[ccp4bb] Research Scientist / Postdoc Position at the Gene Center, University of Munich

Dear CCP4ers, on behalf of Patrick Cramer, I would like to draw your attention to the following open position at the Gene Center, University of Munich. Please, do not reply directly to me, but to the e-mail addresses given at the end of this job offer. Best regards, Dirk Kostrewa. --- App

[ccp4bb] problem with residue numbering and Coot

Hi folks, I'm having a problem with Coot. Molecular Replacement solution to the phase problem. The MR model has one small stretch of residues missing, for which there is density in the maps (both normal and difference density maps). Hence I have built the model into this density. Except that

Re: [ccp4bb] problem with residue numbering and Coot

You can renumber the residues within COOT. Calculate > Renumber Residue Input the residue numbers you wish to change, then by how many you want to offset the sequence. I do not believe you should stick with 'standard numbering schemes'. It would probably be best (and make your refinement's easier

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

Dear all, I do have a question about comparing Rfree and Rwork factors of different refinement trials whereas I always started with the same pdb file and structure factors (phasing by MR). Means I had a protein structure which was (not just by me) refined several times in different ways also wi

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

Dear Jan, an initial increase in Rfree usually means, that either, in case of isomorphous crystal forms, the structure was refined before against a different test set, or, in case of completely different crystal forms, that you have a new test set. In both cases, Rwork and Rfree for the initi

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

Dear Jan, It is hard to compare refinement results from different refinemnt procedures because not all the information you need is stored in the output PDB file. I agree with Dirk that you just have to 'pick your own standard'. Provided all you models are the output of a converged refinemen

[ccp4bb] Alternate configurations blow-up in refmac

Dear all, We recently jump from a local version of ccp4 using Refmac_5.2.0019 to an up-to-date version of ccp4 distributed by sbgrid using Refmac_5.2.0102. From then, refinements with alternate configurations are blowing-up in refmac. A similar problem was solved thanks to ccp4bb ('Refmac dictiona

Re: [ccp4bb] 24-well sitting-drop plates

Jacob There is the MRC Maxi, and also XtalQuest plate, both with 48 wells. Less confusing for filling by hand than 96 wells -- For information and discussion about protein crystallization and automation, please join our bulletin board at http://groups-beta.google.com/group/oryx_group?hl=en pa

Re: [ccp4bb] 24-well sitting-drop plates

We have had dozens of boxes of XtalQuest 42-2 plates sitting on the shelf for three years and I've just been told we've only sold three boxes so far We'll accept any reasonable offers! > -Original Message- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Patrick

[ccp4bb] EMBO Practical Course - PEPC7

EMBO Practical Course - PEPC7 Protein Expression, Purification and Crystallisation EMBL Hamburg, Germany Monday 23 August - Tuesday 31 August 2010 The course, intended for students in the early stages of their research career, will cover over-expression of proteins in prokaryotic and eukaryo

[ccp4bb] [offtopic] shipping dewars : "Because, I like my Skechers, but I love my Prada backpack." [/offtopic]

I like the fact that MVE's plastic shipping cases have a round top, so Fedex can't ship the container upside down. However, I like Taylor-Wharton's wide mouth 91mm (CXR100) vs MVE's 70mm(SC 4/2V). Unfortunately Taylor-Wharton's recommended shippers are square and could be sent upside down.

Re: [ccp4bb] problem with residue numbering and Coot

Dear All, I have received the following suggestion from a crystallographer. The bottom part of the email was indicating that the mail was confidential, so I have removed the name of the author of that email (together with this section about confidentiality) and I am therefore forwarding the m

Re: [ccp4bb] 3D fitting

would ssm serve your purpose? eleanor ebi or ccp4i Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both f

[ccp4bb] Postdoctoral positions in fragment-based drug discovery projects

A number of post-doctoral positions are available in the group of Marko Hyvonen, at the Department of Biochemistry, University of Cambridge. These positions are in multidisciplinary projects aimed at developing novel therapeutic agents and chemical tools against protein-protein interactions in

[ccp4bb] Refmac ligand refinement question

Dear all, I am refining a structure of a protein in a complex with phosphorylated ligand (inositol ring). My problem is that after restrained refinement with Refmac, the ring is distorted in geometrically impossible ways. Could anybody advise me on how to deal with this problem? Ideally, I would

[ccp4bb] Sketcher and Bonds

Hi, I'm using Sketcher to create the following: C=C C=C / \ / \ C CC The problem is that I can't figure out how to keep the carbons cis. I see the "Add Row" button in Sketcher and I can specify the "Sign." There are also spaces to fill in "B/3" F/4" "1/5

[ccp4bb] units of f0, f', f''

Dear all, I just stumbled across the question about what is the unit of f' and f''. The first couple of hits from ixquick.com claim it was e^-. Since e^- is not a unit but symbolises an elemtary particle (of which fractions are considered non-existent), I was wondering whether the unit of f, f',