Re: [ccp4bb] Unknown electron density blob

PEG likes to hang around where it is unwelcome: http://onlinelibrary.wiley.com/doi/10.1002/pro.2923/full Cheers, Robbie Sent from my Windows 10 phone Van: Bernhard Rupp Verzonden: dinsdag 24 januari 2017 23:20 Aan:

Re: [ccp4bb] Bad density for chains

Hi Pooja, Are you positive you have the correct space group and there are no other issues like twinning, etc? If sure, did you define NCS groups in refinement? TLS refinement? Try different refinement programs? How big is the molecule? Was it solved by MR or experimental phasing? You can try

[ccp4bb] Bad density for chains

Dear All, I have a 2.6 A resolution structure having four chains in an asymmetric unit. The chain A and B have density for almost all residues however we don't have proper residue density in chain C and D.What can be tried to build chain C and D ? Many Thanks Pooja

Re: [ccp4bb] add ligand solution onto drop directly

The truth is in the map. Ergo, zap it and rationalize why it worked or not later. Cheers, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Markus Heckmann Sent: Tuesday, January 24, 2017 6:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] add ligand solution onto

[ccp4bb] add ligand solution onto drop directly

Dear all, I wondered if it is OK to pipette ligand soln (X-CoA) *directly* to the drop with crystal (1:1 ratio of protein:precipitant 2µl) instead of dissolving it in precipitant solution and transferring the crystal to this ligand containing precipitant solution. The crystals survive this as I

Re: [ccp4bb] SHELXL refinement with TYR on special position

Dear Francis, You need to put the atoms starting with CG into PART -1 to prevent them clashing, and reset the occupancies to 10.5 (i.e. fixed at 0.5). There must be another disorder component pointing somewhere else (also with half occupancy). SHELXPRO has been made obsolete by Anna

Re: [ccp4bb] Unknown electron density blob

Some general remarks about PEG modelling and associated caveats: http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html Section 3.6.5. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ana Luísa Moreira de Carvalho Sent: Tuesday, January 24, 2017

[ccp4bb] SHELXL refinement with TYR on special position

Hi all I'm trying to refine a structure with a tyrosine sitting on a special position , or maybe it's some disorder.. or Suggestions? https://i.imgsafe.org/7cfbf83a38.jpg Using just FLAT, CHIV,DFIX, and DANG from shelxpro doesn't work. Thanks, Francis

Re: [ccp4bb] Unknown electron density blob

Just to add to this, in our group, we had a funny case where we found PEG around K: https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc Ana Luisa > On 24 Jan 2017, at 17:36, Artem Evdokimov

Re: [ccp4bb] Unknown electron density blob

Hi there, I think it is PEG, very common to have PEG in horseshoe shape with arginine pointing toward to it. Cheers, Mirella Vivoli Mirella Associate Research Fellow Biocatalysis Centre, Henry Wellcome Building College of Life and Environmental Sciences, University of Exeter Stocker Road

Re: [ccp4bb] Unknown electron density blob

PEG. It wraps around K or R residues just like you are showing. Artem www.harkerbio.com "where every blob has candy inside" On Jan 24, 2017 12:19 PM, "Uma Gabale" < 0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all, > While refining a structure at 2.5 A resolution, we observed a

Re: [ccp4bb] Unknown electron density blob

Hi Uma, It is risky to guess based on one-view of of the density from 2-dimensional images. What is the contour-level of 2mFo-DFc (blue) map displayed here?!! If 2mFo-DFc density is continuous from Arg, say at 0.8 sigma, then could it be an alternate conformation of the Arg side-chain. One could

[ccp4bb] 2 year PDRA position in University of Liverpool UK

THE UNIVERSITY OF LIVERPOOL FACULTY OF HEALTH AND LIFE SCIENCES INSTITUTE OF INTEGRATIVE BIOLOGY DEPARTMENT OF BIOCHEMISTRY POSTDOCTORAL RESEARCH ASSOCIATE GRADE 7 £32,958 - £34,956 pa An exciting opportunity has emerged in the Molecular Biophysics group to

Re: [ccp4bb] Unknown electron density blob

On 24/01/2017 17:32, Paul Emsley wrote: On 24/01/2017 17:19, Uma Gabale wrote: While refining a structure at 2.5 A resolution, we observed a semi-circular/crescent shaped electron density blob as shown in the attached picture. We have been unable to identify it so far, and would appreciate

Re: [ccp4bb] Unknown electron density blob

On 24/01/2017 17:19, Uma Gabale wrote: While refining a structure at 2.5 A resolution, we observed a semi-circular/crescent shaped electron density blob as shown in the attached picture. We have been unable to identify it so far, and would appreciate any help in identification. If you have

Re: [ccp4bb] Unknown electron density blob

Hi, Could it be a segment of peg3350?   Cheers,               Boaz     Boaz Shaanan, Ph.D. Dept. of Life Sciences  Ben-Gurion University of the Negev  Beer-Sheva 84105  

Re: [ccp4bb] rigid flexible analysis

Hi, can't you infer this from refined atomic displacement parameters (ADPs; also knowns as B-factors)? Or run a 100 or so SA refinement jobs, each starting with a different random seed. This will generate an ensemble of models with some atoms occupying more conserved positions than the others.

Re: [ccp4bb] Modelling of ligand and Refmac5

Dear Dr Emsley Many thanks for your reply. I have now updated my Coot and am able to run refmac refinement using my ligand PDB and CIF generated from elbow2 under Phenix. This is indeed a lesson on the importance of keeping all softwares updated! Kind regards Sam On 24 January 2017 at 18:29,

[ccp4bb] rigid flexible analysis

Hi everyone! I would like to know the current online servers available for analyzing the rigid and flexible regions of proteins.Looking forward for precious inputs from the community. Sincerely, Dr. Gauri Misra Assistant Professor Amity Institute of Biotechnology Amity University Noida (U.P.)

[ccp4bb] Postdoctoral Research Scientist in Division of Structural Biology, University of Oxford

Dear All, Post-doc positions are available in the laboratory of Dr Jon Grimes, in the Division of Structural Biology (STRUBI) in the Nuffield Department of Clinical Medicine at the University of Oxford. Dr Grimes's group incorporates structural biology and multidisciplinary

Re: [ccp4bb] Modelling of ligand and Refmac5

On 24/01/2017 08:04, Sam Tang wrote: I am trying to fit a small molecule ligand into a protein complex using Coot. The data was processed to P212121, at 2.6 A. What I did was to input a SMILES string, fit the ligand, merge the ligand into the protein molecule using 'Merge Molecules' and save

[ccp4bb]

Dear Colleagues  A reminder: applications close on 31 Jan 2017.  Dear colleagues, Applications are open for a cryo-electron microscopy scientist at the Francis Crick Institute in London to work in the Structural Biology Science Technology Platform.  We are looking for a motivated, skilled

[ccp4bb] Tenure Track Research Group Leader Position “Cryo-Electron Microscopy of Membrane Protein Complexes”

Dear ccp4 community, I just would like to call your attention about this opening at the Martin-Luther-University Halle-Wittenberg, Germany. Further information can be found in the attached PDF. Kind regards, Christoph HALOmem_8p138x255_09-01-17_s1.pdf Description: Adobe PDF document

[ccp4bb] Modelling of ligand and Refmac5

Dear all I am trying to fit a small molecule ligand into a protein complex using Coot. The data was processed to P212121, at 2.6 A. What I did was to input a SMILES string, fit the ligand, merge the ligand into the protein molecule using 'Merge Molecules' and save coordinates. After fitting the