Re: [ccp4bb] Low 280 absorbance imidazole?

Hi Bernhard, this one works for us: Sigma BioUltra imidazole, >99.5% by GC, 56749 Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On Aug 21, 2013, at 7:33

Re: [ccp4bb] A quick question about making PEG cryo-protectant

small PEGs will help. Glycerol, MPD, sugars or oils might be helpful. Cheers, Jan -- Jan Abendroth Beryllium Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_be4.com http://www.be4.com On Oct 13, 2014, at 6:08 PM, Xiao Xiao wrote: > Hi Mayer a

Re: [ccp4bb] CrystalClear tape rolls

… and there is RigakuReagents, formerly EmeraldBio, too: https://www.rigakureagents.com/p-595-crystallization-plates.aspx <https://www.rigakureagents.com/p-595-crystallization-plates.aspx> Or google for HD clear duck tape. Several office supply retailers in the US sell it. Cheers, Jan

Re: [ccp4bb] Crystallization buffer pH optimization

solutions. Good luck! Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbios.com On Jan 16, 2013, at 9:38 PM, Mike John wrote: > Hello, > > Shameful and sorry for asking this

Re: [ccp4bb] PILATUS data collection

ons at different distances should remedy that. Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On May 6, 2013, at 4:04 PM, Theresa Hsu wrote: >

Re: [ccp4bb] question about CCP4 scripts

Hi Joe, this line of code for csh/tcsh is awfully rickety-raggedy, it does the trick though. Jan setenv spacegroup P3121 setenv noresidues 350 setenv lambda 1.5418 set unitcell = `head -3 ../hkl/output.sca | tail -1 | cut -b 4-60` scalepack2mtz \ hklin ../hkl/output.sca \ hklout

Re: [ccp4bb] cryo condition

Hi Faisal, 3 - 3.5M Ammonium sulphate with your buffer should work too. Take a small loop. Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On May 23, 2013, at 2:42

Re: [ccp4bb] Figure of merit in refinement

iple reflections - I guess this is possible but I wonder if you could get easily say a 25 sigma I in this way. And as we often end our beer-discussions - may be all protein space groups are actually true P1, just close enough to satisfy the high symmetry rules .. but this is getting a bit philosop

Re: [ccp4bb] powdery residue on pucks?

We call this 'synchrotron dust', but our suspicion is the same that is is a breakdown product of the foam. It happens more often with old dewars than with newer ones. Once this happens, it is a good time to test the dewars. Cheers, Jan On Fri, Feb 21, 2020 at 4:40 PM Dian

[ccp4bb] Project applications to CMS, IBT Biocev - Covid-19

financial contribution will be requested for the measurement/service. Stay safe The CMS team http://www.ibt.cas.cz/core-facility/CMS/index.html -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech

Re: [ccp4bb] dewar horror stories

issues - they even did not reply ... Jan On Wed, Jun 24, 2020 at 9:27 PM Patrick Loll wrote: > Hello community, > > We recently had a dry shipping dewar fail catastrophically (while en route > to the beam line, so, major trauma). I sent it to a company that > specialize

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories

The trouble is no other company does international LN2 shipments here ... So we stopped shipping dewars completely. Jan On Thu, Jun 25, 2020 at 2:27 PM Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > I had a similar one-sided discussion with FEDEX about their ignoring

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories

(which can be determined by the S/N number printed on the dewar). > > Best, > Syun-Ru > > --- > Syun-Ru Yeh, Professor > Department of Physiology and Biophysics > Albert Einstein Collage of Medicine > Bronx, NY 10461 > > > ------ >

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories

, there is a lot more value being shipped in each shipment. Cheers, Jan On Thu, Jun 25, 2020 at 6:47 AM Syun-Ru Yeh wrote: > We had a similar experience with a CX100 a few years ago. We found some > small chunks of white powder leaking out of the inner chamber of the dewar, > which was a

[ccp4bb] diffdump in CCP4 7.1

Hi all, It looks as if the utility ‘diffdump’ is no longer part of the standard linux CCP4 7.1 distribution. It has been a very handy tool for preparing XDS input files. Does anyone know if there is an equivalent script in CCP4 7.1? Thanks, Jan -- Jan Abendroth UCB BioSciences Seattle

Re: [ccp4bb] metal coordination at low resolution - restraints

These are structural. They form the active site of our enzyme. Normally there is no need to restrain these, they "behave". But in general having such standard "restraint angles" available would be of use, I agree. Jan On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov wrot

Re: [ccp4bb] metal coordination at low resolution - restraints

Hi Garib, > > On 8 Sep 2020, at 11:39, Jan Dohnalek wrote: > > These are structural. > > > Are they tetrahedral or octahedral? From the list of neighbours they do > not look like tetrahedral. Some of them do look like octahedral. > > They are involved in reaction

Re: [ccp4bb] metal coordination at low resolution - restraints

It is the active site which is very well defined, with high occupancy and tight binding. We also have high resolution structures of these .. However, restraints (for protein-metal contacs) were not necessary to refine these sites. Atoms site where they should be ... Jan On Tue, Sep 8, 2020 at 2

Re: [ccp4bb] (off-topic) beamline for XAFS

Dear Banu, I would recommend looking also at SSRL beam line 7-3 and 9-3 as they are well set up for protein EXAFS. Greetings, Jan On Tue, Nov 10, 2020 at 11:03 AM PULSARSTRIAN wrote: > Dear all, > Sorry for the off topic. > Looking for suggestions on beamlines for XAFS on

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

We also recently encountered this way of coordinates treatment - did not find it useful but just left it as it was (life has other more exciting adventures waiting ...). I strongly support the solution suggested by Luca, A nice day to all, Jan Dohnalek On Fri, Dec 4, 2020 at 8:48 AM Luca

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

involve more machine learning. Jan On 04/12/2020 00:49, Paul Adams wrote: I agree completely Tom. Having been recently involved in some efforts to identify interesting compounds against SARS-CoV-2, I can say that the current AI/ML methods for docking/predicting small molecule binding have

[ccp4bb] Up-to-date 3D stereo solution

controls. We played a bit with PS VR, VR solutions prsented last year at CCP4 weekend seem to be still far from usable. Did anyone try AR? Best regards, Jan To unsubscribe from the CCP4BB list, click the following link: https

Re: [ccp4bb] Do manufacturers change their crystallogenesis screens?

I have witnessed a change in the Hampton additive screen some years ago - on purpose - the formulation simply did not work OK. So I guess there are changes occasionally. Jan On Wed, Aug 24, 2011 at 5:21 PM, Chris Morris wrote: > HI, > > I've recently seen two examples where the

Re: [ccp4bb] Trying to "digest" PISA results

. We should not be getting such contradictions on a regular basis. Possible I misunderstood the original point ... Jan On Thu, Sep 1, 2011 at 7:46 AM, Karthik S wrote: > http://www.ebi.ac.uk/msd-srv/prot_int/pi_ilist_css.html > so it depends on how many 'stable assemblies'

Re: [ccp4bb] Trying to "digest" PISA results

n state is biologically relevant. I wish we had a method that delivers a reliable answer regarding the "real state" of any protein studied... Jan On Thu, Sep 1, 2011 at 8:41 AM, Ethan Merritt wrote: > On Wednesday, 31 August 2011, Jan Dohnalek wrote: > > Wasn't the

[ccp4bb] CCP4MG 2.5.0 troublesome start

ideas? Jan -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410

[ccp4bb] Vivaspin vs Amicon Ultra

? Thanks, Jan -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066

Re: [ccp4bb] Akta Prime

ourse, is not nearly as sophisticated as a Prime... Best, Jan Am 12.10.2011, 20:28 Uhr, schrieb Michael Colaneri : Dear all, We have an AktaPrime and GE Lifesciences stop servicing these instruments because they are getting old. Does anyone know of a third party company that gives contracts to m

Re: [ccp4bb] should the final model be refined against full datset

ld probably get away with > depositing an unfree R-free set ;) > > > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410

Re: [ccp4bb] Laptop stereo

le windows... (most likey due to driver restrictions). So, AFIAK there is no mobile 3D-platform available for crystallographers. Regards, Jan PS: If I'm wrong I would be happy to know! Am 20.10.2011, 15:01 Uhr, schrieb David Schuller : There are a some models of laptop which contain a

[ccp4bb] Installation of CCP4 under Windows 7

does not seem to create anything "runnable" - please any experience here? I downloaded the latest Windows package "all users" - type. Installed under admin (as it would not let me otherwise). Now as a user I cannot start the interface no matter what I try. There is no ccp4

Re: [ccp4bb] image compression

compression format for our type of data - our data sets have some very typical repetitive features so they can be very likely compressed as a whole set without loosing information (differential compression in the series) but this needs experts .. Jan Dohnalek On Tue, Nov 8, 2011 at 8:19 AM, Miguel

Re: [ccp4bb] Disappearing crystals

We have seen such behaviour connected to temperature fluctuations. Jan On Mon, Nov 28, 2011 at 6:04 PM, Harman, Christine < christine.har...@fda.hhs.gov> wrote: > Hi All, > I have just noticed a very strange thing and need some help in > understanding it. I recently found tw

[ccp4bb] Postdoctoral positions in protein crystallography, computational and biophysical techniques

, fixed term, 3 years, starting 1st July 2012, EU funded via the Czech Ministry of Education. Please, send your expression of interest via e-mail as soon as possible to myself at dohnalek...@gmail.com. You will receive further details necessary for a full application. -- Jan Dohnalek, Ph.D

[ccp4bb] Postdoctoral position in structure-function studies of enzymes for biotechnologies

/aktuality.htm?id=97 The deadline for full applications is February 29! Jan Dohnalek IMC Prague -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410

Re: [ccp4bb] Any calculation function in CCP4 to analyze coordinate file?

We have been doing a bit of this using a simple program under Linux - pdbskim. A linux binary available on request. Very simple output though, focused on infromation on occ, Bs alternatives, etc to help make decisions during structure refinement. Jan On Sat, Feb 25, 2012 at 11:59 PM, WENHE

Re: [ccp4bb] Postdoctoral position in structure-function studies of enzymes for biotechnologies

Apologies - the limiting date for PhD title is different, as stated here: The applicant has received PhD degree after March 28, 2008. Jan Dohnalek IMC Prague On Sun, Feb 26, 2012 at 9:52 PM, Jan Dohnalek wrote: > DEADLINE APPROACHING! > Our group has been involved in structural stud

Re: [ccp4bb] "resolution" on PDB web page

lso noticed that the reported resolution values are nonsensically advertised with three decimal positions after the point which is not the way we would put it, is it? Either fight it or live with it ... Jan Dohnalek On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice wrote: > I just noticed that

Re: [ccp4bb] "resolution" on PDB web page

We indeed used the US portal for deposition which may be "the difference". Nevertheless the recent reported resolution values etc. are projected also to the PDBe portal. Jan On Wed, Apr 25, 2012 at 10:10 AM, Mark J van Raaij wrote: > Phoebe, Jan, PDB, > is this something part

Re: [ccp4bb] effective iodide conc. for SAD data

! Cheers, Jan -- Jan Abendroth Emerald Bio Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On May 3, 2012, at 6:51 AM, Rajesh Kumar wrote: > Dear All, > > I have very thin crystals but diffracting. I was

[ccp4bb] Drawing plt and libXaw lib

system - the 64 bit version though. Anybody knows the way out? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410

Re: [ccp4bb] Drawing plt and libXaw lib

Thanks a lot for help. libXaw.i686 does the job, 386 is not available .. In Windows 7 I have the same trouble but no idea what to do there ... Jan Dohnalek On Thu, May 17, 2012 at 3:53 PM, Edward A. Berry wrote: > Jan Dohnalek wrote: >> >> Dear all, >> in Fedora 15 I

Re: [ccp4bb] Additional band on gel due to his-tag: any references?

Hi Sebastian, Under the assumption that the SDS in your assay does not completely unfold the protein during electrophoresis (chemical impurity can be excluded because of MS experiments, right?), how about adding some urea additionally to the SDS-PAGE (or changing SDS concentration)? GL Jan

[ccp4bb] Older cryocooling system

Would anybody offer an older crystal cooling system to go? -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410

[ccp4bb] UNESCO/IUPAC course 2011/12

on on the course and participants status, etc. can be found at: http://www.imc.cas.cz/unesco/index.html as well as instructions regarding conditions and applications. Jan Dohnalek IMC Prague -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyr

Re: [ccp4bb] crystallizing a complex that's sensitive to ionic strength

). Greetings, Jan --- Dr. Jan Kern Lawrence Berkeley National Laboratory Physical Biosciences Division One Cyclotron Road, MS 66-326 Berkeley, CA 94720 On Sat, Feb 26, 2011 at 6:13 PM, Hua Yuan wrote: > Dear CCP4 community members, > > I've been trying to crystallize a protein compl

Re: [ccp4bb] while on the subject of stereo

see properly in three dimensions and rely on depth cues alone. I personally prefer people with A) when I am their passenger in a car since they do not need to rotate by 90° to see how far the braking lights of the car in front are away :-) jan On 01/03/2011 21:35, Jim Pflugrath wrote: I

Re: [ccp4bb] xds question: inverse beam, lots of wedges

s one continuous sweep. Monitoring scalefactors might be a good indicator. Good luck Jan On Mar 31, 2011, at 3:08 PM, Patrick Loll wrote: > We've just collected a number of inverse beam data sets. It turns out the > crystals showed little radiation damage, so we have a lot of data: 2 x 360

Re: [ccp4bb] Problems in refinement

We did not investigate much further as most of the time use of two or three versions gave us a good picture of what's going on ..probably a feature which would disappear with newer versions anyway. What's the version of Refmac you use, Petr? Jan Dohnalek On Thu, May 26, 2011 at 12:11 PM,

Re: [ccp4bb] Criteria For Solvent Components

the best guestimate .. Na+ is and will be always uneasy. Jan D. On Tue, Jun 14, 2011 at 11:34 PM, Jacob Keller wrote: > Dear Crystallographers, > > While I acknowledge that assigning solvent/ions/waters to blobs of > density is prone to subjectivity, does anyone here know of any

Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms

DO model a few waters in the closest H-bonding positions to protein. If the ligand was not there water would probably occupy that space anyway and who knows - may be our "ligand" is present only 50% and the other 50% is water ... Modeling more UNKNOWN atoms might be the future for thes

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

kept clean! Jan D. On Fri, Jun 17, 2011 at 3:36 AM, Richard Edward Gillilan wrote: > > Hi Chelsy, yes we had a lot of trouble with the nanoview during that run. >  Even after going through the calibration procedure with the special fluid > provided, we still had inconsistent res

[ccp4bb] SLOW CCP4 Interface

Dear all, my ccp4 interface 6.1.3 became REALLY slow in response on a new i7 PC with Fedora core 15 2.6.38.8-35.fc15.x86_64 . Any ideas where to go from here? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2

Re: [ccp4bb] SLOW CCP4 Interface

Was a SELinux issue. Jan Dohnalek On Thu, Jul 21, 2011 at 1:44 PM, Jan Dohnalek wrote: > Dear all, > my ccp4 interface 6.1.3 became REALLY slow in response on a new i7 PC with > Fedora core 15 > 2.6.38.8-35.fc15.x86_64 . > > Any ideas where to go from here? > > >

[ccp4bb] pdb_extact and refmac5.6

/mmcif_pdbx_2.items) in get_lines_from_file pdb_extract version-3.010, as downloaded form the rcsb webpage also chokes on the refmac5 logfile with a segmentation fault. Any ideas how to treat the new refmac log files in pdb_extract? Thanks a lot. Jan -- Jan Abendroth Emerald Biostructures

Re: [ccp4bb] ARP/wARP install on 6.2.0 & RHEL 6?

... strange, I have not seen any problems installing ARPwARP 7.1 on a new CCP6-6.2.0 install on - linux centos - os-x snow leopard, here I initially ran into write permissions issues and wound up changing the ownership of the /Applications/ccp4-6.2.0 directory Cheers Jan On Jul 27, 2011, at 9

Re: [ccp4bb] SHELXL eating REFMAC5 waters - whom to trust?

My way was to leave this water fiddling to the very last cycle and not let them go away too much. Those that went completely wrong were deleted. I wish I had a more satisfying answer. Jan On Thu, Nov 12, 2009 at 8:53 AM, Wulf Blankenfeldt < wulf.blankenfe...@mpi-dortmund.mpg.de> wrote: >

[ccp4bb] AW: [ccp4bb] off-topic: crystal optimization without buffer

might change maybe if your crystallization experiments give you some more hints about the solubility of the protein. Good luck, Jan --- Katja Schleider schrieb am Do, 19.11.2009: Von: Katja Schleider Betreff: [ccp4bb] off-topic: crystal optimization without buffer An: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] Methylation of macromolecular complexes

contributions by lysines might be a cause for not obtaining crystals, or is there any other better ways? thanks, Jan Rash

Re: [ccp4bb] Methylation of macromolecular complexes

Hi all, What I really want to know is whether macromolecular complexes ( more than 200kDa) can tolerate methylation? thanks, Jan Rash 2009/11/24 Hüsnü Topal > Hi Jan, > > > > Maybe this link > http://www.jenabioscience.com/cms/en/1/catalog/529_jbs_methylation_kit.htmlor

Re: [ccp4bb] Arp/wArp error

Hi all, I ran into that several times in the monoclinic space groups. ARP/wARP does not seem to like the C121 notation, yet likes the C2 notation. Same for P121 vs. P2. Re-assigning the SG eg. in CAD using the correct notation or the SG number is an easy remedy. Cheers Jan On Tue, Dec 1, 2009 at

[ccp4bb] AW: [ccp4bb] FW: [ccp4]: TDS upon flashcooling

Did you also try a cryo salt (e.g. Li+)? In the best case the xtals might even grow in there. GL Jan --- Natalie Zhao schrieb am Di, 15.12.2009: Von: Natalie Zhao Betreff: [ccp4bb] FW: [ccp4]: TDS upon flashcooling An: CCP4BB@JISCMAIL.AC.UK Datum: Dienstag, 15. Dezember 2009, 13:20

[ccp4bb] AW: [ccp4bb] off topic: multiple structural sequence alignment

Hi Ronnie, the (a) Mammoth tool might also work (but I just tried 6 structures or so when I used it a couple years ago - not 20). Jan --- Ronnie Berntsson schrieb am Di, 12.1.2010: Von: Ronnie Berntsson Betreff: [ccp4bb] off topic: multiple structural sequence alignment An: CCP4BB

[ccp4bb] Refmac and links between ligands

.pdb file contains the LINK records newly created for these atoms. The actual distances look pretty much as if they were restrained ... Is there a way to make Refmac ignore these links? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czec

Re: [ccp4bb] Refmac and links between ligands

Problem solved. One must also switch to the "make sugar NO" keyword. Otherwise Refmac tries to use the discovered sugar and ion as if it was sugar-peptide bond. Jan Dohnalek On Mon, Feb 1, 2010 at 2:52 PM, Jan Dohnalek wrote: > Dear all > I understand that when I use the Refma

[ccp4bb] refmac5 and spericity restraints

Hi there, I am refining a 1.3AA structure for SSGCID using -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

[ccp4bb] refmac5 and sphericity restraints, 2nd attempt

ill active? Cheers Jan On Mon, Feb 8, 2010 at 6:29 AM, Jan Abendroth wrote: > Hi there, > I am refining a 1.3AA structure for SSGCID using > -- > Jan Abendroth > Emerald BioStructures > Seattle / Bainbridge Island WA, USA > home: Jan.Abendroth_at_gmail.com > wor

[ccp4bb] Example of a good crystallization facility design?

not mean robotic setups by this .. Jan Dohnalek, IMC Prague -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410

Re: [ccp4bb] Distinguishing Between Na+ and H2O

a "sodium detector" for such structures .. Jan On Tue, Feb 16, 2010 at 12:00 PM, George M. Sheldrick < gshe...@shelx.uni-ac.gwdg.de> wrote: > A few years ago we thought that the bond valence method might provide > an answer to this problem and wrote a paper on the subje

Re: [ccp4bb] Distinguishing Between Na+ and H2O

distances can result just from bad structure refinement or relatively low resolution of the data (there are even examples of non-refined structures in the PDB) and in those cases making this kind of changes would be a complete disaster... Jan On Wed, Feb 17, 2010 at 6:32 PM, Jacob Keller wrote

[ccp4bb] about comparing Rwork and Rfree factors of different refinement trials

rable? (E.g. it did not work for me to do a 1 cycle rigid body refinement in refmac hoping that the R factors are measured well and the structure does not change much. In fact, the R factors increased dramatically, lets say Rfree from 30% to 40%.) Many thanks for y

[ccp4bb] crystallization of a macromolecular complex

genuine hit. Any suggestions for growing the crystals of this macromolecular complex will be highly appreciated. Thanks, Jan

Re: [ccp4bb] inexpensive source of DDM

). Hope that helps, Jan Tony Wu wrote: Hello, I am looking for an inexpensive US source for large quantities of dodecylmaltoside. Can anyone help me? Thank you!

[ccp4bb] looking for people interested in fast (0.8 ms) x-ray shutter

ional $1095. So I was wondering if anyone else would be interested in buying this shutter, so we could combine the orders. Please answer directly to me. Thanks a lot, Jan Dr. Jan Kern Physical Bioscience Division LBNL Berkeley phone: +1-510-486-4330 e-mail: jfk...@lbl.gov or

[ccp4bb] AW: [ccp4bb] freezing crystals grown in isopropanol condition

after freezing (or check the loop under the microscope/camera of the xray source). Evaporation of isopropanol (comparable to EtOH) during mounting should not be a serious problem. HTH Jan --- Chris Meier schrieb am Fr, 9.4.2010: Von: Chris Meier Betreff: [ccp4bb] freezing crystals grown in isopro

[ccp4bb] Protein-antibody complex

will be highly appreciated. Thanks, Jan

Re: [ccp4bb] Clarification and another question . . .

grown crystals ... Jan On Sun, May 9, 2010 at 8:26 PM, Jack Reynolds wrote: > --- On Sun, 5/9/10, Klaus Fütterer wrote: > >> Dear Jack, >> >> I believe your venture would enter a mature market, and, if >> you were to offer growing growing crystals in microgravity

Re: [ccp4bb] Micro-g Crystal Growth and the literature

does not overcome either of those. Jan On Mon, May 10, 2010 at 5:49 AM, Jack Reynolds wrote: > TITLE: "Extracting trends from two decades of microgravity macromolecular > crystallization history" (2005) (Judge, Snell and van der Woerd). > > "Significant enhanceme

[ccp4bb] mosflm in script mode

starting the old gui. Is there a command in the current mosflm versions to run it in shell mode only? Below the script that I have been using. Any ideas? Thanks Jan --- ipmosflm summary integrate02.sum <http://www.emeraldbiostructures.com

Re: [ccp4bb] Off-topic: hollow protein crystals

Many times. Jan Dohnalek On Wed, Jun 2, 2010 at 9:07 PM, Andre Ambrosio wrote: > Dear all, > > > > We have recently obtained crystals from a small protein, and interestingly, > at least for me, they are hollow trigonal rods (please see pictures > attached). > >

[ccp4bb] AW: [ccp4bb] Heme Proteins

the bottom than the Erlenmeyer flasks). I wonder if this really makes sense for the CYP51 expressions though, because the idea of these bottles is to INCREASE the interface of bacterial medium and air HTH Jan --- Hari Namboodiri schrieb am Do, 26.8.2010: Von: Hari Namboodiri Betreff

[ccp4bb] AW: [ccp4bb] Heme Proteins

pete with these guys... Maybe someone else has other ideas about that? Good luck! Jan --- Hari Namboodiri schrieb am Fr, 3.9.2010: > Von: Hari Namboodiri > Betreff: [ccp4bb] Heme Proteins > An: CCP4BB@JISCMAIL.AC.UK > Datum: Freitag, 3. September, 2010 19:30 Uhr > Dear CCPeers

Re: ccp4bb on new site

son asking rather than bothering the entire community with my advice. Some of the nice collection of answers indicate that several other think so too. Unless this only happens in my computer setup, one option might be that the original sender of a post is included in "reply to all".

Re: [ccp4bb] Bio-rad DuoFlow

only systems, at least on the US market. -Jan Frank Lee wrote: Dear all, Thanks a lot for all the feedbacks on AKTA prime. They are so helpful that I have abandoned the idea of buying one. Now it is a choice between AKTA FPLC and Bio-rad DuoFlow. I heard that DuoFlow is not as robust as

[ccp4bb] RMSD of pairs of atoms?

A41 A50 Atom types | CA | B-factor range used: -1000.00 - 1.00 A2 Nr of atoms to match : ( 3) Nr skipped (B limits) : ( 0) Many thanks, jan -- Jan Lowe

[ccp4bb] TeachSG Workshop on ligand searching and docking in Prague

expression of interest explaining the reason for participation, and a letter of support from their group or laboratory head. The applications should be send by e-mail to Sarit Goren [EMAIL PROTECTED])or to Jan Dohnalek ([EMAIL PROTECTED]) as soon as possible. The participants have to fund their travel

[ccp4bb] mosflm getbox error

Mosflm experts, mosflm dies on me with the error message below. Granted, it is really crappy data I am working with... Cannot find the getbox command in the documentation. Which would be appropriate values for xlines etc at low double digit resolution? Any ideas? Cheers Jan ... mosflm.lp

[ccp4bb] scala and cell dimensions

Hi mosflm experts, last week's problem with mosflm solved, another one appearing. Scala fails with the error message below. These are ~10AA data. Scala finishes in p422, however dies in p222... Any ideas? Cheers Jan ~ scala.log Run(s):1 * Wavelength and cell extr

Re: [ccp4bb] scala and cell dimensions

Thanks a lot, Graeme, using scala from ccp4 6.0.1 indeed did the trick (osx binaries). The data were processed with mosflm in fact. Cheers Jan Winter, G (Graeme) wrote: Hi Jan, This data is from XDS I'm guessing. Try Scala from CCP4 6.0.1 - this is a problem only with 602 I think. C

[ccp4bb] Douglas Instruments Oryx crystallisation robots

We are thinking about getting the Oryx8 robot (Douglas Instruments) for crystallisation experiments. Is anyone out there with any kind of experience with these? Jan Dohnalek IMC Prague

[ccp4bb] MSGPP cocktails for fragment crystallography

posted on behalf of Christophe Verlinde, MSGPP, University of Washington, Seattle Replies only to him, please. MSGPP: The recipes for our cocktails for fragment crystallography designed to aid in drug design are now available. More info is at this URL: faculty.washington.edu/verlinde/ _

[ccp4bb] xds, saturn94 and 2theta

d to be changed? - I also tried to use only a few or plenty of images for indexing. I know there are other programs for processing data, however, there are good reasons why I'd like to get this data set integrated with xds. Any ideas would be greatly appreciated! Cheers Jan -- Jan Abe

[ccp4bb] mosflm and APS BM17

. Probalby just a parameter or so set wrong. My input file in the attachment. The last three lines do not make much of a difference. Any ideas? Thanks! Cheers Jan mosflm.in: detector marccd directory ../Images template Image_0###.img image 001 nullpix 1 separation 0.95 0.95 close

Re: [ccp4bb] mosflm and APS BM17

case. Cheers Jan On 8/22/07, Harry Powell <[EMAIL PROTECTED]> wrote: > Hi > > I'd guess from the input file that the beam centre may be defined in a > different reference frame to that which Mosflm expects in the image > header; other possibilities are that the distance,

[ccp4bb] Thermal melt and heme in the protein

ts with an appropriate dye instead or does Thermal melt never work with heme in the protein? Many thanks! Jan - Die etwas anderen Infos rund um das Thema Reisen. BE A BETTER WELTENBUMMLER!

Re: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds

Just to add to the outliers in Refmac - careful when some of your atoms have zero occupancy. The bond restraints are not applied any more to these atoms (my feeling) and CERTAINLY are NOT CHECKED FOR OUTLIERS by Refmac at the end of the refinement. Jan Dohnalek Eleanor Dodson wrote: No

[ccp4bb] refmac and ramachandran troubles

POSITIVE" problems. Any ideas? Cheers Jan -- Jan Abendroth deCode Biostructures Seattle/Bainbridge Island, WA, USA work: [EMAIL PROTECTED] home: [EMAIL PROTECTED]

[ccp4bb] phaser and rotation function solutions

ver, 50 peaks when I chose the brute rotation function. Any ideas? Thanks Jan

[ccp4bb] tricky molecular replacement

s procedure make sense at all? - any other ideas? Thanks a lot Jan almn.log: ## Peaks must be greater than 2.00 times RMS density 52.2161 Eulerian angles Polar angles Alpha Beta Gamma Peak Omega

Re: [ccp4bb] tricky molecular replacement

maprot dies with "ccpmapin - Mask section > lsec: recompile" Any ideas? I btw. use the osx binaries from the ccp4 webpage. Thanks for any input! Cheers Jan On 11/2/07, Edward A. Berry <[EMAIL PROTECTED]> wrote: > > One other idea idea: > 1. Solvent flattening on the

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