: [ccp4bb] questions about hydrophobic core

t; > 20139 Milano > > Italy > > > > tel +39 02 9437 5094 > > fax +39 02 574 303 310 > > > > > -------- > > > > > > > > No virus found in this outgoing message. > &

[ccp4bb] experiences on fluidigm topaz system

). 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: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9

Re: [ccp4bb] recommendation for heavy atoms used in lithium sulfate and ammonium sulfate

d 0.5M ammonium sulfate? > I read from Hampton user guide of heavy atom kit that "high salt > concentrations are not the ideal medium for heavy atom reactions with > macromolecules", so is there any type of heavy atom we should avoid > using? We do not have any experience in

Re: [ccp4bb] cryo was:bigger size - > better diffraction?

ed NaCl as the salt, in a 4*6 tray, the > >> [NaCl] is going from 2.0,2.05,2.1,2.15,something like > >> that and 0.05M does make big difference.I used Urea as the > >> additive in this case ( 25 m ~ 100 mM) and tried > >> 2+2,3+1,3+2, 3+1 ( 3 uL prot

Re: [ccp4bb] High overall b-factor

where the > > protein density and ligand density can be distinguished at such high > > B-factors. Does anyone have any suggestions if there is something > going > > wrong here? > > > > Thanks, > > > > George > > > > > > > _

[ccp4bb] met-Pb-acetate

Hi, would anyone know a commercial source for methyl lead acetate? thanks in advance, 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