[ccp4bb] Vacancy at Evotec UK (Abingdon)

Dear All, There is an opportunity to join the Structural Biology team at Evotec based in the UK as a Senior Scientist (Protein purification). Please see the advert in the link below. Interested candidates should apply directly through our website. Please do not send applications through to me d

[ccp4bb] Crystallographer position at Evotec

applications through to me directly. Closing date is June 30th and applicants must be eligible to work in UK. https://recruitment.evotec.com/VacancyDetails.aspx?FromSearch=True&MenuID=QSAukis1tlc=&VacancyID=646 Kind regards, Matthias Zebisch STATEMENT OF CONFIDENTIALITY. This e

Re: [ccp4bb] Anisotropic diffraction

- Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk

Re: [ccp4bb] merging anisotropic datasets

- Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk

Re: [ccp4bb] ATP library file in REFMAC

Cant you edit the ATP.cif on your computer to have the correct expected bond length? Best, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

Re: [ccp4bb] double bonds in oleoyl-CoA

value. Be careful that you edit the correct bond. Your numbering might be different. Are you sure that there is no cif file for your ligand already existing? Best, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human

Re: [ccp4bb] SO4 geometry

, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strub

Re: [ccp4bb] large domain motion and calculation of flip flop angle

As usual, I'd recommend the program Dyndom which is available from CCP4i. This will identify domain borders + hinge regions as well. Best, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Unive

[ccp4bb] pymol multiple transparent surfaces

my object in the back drawn? Thanks a lot, Matthias -- - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865

[ccp4bb]

Dear Avinash, in addition to Eleanors suggestion you might want to consider using Dyndom in CCP4 or via its web server. It will also identify hinge regions and percent twist motion vs. closure motion. Best, Matthias - Dr. Matthias Zebisch Division of

Re: [ccp4bb] cryoprotection condition

Hi Rana, you are almost there. For the first one I'd add (if at all) 5% PEG200 and for the second I'd mix in 10% PEG200. Only very big crystals might need even more cryoprotectant. Best, Matthias - Dr. Matthias Zebisch Division of Structur

Re: [ccp4bb] seeding, reproducibility

Dear Mahesh, cross-seeding into other conditions often works but still the chances are much lower than seeding the same form. Best wishes, Matthias (Please desist from sending so large attachments to half the planet!) - Dr. Matthias Zebisch Division

Re: [ccp4bb] Best compounds for heavy atom soaks

free cysteines? - pCMB phosphate-binding? - tungstate Best, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax

[ccp4bb] Membrane protein structures from mammalian expression

- Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk -

Re: [ccp4bb] Fwd: undefined edensity blob at glutamine sidechain

check an anomalous map! The obvious thing to do to rule out gold binding - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549

Re: [ccp4bb] the f' and f'' of heavy cluster

Dear Lisa, if you have proper anomalous data I rather recommend using the Phaser SAD pipeline and specify cluster search. Worked instantly for me. Good luck! - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human

Re: [ccp4bb] off topic

eparations serve as nucleation points. Well done, shoot'em! Matthias ----- Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549;

Re: [ccp4bb] High Rsyms between 5-7 A

- Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk

Re: [ccp4bb] Off Topic- DNA length

. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk

Re: [ccp4bb] visualizing G310 helices in PYMOL

this helps, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk We

Re: [ccp4bb] Low 280 absorbance imidazole?

Hi everybody, I would just like to contribute that absorption at 280 results from methylated imidazole, a contamination hard to get rid of. Imidazole itself does not absorb at 280. Bye, Matthias - Dr. Matthias Zebisch Division of Structural Biology

Re: [ccp4bb] Where to cut the data in this medium resolution dataset

se. bye, Matthias ----- Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http:/

Re: [ccp4bb] laboratory phage infection [SEC=UNCLASSIFIED]

Dear Aidong, we never had that problem but I heard that only long dry(!) heat treatment of glassware destroys the phages. No need to say that you have to do it with ALL your glassware. Good luck, Matthias - Dr. Matthias Zebisch Division of Structural

Re: [ccp4bb] Superpose, SSM

doing something wacky with files in certain cases...why don't you get the excellent text editor NoteTab Light [sic] (I use it all the time--free and works great), then take a look at your files and see whether MS notepad altered the files. JPK On Mon, Sep 26, 2011 at 2:42 PM, Matthias Zebis

[ccp4bb] Superpose, SSM

Dear CCP4 users, I am using the ccp4i version 6.2.0 under windows 7. I've come across a problem with superpose. The outputfile appears to have additional line feeds (see picture) which, however are not seen in the windows notepad. The structure can also be opened in coot and pymol. However, it

Re: [ccp4bb] large R-Rfree difference in "final" structure

Hi Careina, in our lab we once had the problem, that the asymmetric unit contained 8 molecules, whereas 7 had only been modeled. Somehow the 8th monomer had evaded detection. So be careful not to miss density. Matthias On 7/13/2011 7:54 PM, Robbie Joosten wrote: Hi Careina, Assuming you

Re: [ccp4bb] Question about movie making

PNG files on windows? What is your experience with quality of product and especially with user friendliness? If you have any insight, we would appreciate your comments. Thanks! Mark van der Woerd Colorado State University -- **** Dr. Matthias

Re: [ccp4bb] A quick question - monomer lib cif

-- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi

Re: [ccp4bb] sketcher

****** Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de

[ccp4bb] CCP4

****** Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de

[ccp4bb] Anisotropic Diffraction Examples

along good and bad directions as well? Thank you a lot, Matthias -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97

Re: [ccp4bb] TCEP effect on protein

thanks and regards -- -- **** Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de

[ccp4bb] sulfur sad phasing

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 be appropriate to maximize anomalous scattering to position chlorides, calcium, sulfate in already phased structures? Thanks in a

[ccp4bb] Problem with TLS

Dear BB! I have a strange problem with TLS refinement and refmac. In my AU there are 4 monomers of the same protein. Based on structural subdomains I defined 3 TLS groups for each of those monomers so that the overall TLS group number is 12. When I do TLS and restrained refinement from the GUI u

[ccp4bb] statistics

Dear everybody! I recently tried out the anisotropy server at http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/ I also see that there is much discussion going on about the correctness of this method. In any case, does anyone know a tool that gives me the datacollection statistics that I normally

Re: [ccp4bb] Alignment of Electron Density Map for structures that have different space groups

Dear Milya! I had this problem before to. This was showing active site ligands from the same view (i.e. after superposition of totally diffeent crystals). You can use the superposition matrix fom your PDB superposition and apply it using the program MAPROT in the "INVERT" mode and using "SYMMET