[ccp4bb] On the rotamer of Arg

Dear All, I have a set of data, in which there are  very nice electron density for several Arg residues. However MolProbity analysis demonstrated that the percentage of the Arg rotamer in my data is 0%. Although there is the possibility that the Arg rotamer in my data is 0%, I still wonder is an

[ccp4bb] Hydrogen adding and real space refinement

Dear All, I find when I add H in the PDB file, in a refinement by Phenix, there is no real space refinement step (rsrl). If I do not add H in the PDB file, there is the rsrl step in the refinement. Somebody told me it was because there was a bug in the Phenix I downloaded, somebody told me if H

Re: [ccp4bb] Peptide flips in electron density?

It looks like I'm seeing density for both conformations I just wasn't sure how to build both in Coot. (Or in another program if necessary.) On Thu, Feb 12, 2015 at 3:18 PM, Dale Tronrud wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > >I'm a little confused. If you see from the

[ccp4bb] Postdoc Position in Multi-targeting of aminoacyl tRNA synthetases: a paradigm shift in combatting AMR.

>> Dear Colleagues >> >> Multi-targeting of aminoacyl tRNA synthetases: a paradigm shift in >> combatting AMR. >> Applications are invited for an enthusiastic postdoctoral research scientist >> to join a research group at the School of Life Sciences, University of >> Warwick supervised by a te

Re: [ccp4bb] how to switch on probe clashes (disabled in coot)

On 11/02/15 20:19, sreetama das wrote: Dear Users, The option "Validate>Probe > clashes" is disabled in coot (version 0.8/CCP4-6.5, OS - ubuntu 12.04). How can this be enabled? Can I toggle between 'enable' and 'disable' according to need? The menu items will be enabled when you tell coot w

Re: [ccp4bb] Peptide flips in electron density?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I'm a little confused. If you see from the density that a peptide flip is required, can't you just fix it? Or is it the case that the density is telling you that both conformations are present? In that case build alternative conformations and re

[ccp4bb] Peptide flips in electron density?

Hello all, I am in some of the final stages of refinement of a 1.5 A resolution oligomeric protein and I'm noticing what appears to be extra density corresponding to a carbonyl peptide flip near the N-terminus of one of the chains. I was wondering if anyone had any experience with this before and

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 1, 2015 is approaching

Next MX-proposal application deadline: March 1, 2015 is approaching BAG proposal applications are now possible Single 8h-shift beamtime bookings are now possible We kindly invite new MX-proposals for beamtime applications for the next beamtime period. In order to apply for beamtime, please regist

Re: [ccp4bb] Superposition of select residues

Hi Yanfeng, You need to supply the two imol numbers in the apply_lsq_matches() function (defined in WinCoot\share\coot\python\coot_lsq.py). For example: clear_lsq_matches() add_lsq_match(12,18,"B",12,18,"D",2)#match-type is 0 for all-atom, 1 for mainchain and 2 for CAs add_lsq_match

Re: [ccp4bb] off topic pymol

Dear all, thank you very much for all your suggestions. The one that worked for me was Sam's actually. Indeed in that column I had As, then nothing, then also Ds, and Vs or some other letters... I don't know. I just removed the whole column and now when I open it in pymol it looks good! Super tha

[ccp4bb] Twilight 2014 update

Dear All, Chris Weichenberger just released the 2014 update for TWILIGHT. It is available from my web site http://www.ruppweb.org/twilight/default.htm http://journals.iucr.org/d/issues/2013/02/00/issconts.html http://journals.iucr.org/f/issues/2013/02/00/issconts.html Please note: The

[ccp4bb] Postdoc position in Structural Characterization of a membrane-associated enzyme

Postdoc position in Structural Characterization of a membrane-associated enzyme Lookingfor an outstanding and highly motivatedindividual to start immediately in a postdoctoral position to study structureand mechanism of a membrane-associated enzyme involved in co-translationalmodification. The p

Re: [ccp4bb] Collecting Spread-Out Molecules

That what PISA will do for you - make a sensible assembly Eleanor On 12 February 2015 at 05:02, Kevin Jude wrote: > In coot: > Extensions>Modelling>Symm Shift Reference Chain Here > > Quick, but not automatic. > > On Wed, Feb 11, 2015 at 7:07 PM, Keller, Jacob > wrote: > >> Dear Crystallographe

[ccp4bb] Post-doctoral position in GPCR crystallography

Dear All, Several post-doctoral positions are available in the Laboratory of GPCR Biology in the Department of Biological Sciences and Bioengineering at the Indian Institute of Technology in Kanpur, India. The positions are funded by the Wellcome Trust - DBT India Alliance for a period of up to fi