[ccp4bb] tricky molecular replacement III

55% for 4AA data. This huge gap of R-factors from Molrep and Refmac is really puzzling to me. Any ideas? Cheers Jan

[ccp4bb] external phases in sharp

to need a DANO column. Thanks a lot Jan

[ccp4bb] ciftr troubles - now with logfile

... meant to include this logfile in my previous post: -Jan /sw/xtal/ciftr/ciftr-v2.053-prod-bin-darwin/bin/CIFTr -i output.cif Translating a mmCIF file [1] output.cif to PDB file output.cif.pdb Warning skipping item _computing.pdbx_density_modification is NOT in dictionary. Warning skipping item

[ccp4bb] ciftr troubles

during "obj/regcomp.o". Could be a very handy tool! Any help how to get it running would be greatly appreciated. Thanks Jan

Re: [ccp4bb] Tough Low-Res MR

correct, however model bias did not allow to get further. Sometimes it turned out to be helpful to increase the numbers of rotation solutions that are considered for the translation search. Cheers Jan ## deCODE biostructures Bainbridge Island 2008/2/21, Roger Rowlett <[EMAIL PROTEC

[ccp4bb] ELRIG crystallography meeting

scientists interested in robotic crystallisation and and a strong list of speakers has been assembled this year. Please see http://www.elrig.org/ for details. jan Jan Löwe Laboratory of Molecular Biology Medical Research Council Hills Road

[ccp4bb] Color of heme containing Xtals

! Jan - Lesen Sie Ihre E-Mails jetzt einfach von unterwegs..

[ccp4bb] Peltier Crystallisation Incubators

hanks Jan Dohnalek PS: I have found these, there might be more http://www.memmert.com/en/products/product-range/peltier-cooled-incubators/overview/ http://www.analis.be/products/product.asp?idP=282&prodCatg=1778&prod=1471 -- ====== Mr. Jan Dohnalek, Ph.D

Re: [ccp4bb] into the looking glass

Hey guys, what day is today? I think this was very funny... James Holton <[EMAIL PROTECTED]> schrieb: Dear CCP4BB, I think it prudent at this point for me to announce what could be a very old, but serious error in the fundamental mathematics of crystallography. To be brief, I have unco

Re: [ccp4bb] How to obtain an oca file?

We miss the MSD target service a lot. Is there a real reason why it's gone? Jan Dohnalek Eleanor Dodson wrote: Thwe MSD target service has gone, and that was the way I created oca files comparing sequences? Is there another web site which will give back the same format? El

Re: [ccp4bb] Finding NCS operator from one heavy atom site?

wever, almost needles to say that cloning, expressing, purifying, crystallizing and solving the same construct of an 85% seq. identical ortholog took less effort than messing around with the bad maps... Good luck Jan 2008/5/22 Partha Chakrabarti <[EMAIL PROTECTED]>: > Hi, > > Apol

[ccp4bb] ccp4mg and speed

: - ccp4mg-1.1.1-Linux-Fedora-Core - coot-Linux-i386-fedora-6 - python2.4 - Fedora Core release 6 Thanks a lot for any hints. Jan

[ccp4bb] monomer library sketcher troubles

Any ideas? Thanks a lot! Jan tmp file # --- LIBCHECK --- /Vers 4.1.3 ; 19.12.2002/ Do you want to have FILE-DOCUMENT /libcheck.doc/ ? //Y/A : N - means without DOC-file Y - with new contents A - means to keep old contents a

[ccp4bb] sketcher and nitrogen in rings

geometry or fiddle around with the cif file. Is there a proper way to make it right in the first place? Thanks Jan

Re: [ccp4bb] Change reflection file names

try the unix tool mmv. jan On Aug 7, 2008, at 1:40 AM, yanming Zhang wrote: All UNIX gurus, I need to change 300 image file names sequentially, such as: XXX_10001.img to XXX_101.img XXX_10002.img to XXX_102.img Obviously, using UNIX 'mv' to work on 300 files

[ccp4bb] refmac, twin - really low Rfactors

y low for a 1.9AA structure. As expected, the maps from the twin treatment are a bit nicer that for the non-twinned treatment. Any reasons for concerns or just a very rigid structure that refines really well or refmac handling twinning really nicely? Thanks for any input Jan -- Jan Aben

[ccp4bb] AW: [ccp4bb] hi / cloning stuff

hen gave it up! So this vector really seems to be a tough one. Thats why if nothing works, you might take another vector into consideration. But before that you should check buffers, ligase, restriction enzymes etc. and do in silico cloning. Another idea would be do to de/phosphorylation (s

[ccp4bb] xds and Saturn troubles

: !!! ERROR !!! ILLEGAL RAXIS_COMPRESSION_RATIO Any ideas what this might be? Thanks a lot Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

Re: [ccp4bb] xds and Saturn troubles

Hi all, thanks a lot for all the replies! Using the very current version of XDS fixed all the problems, really nice data, structure solved, yet another one for SSGCID. re input file: attached the XDS.INP file that worked for the Saturn 944+ detector. Thanks again! Jan 2008/9/4 Jan Abendroth

[ccp4bb] Topp fails: TOP: Open failed: File: /people/...../myfile.pdb

elped. I have tried moving to various Linux versions (64bit,32bit, var. levels of Fedora or RHEL) Any ideas? Jan Dohnalek -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Struc

[ccp4bb] Xtals: protein or something else?

DS-PAGE or glutaraldehyde? Or is there another method (like unsuccessful staining with IZIT) I am not aware of, that would allow an SDS-PAGE or staining by glutaraldehyde afterwards? Many thanks for your suggestions! Jan

[ccp4bb] low B factors

, Rfree=0.286, bonds=0.018, angles=1.89 ... obviously I could retrain a bit more... Any ideas how to handle this? Basically, my question is: how do I get the overall B factor to realistic numbers? Thanks a lot for any hints Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA

Re: [ccp4bb] iMosflm 1.0.0

eters with two wedges 90 deg apart and want to integrate the full data set. At this point it seems that I can only add one image at a time. Thanks a lot for any pointers Cheers Jan On Nov 13, 2008, at 9:18 AM, Luke Kontogiannis wrote: Dear all, When we released iMosflm 1.0.0 on 17th Oc

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

ike their crystals to really behave like solids (stability, localization of disordered regions, etc.) no need for cryoprotection and it is hard to make them ... Jan Dohnalek IMC Prague Jayashankar wrote: Here we are dealing with two different state of chemistry, solid state and solution sta

[ccp4bb] refmac 5.5.063 vs. 5.5.066

Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

Re: [ccp4bb] refmac 5.5.063 vs. 5.5.066

Thanks a lot, Pavol, that indeed did the trick. refmacRwork Rfree RMSDb RMSDan 5.5.0063 0.1682 0.2118 0.0204 1.717 5.5.0066 0.1781 0.2247 0.0205 1.764 5.5.0070 0.1663 0.2102 0.0204 1.719 Cheers Jan On Dec 19, 2008, at 2:21 AM, Pavol Skubak wrote: Hi Jan, the

[ccp4bb] TeachSG workshop Expertise in Macromolecular Structure Refinement in Prague April 3-4

ease, send an e-mail to myself (Jan Dohnalek, cc: dusk...@imc.cas.cz) containing a motivation letter (within the e-mail message is OK), a letter of support from your supervisor or head of group, and a short professional CV (one page). It should be clear from your documents why participati

[ccp4bb] TeachSG workshop Expertise in Macromolecular Structure Refinement in Prague April 3-4

This is a reminder - the application deadline is approaching - 24th February. Jan Dohnalek A two-day workshop focused on both the basics and the current development in macromolecular single crystal structure refinement techniques will be held in Prague on April 3-4 2009. The workshop is

[ccp4bb] unit cell flags in mtz files and refmac

s a rather annoying shift of the electron density that is displayed in coot based on different unit cell in the mtz file. Is there a way to tell refmac which of the two unit cells to put in the output mtz file? Intuitively, it should be the one from which the amplitudes originate? Cheers Jan *mtz

Re: [ccp4bb] unit cell flags in mtz files and refmac

Thanks a lot, Garib, as always, there is a new version of refmac just out that fixes all the problems. Cheers Jan 2009/2/26 Garib Murshudov > I think we have fixed this problem just recently. The problem was related > with refmac not being able to pick correct dataset from mtz. IF the

[ccp4bb] Problem with setting up ccp4 gui

s from def file source [file join $env(CCP4I_..." (file "/opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i.tcl" line 163) invoked from within "source [file join $env(CCP4I_TOP) bin ccp4i.tcl]" (file "/opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i" line 5) Can anyone

[ccp4bb] ccp4i / refmac issue

also occurs for files that refined w/o any problems before. Any ideas what is going on here? Thanks for any input. Jan ~~~ Top level CCP4 directory is /usr/local/ccp4-6.1.1 Using CCP4 programs from /usr/local/ccp4-6.1.1/bin can't set "ATOM(0)": variable isn't array

Re: [ccp4bb] ccp4i / refmac issue

Hi all, yes, re-running jobs was the issue. So, creating a new job did the trick. Thanks for all the various feedback! Jan On Mar 6, 2009, at 12:43 AM, Paul Fyfe wrote: Hi Jan, I had exactly the same problem. It happens (for me) when you try and re-run a job created for a previous version

[ccp4bb] nad woes

* nomenclature. Cheers Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

[ccp4bb] AW: [ccp4bb] Refolding of Denatured Protein

Urea can modify your protein. Maybe you should also try guanidine HCl. Also, did you try any detergents? Good luck! Jan --- Sanjiv Kumar schrieb am Di, 5.5.2009: Von: Sanjiv Kumar Betreff: [ccp4bb] Refolding of Denatured Protein An: CCP4BB@JISCMAIL.AC.UK Datum: Dienstag, 5. Mai 2009, 13:27 I

Re: [ccp4bb] Lost my protein

When using spin concentrators, always remember to not spin more than 4-6min before remixing the content of the concentrator by pippetting, to prevent concentration gradient and subsequent precipitation at the bottom. Jan Jan K Jensen, Pl-R, Ph.D. Post doctoral fellow at University of Illinois

[ccp4bb] ccp4i problem - bad marshal data

e advanced functions may not be available. Next time you start CCP4i it will try again to use the database server. If you wish to disable this behaviour then select the option to automatically disable use of the server in future sessions. Any ideas how to get out of this? Thanks Jan -- -- Jan Abendr

[ccp4bb] ccp4i problem - bad marshal data

e advanced functions may not be available. Next time you start CCP4i it will try again to use the database server. If you wish to disable this behaviour then select the option to automatically disable use of the server in future sessions. Any ideas how to get out of this? Thanks Jan -- -- Jan Abendr

[ccp4bb] ccp4i problem - bad marshal data

e advanced functions may not be available. Next time you start CCP4i it will try again to use the database server. If you wish to disable this behaviour then select the option to automatically disable use of the server in future sessions. Any ideas how to get out of this? Thanks Jan -- -- Jan Abendr

Re: [ccp4bb] ccp4i problem - bad marshal data

ne 27, in ? from Handlers.Streams import Chatter ValueError: bad marshal data *ccp4* provides /usr/local/ccp4-6.1.1/Python-2.4.5/bin/python *centos5.3* runs python-2.4.3-24 Any ideas what happens there? Cheers Jan On Wed, Jun 3, 2009 at 3:31 AM, Ballard, CC (Charles) < charles.ball...@st

[ccp4bb] refmac twin operator problems

Dear all, I assume that the current versions (from 5.5.0072) take the input line twin operator parameters. However we are getting the Problem get_symm_from_text message whatever we do. What is the correct format here? We do for example twin operator h,-k,-l thanks Jan

[ccp4bb] LINKR in refmac

created with bond_lenth = 1.260 So, in my understanding it comes down to the question: how is a peptide bond referenced to in the dictionary? Any ideas are welcome! Thanks! Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home

[ccp4bb] LINKR in refmac

created with bond_lenth = 1.260 So, in my understanding it comes down to the question: how is a peptide bond referenced to in the dictionary? Any ideas are welcome! Thanks! Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home

[ccp4bb] Discussion workshop on Eukaryotic expression

provide a limited assistance with finding your hotel accommodation in Prague. Jan Dohnalek, Institute of Macromolecular Chemistry, Prague, Tel: +420 296809390 Ondrej Vanek, Institute of Microbiology, Prague Workshop organizers DiscussionWorkshoponEukaryoticExpression_Prague26Oct2009_preliminary.pdf

[ccp4bb] xds and cell refinement in cP

. When I reduce the symmetry to tetragonal and run an otherwise identical XDS.INP script, the cell parameters are refined again. Any ideas? Thanks a bunch Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

Re: [ccp4bb] xds and cell refinement in cI

t run INTEGRATE and CORRECT, the cell parameters won't refine any further, they stay right at the value given by XPARM.XDS. As Kay suggested, no cell parameter refinement in cubic (cI)? Cheers Jan On Oct 8, 2009, at 12:28 AM, Graeme Winter wrote: Hi Jan, Always worth a try is to proces

[ccp4bb] Discussion workshop on Eukaryotic Expression - last call

. Jan Dohnalek, Institute of Macromolecular Chemistry, Prague, Tel: +420 296809390 Ondrej Vanek, Institute of Microbiology, Prague Workshop organizers DiscussionWorkshoponEukaryoticExpression_Prague26Oct2009.pdf Description: Adobe PDF document

[ccp4bb] Crystallization of lysine and arginine rich proteins

Dear All, I have a question regarding the crystallization of lysine and arginine rich protein around 13%. So far our attempts to crystallize this protein have not been successful although the secondary structure predictions, CD spectroscopy measurements clearly show that this protein is folded. I

[ccp4bb] Special position refinement

Dear all, we have seen again with the 5.5.0102 version that water O or Fe ion are not held on the crystallographic axis automatically. What should we do except using possibly the restrain keyword? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of

Re: [ccp4bb] sulfur sad phasing

. ... has given us 2 structures for SSGCID during the past month... Cheers Jan On Nov 11, 2009, at 4:16 AM, Matthias Zebisch wrote: Dear bb! What is the optimal wavelength for Sulfur SAD phasing? Is it 1.9A or should one go below that to reduce absorption/damage. Also, would the same wavelength

[ccp4bb] mar345 version of generate_XDS.INP

Dear all, sorry for the slightly off-topic question: Does anyone have a modified version of generate_XDS.INP for the mar345 image plate detector? I know I could -relative easily- make it on my own, but why inventing the wheel twice? Regards, Jan -- Dr. Jan Gebauer AG Prof. Baumann

Re: [ccp4bb] mar345 version of generate_XDS.INP

t, to generate XDS.INPs automatically... It's very handy if you have datasets from multiple detectors. (here the wiki: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP) Best, Jan Am 21.06.2013, 10:23 Uhr, schrieb Jan Gebauer : Dear all, sorry for the sl

[ccp4bb] Superposition of electron density

, Jan

[ccp4bb] Molecular Replacement using low sequence identity templates

the crystals might be though.. Thanks for any tips and best regards, Jan

Re: [ccp4bb] Validity of Ion Sites in PDB

teach in my lectures). Therefore also an easy and uniformly reliable evaluation of ion sites in the PDB is not possible (too many details to be included in the analysis which are not part of the PDB record). In many cases though it is fairly easy to say "wrong ion". Jan Dohnalek IBT Prague

[ccp4bb] Acrimboldo BORGES standard libraries

$CCP4/bin/destination/BORGES_LIBS I selected 'edit set up file' while running 'ccp4sm'. Still, the standard libraries show in ccp4i remain greyed out, only CUSTOM is an option. The ccp4.setup-sh file does not seem to have a reference to BORGES. I wonder what I am missing to ge

Re: [ccp4bb] Unidentified electron density blob

e? For example HEPES has a group with sulphur, which might be seen in anomalous map. If you see anomalous peaks on sulphurs of your protein, it might not be that unreasonable even on 1.0A-ish wavelength. Best regards, Jan Dne 06.07.2018 v 16:02 Robbie Joosten napsal(a): I'd like to

Re: [ccp4bb] Last few months updates, updated coot, ccp4i2, imosflm, etc

Dear Charles, is there a plan to release new base package of CCP4 which would contain all updates, so we don't have to go through the already quite lengthy update process with new installations? Best regards, Jan On 07/05/2018 03:15 PM, Ballard, Charles (STFC,RAL,CSE) wrote: > For thos

Re: [ccp4bb] Can H-clashes be ignored ?

serious H-clash is checked, otherwise mostly not. Jan Dohnalek On Fri, Aug 17, 2018 at 6:27 PM Firdous Tarique wrote: > Hello everyone. > > I have a basic question. When a validation report of a coordinate is > generated we often come across a term known as "Too-Close Co

Re: [ccp4bb] 3D stereo and pymol

seems that 3d vision is not very supported by NVIDIA, even for gamers... Was anybody able to mke it work with Geforce cards, to save few bucks? Best regards, Jan Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a): > I answer a bit late, but I repost a message on 3D graphics from Mai > 2017 : >

Re: [ccp4bb] AW: [ccp4bb] 3D stereo and pymol

Awesome solution :-) I am sure, users will appreciate it. And I don't need stereo personally :-) Jan On 1/31/19 9:26 AM, Hughes, Jon wrote: > ...just open pymol, go to display - stereo mode - cross-eye then click > stereo. it might need a little practice and it makes one look even >

Re: [ccp4bb] 3D stereo and (pymol) Win 10

. I will let you know, once I know the results. Best regards, Jan On 2/1/19 3:19 PM, Pedro Matias wrote: > Hi all, > > Thanks Philippe, for the comprehensive discussion of the problem. > > I may also add that about 2 years ago I inquired our local DELL reseller > about laptops

Re: [ccp4bb] Fwd: [ccp4bb] SO4 or PO4

This can be done at Diamond I23 beamline. https://doi.org/10.1016/j.nimb.2016.12.005 Best regards, Jan Dne 16.02.2019 v 18:49 Patrick Loll napsal(a): > S has about 0.56 anomalous electrons at 8 keV, whereas P has about > 0.44. This is a small difference between two weak signals—unlik

[ccp4bb] Visualisation software supporting ChromaDepth

s from the viewer in Chimera -- I could write my own python script then... Thanks for all help, Jan Gebauer -- Dr. Jan Gebauer Structural Biologist px.uni-koeln.de / c2f.uni-koeln.de / pipc.uni-koeln.de To unsubscribe

Re: [ccp4bb] 3D

We have tried PS VR, and it works even with coot. It has some obvious drawbacks with toolbars, so it is not perfect for model building, unless you have good set of keybindings configured and perfect muscle memory. I could also imagine to configure a gamepad, but we are not there yet. Jan On 3/11

[ccp4bb] map rotation

molecule A and B (not a big deal), more importantly, it cuts of certain areas on both molecules. Molecule A and B have low RMSDs (0.5Å). I must be missing something fairly obvious, have not been able to see what. Feedback would be much appreciated. Scripts are below. Thanks! Jan mapmask \ mapin

Re: [ccp4bb] map rotation

. I guess I am missing something in maprot. Any input would be appreciated. This is public data, so I would be happy to share the data. Cheers, Jan On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth wrote: > Hi all, > this should be easy, scripting the rotation of a map. > Purpose for t

Re: [ccp4bb] map rotation

100 228 112 MODE to AVER rota euler 1 0 0 TRANS 0 0 0 end eof Cheers, Jan On Mon, Mar 25, 2019 at 3:49 AM Eleanor Dodson wrote: > Hmm - I find maprot extremely confusing, but remember a wrkmap does not > use any symmetry so maybe that is why some is lost. > > I woul

Re: [ccp4bb] A ccp4I2 question

I can comfirm, it is my favourite feature of i2. I would like to see it automated (or -able using CLI) for flawless backup recovery. Cheers, Jan On 16/04/2019 14:22, Christian Roth wrote: > yes one can > > Cheers > Christian > > On Tue, Apr 16, 2019 at 1:19

Re: [ccp4bb] Off-topic question

Hi, there is a guide here, but you should get the proper script for Pymol from the Consurf server. http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/consurf.php Jan On 6/22/19 10:24 PM, khaja faisal tarique wrote: > Hi everyone, > > I was wondering can anyon

[ccp4bb] Rescuing CCP4i2 projects after a loss of CCP4 installation

eems to expect compressed database files, which presumably needs to be exported. Unfortunately, I only have the folder structure left. Is there a way to do that? Best, Jan PS: I can easily import ccp4i (old) projects - but that's of no help for the new projects. -- Dr. Jan Gebauer

[ccp4bb] Postdoctoral position for XFEL crystallography/spectroscopy at Berkeley Lab

We are looking for a postdoctoral fellow to study metalloenzymes using X-ray crystallography and spectroscopy at X-ray free electron lasers. The fellow will work in the Kern/Yachandra/Yano group ( http://www2.lbl.gov/vkyachan/ and http://biosciences.lbl.gov/profiles/jan-florian-kern/) at Berkeley

Re: [ccp4bb] SCRIPT FOR RUNNING MULTIPLE RUNS OF SHELX C DE FOR RIP

See both scripts enclosed, at least for inspiring. Best regards Jan -- Původní zpráva -- Od: Arka Chakraborty Komu: CCP4BB@JISCMAIL.AC.UK Datum: 28. 7. 2014 14:19:08 Předmět: Re: [ccp4bb] SCRIPT FOR RUNNING MULTIPLE RUNS OF SHELX C DE FOR RIP " Dear Dr. Tim Gruene,

[ccp4bb] Position of a manager of central laboratories

nswer your questions via email. Jan Dohnalek Guarantor of CMS, Biocev Coordinator of Central facilities -- Jan Dohnalek, Ph.D Institute of Biotechnology Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 2

[ccp4bb] Postdoctoral Position in Structural Biology of Chromatin Regulators in Grenoble

Postdoctoral Position in Structural Biology of Chromatin Regulators in Grenoble A 2-year post-doctoral position is available in the newly established group of Jan Kadlec at the Institut de Biologie Structurale (IBS) in Grenoble, France to study the structure and function of chromatin

[ccp4bb] Privateer fails to run

Dear all, I am experiencing some troubles with running Privateer. It seems to fail to read a PDB file. The Error message: Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb :3 terminate called after throwing an instance of 'clipper::Message_fatal' Aborted Any ideas? Best regards, Jan

Re: [ccp4bb] Privateer fails to run

Dear Jon, yes indeed, as it was figured out with Eugene, it is my case. The problem was PDB ID in the header, which was putted there by refmac5. Removing or changing to PDB ID 1XXX solves the problem. Thank you both for help. Best regards Jan Dne 12. 1. 2015 v 17:28 Jon Agirre napsal

[ccp4bb] Postdoctoral Position in Structural Biology of Chromatin Regulators in Grenoble

Postdoctoral Position in Structural Biology of Chromatin Regulators in Grenoble A 2-year post-doctoral position is available in the newly established group of Jan Kadlec at the Institut de Biologie Structurale (IBS) in Grenoble, France to study the structure and function of chromatin

Re: [ccp4bb] PAD images

Some software enables overlay of a batch of images so that you simulate the classical crude phi slicing and get visible patterns. I think we tried with d*Trek. Jan On Tue, Apr 28, 2015 at 9:20 AM, Graeme Winter wrote: > Looking at PAD images is something we have had to get used to at Diam

Re: [ccp4bb] Instrument help: any comments on bench-top SPR

e the peptides to the sensors. More sensitive and more convenient are the higher priced machines (K2), however as their price tag is in the range of an SPR, I would buy them only if I need some screening capabilities. Best, Jan PS: I have no relations to fortebio, other than that we own one..

[ccp4bb] Aimless on MS Windows?

Regards, 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] Phaser Fatal runtime error.

Data from Crysalis in mtz format are not merged I think - you have to go through the scale and merge step in Scala first ... Jan Dohnalek On Tue, Jun 26, 2012 at 11:21 PM, Steiner, Roberto < roberto.stei...@kcl.ac.uk> wrote: > Don't know where the exact problem is. However, it

Re: [ccp4bb] Large unit cell, overlaps

most valuable in several cases. Good luck. 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 Jul 16, 2012, at 8:28 PM, Jason Busby wrote: > Hi,

[ccp4bb] refmac5, SIGF/SIGIMEAN labels

, while Refmac 5.7.0029 outputs F/SIGIMEAN, see mtzdmp output below. Any ideas? Cheers, Jan CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11 Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. Low

[ccp4bb] Phaser and space groups

the two lines mentioned above with SPACEGROUP P41 This is a bit inconvenient though. Any ideas what is going wrong with the standard way? Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com

Re: [ccp4bb] is it valid to compare the B factors of corresponding domains or regions of molecules from different crystal structures

I think that a simple and straight answer is NO. Individual crystal structures compensate for various and differing factors by their individual Bs. Jan D. IMC Prague On Fri, Aug 24, 2012 at 8:29 PM, Michael Murphy wrote: > I am looking to compare the B-factors of a particular stretch of

Re: [ccp4bb] Tricky MR problem

h the great software packages available nowadays, you can have an initial structure within minutes after finishing the data set. For a recent review of this old technique see here: http://www.ncbi.nlm.nih.gov/pubmed/21359836 Best wishes, Jan -- Jan Abendroth Emerald BioStructures / SSGCID Se

Re: [ccp4bb] Strange diffraction image

Could be an organic crystal - what's the resoution of the lowest order reflections? Jan D. On Fri, Oct 12, 2012 at 8:11 AM, Chang Qing wrote: > Hi, everyone: > > I just got some strange diffraction images from crystals with > triangular pyramid shape. I think this shou

Re: [ccp4bb] On maps and doubts

Have you got two very similar datasets (isomorphous) inbetween which the mentioned difference should be pronounced? You could try a cross-crystal difference map as well. Jan On Fri, Oct 5, 2012 at 8:40 AM, wrote: > ** > Dear Israel, > > I wonder why you do not see anything in you

Re: [ccp4bb] Open position - data management in biophysics

On Fri, Jan 22, 2021 at 10:54 AM Pearce, N.M. (Nick) wrote: > Academia, one of the only careers where _success_ is rewarded with > perpetual impending employment every two+ years. > > Which translates "If you do your work well, you will get more .." Jan > Nick >

Re: [ccp4bb] Open position - data management in biophysics

r 10 years ..." Fineprint - assuming nobody asks for reports, further applications, silly record tables, appraisal documents, in that period .. Back to real world. Jan On Fri, Jan 22, 2021 at 11:49 AM Pearce, N.M. (Nick) wrote: > "If you do your work well, you will get more ..”

[ccp4bb] postdoctoral position in cryo-EM at LMB in Jan Löwe's group

here: https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-studies-dr-jan-lowe-lmb-1485-medical-research-council-laboratory-of-molecular-biology-736334 <https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-studies-dr-jan-lowe-lmb-1485-medical-resea

[ccp4bb] Joint webinar of Centre of Molecular Structure and Excillum - 28th April

-capabilities-at-cms/ Best regards, Jan Stransky P.S. You can now follow news from Centre of Molecular Structure at Twitter, @CmsIbt (https://twitter.com/CmsIbt) -- Jan Stránský, PhD. Institute of Biotechnology, AS CR Centre of Molecular Structure Průmyslová 595 252 50 Vestec Czech Republic Email

Re: [ccp4bb] off-topic: structural motif / domain comparison

Like PDBeFOLD search? https://www.ebi.ac.uk/msd-srv/ssm/ Jan On Fri, Aug 6, 2021 at 8:43 AM Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain ju

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

This is good to know indeed. Will improve my teaching now, I also did not know this is now done automatically. Thanks for pointing it out. Jan On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear Eleanor, > > Thanks for pointing out that

[ccp4bb] LMB Kendrew Lecture on AlphaFold

With best wishes, Jan To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a m

[ccp4bb] Computational modeling job opportunities in the Kosinski lab at EMBL Hamburg

s of the job opportunities <https://www.embl.org/groups/kosinski/open-positions/>. We offer access to superb computational infrastructure, experimental data from electron microscopy and other techniques, competitive salaries, and excellent working conditions. Best regards, Jan Kosinski -- Gr

Re: [ccp4bb] Validation of structure prediction

density is actually not that appropriate. The only "improvement" to this I think is the multiple model approach. My 2 c. Jan On Sat, Jan 15, 2022 at 9:29 PM James Holton wrote: > > On 1/13/2022 11:14 AM, Tristan Croll wrote: > > (please don’t actually do this) > >

[ccp4bb] Survey on Data Standards and Databases in Molecular Biophysics

e your answers The survey will close on 4 March 2022 *Feel free to contact us at mosbri-d...@ibt.cas.cz * Jan Dohnálek & Jan Stránský for the team of Standards for data archiving & exploitation MOSBRI -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech R

Re: [ccp4bb] PDB deposition of structure solved with a Robetta model

that might select domains from various sources, etc. Cheers, Jan On Mon, Feb 7, 2022 at 5:24 AM Loll, Bernhard wrote: > Dear all, > > I have recently solved a structure by molecular replacement with a > search model calculated by the Robetta server. > > I am in the process to deposi

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