Re: [ccp4bb] DipCheck Webservice

as a matter of interest - which conformations differ? Eleanor On 4 September 2017 at 16:29, Victor Lamzin wrote: > > Dear Ameya, > > DipCheck uses a novel 3-dimensional parameter space for validation of the > backbone geometry, and we hope that it can be more informative than some of > the exist

[ccp4bb] Postdoc positions in cryo-ET and single particle cryo-EM

Dear colleagues, I would like to draw your attention to the following job opportunities. Best Stefan PostDoc Positions in Electron Microscopy at Max Planck Institute of Molecular Physiology The positions are available immediately in the Department of Structural Biochemistry (Director: Stefan Rau

Re: [ccp4bb] maltodextrins on superdex columns?

Hi, Sebastiano, I 've never heard about issues with purification of carbohydrates or glycoproteins of this type of sorbent. But I would recommend to perform analytical purification to evaluate your product yield. We usually add 150 mM NaCl to avoin non-specific binding. 2017-09-04 17:41 GMT+03:00

[ccp4bb] Reminder - Sep 15 deadline: 2 Postdoctoral Fellowships in Structural Biology and Drug Development at NCMM, University of Oslo

Postdoctoral Fellowships in Structural Biology and Drug Development Two postdoctoral positions (three years) are available in the Group of Structural Biology and Drug Development (Luecke group, hu...@ncmm.uio.no) at the Nordic Centre for Molecular Medicine (NCMM), the

Re: [ccp4bb] DipCheck Webservice

Dear Ameya, DipCheck uses a novel 3-dimensional parameter space for validation of the backbone geometry, and we hope that it can be more informative than some of the existing validation approaches. We also hope that DipCheck can be a good validation tool as its inverse task does not seem to b

Re: [ccp4bb] DipCheck Webservice

Dear Victor, I used the server. However I found that the % of residues in disallowed region given by your server and PDB validation server differs. What could be the probable reason? regards, Ameya On Mon, Sep 4, 2017 at 8:12 PM, Victor Lamzin wrote: > > Dear Colleagues, > > We announce the Di

[ccp4bb] DipCheck Webservice

Dear Colleagues, We announce the DipCheck Webservice for validation of backbone geometry in protein structures as described in: https://doi.org/10.1107/S2052252517008466 The Webservice is available at: http://cluster.embl-hamburg.de/dipcheck Joana Pereira, Umut Oezugurel, Philipp Heuser and

[ccp4bb] maltodextrins on superdex columns?

Hi all, a group in the department here has a sample with high amount of maltodextrins (~40 mg/ml) that they would like to load on a superdex column. Anyone has advices on whether this is doable / not recommendable / absolutely to avoid? So far, I have just found that people are separating dextra

Re: [ccp4bb] Fix sidechain outliers

Fitmunk works pretty well in the initial stages of model fitting. You will still need to manually check the results of any automated model fitting program to see if it makes sense; your brain is still your best tool, in the final analysis. Diana > On Sep 4, 2017, at 1:29 PM, Dominika Borek wr

[ccp4bb] Risk assessment for heavy atom soaking - examples?

Hi all, (This email is aimed primarily at my UK colleagues, but feel free to read on and gloat that you don't have to write safety forms in your lab/country!). I need to sort out written risk assessments for heavy atom soaking of crystals in my lab. I wondered whether anyone would be willing to s

Re: [ccp4bb] Fix sidechain outliers

Hello Rohit, did you inspect the structure and map in Coot ; are the outliers really outliers, are other orientations possible? In Coot there are several options, e.g. - under Extensions -> all molecule-> Fit protein, step refine or optimize Ramachandran - using the icons on the right side of

Re: [ccp4bb] Fix sidechain outliers

You may try Fitmunk for side chains: http://kniahini.med.virginia.edu/fitmunk/server/ D. On 2017-09-04 09:36 AM, rohit kumar wrote: Dear All, Could anyone help me, how I can fix my sidechain outliers or clashscore in coot or in CCP4 tools. Or by using any online severs. Its urgent Thank You

[ccp4bb] Fix sidechain outliers

Dear All, Could anyone help me, how I can fix my sidechain outliers or clashscore in coot or in CCP4 tools. Or by using any online severs. Its urgent Thank You in advance -- WITH REGARDS Dr. Rohit Kumar Singh School of Life Sciences, Jawaharlal Nehru University New Delhi -110067