[ccp4bb] modelling in coot

Dear Community, I had a problem in correcting cis and tran peptide of structure in coot. how i can resolve it. -- Regards, Smita Yadav Ph.D JRF Regional Centre for biotechnology, Haryana-121001. To

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

THE PROBLEM IS SOLVED! Thank you all for you suggestions. I applied all the suggestion across all datasets collected (not just the one shown above). The error & solution: Incorrect space group assignment (new space group P 21 2 21) and ignoring tNCS. This is the BEST Christmas gift a

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

Hello, I would guess that the badly fitting molecule may be upside down (related my an 2-fold axis). I would use the first, partially refined structure for another round of molecular replacement in P212121 with molrep, using the model as well as a partial solution as as asearch model. The

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

Hi Jessica You may try the following (if you haven't already): 1. Try solving it using P222 space group. 2. Re-index using different axes. *Regards* *Adarsh Kumar* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Mon, Dec 16, 2019 at 2:30 PM Jessica Besaw

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

There have been two potential space groups: P212121 - Rfree = 36% P21212 - Rfree = 45% Xtriage reports that twinning is unlikely. Cheers! Jessica On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch wrote: > What’s your spacegroup ? RWork / RFree? > > Twinning by any chance? > > Jürgen > >

Re: [ccp4bb] Problem with structural alignment

Dear Ishan Would it be possible for you to use a fitting of the atoms of the ligand? I've done that with success before. Hope this helps Folmer man. 16. dec. 2019 07.38 skrev Ishan Rathore : > Hi, > > I am trying to compare multiple homologous structures of a protein, where > I am analysing

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

What’s your spacegroup ? RWork / RFree? Twinning by any chance? Jürgen __ Jürgen Bosch, Ph.D. Division of Pediatric Pulmonology and Allergy/Immunology Case Western Reserve University 2109 Adelbert Rd, BRB 835 Cleveland, OH 44106 Phone: 216.368.7565 Fax:

Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

On Monday, 16 December 2019 09:25:59 PST Jessica Besaw wrote: > Dear community, > > I am having a lot of trouble solving a protein structure. I think my > problem may caused by incorrectly placed proteins in molecular replacement. > I have two proteins in my asymmetric unit. It appears that one

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Problem with structural alignment

Dear Herman et al, On Dec 16, 2019, at 17:52, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear Ishan, A structural alignment should be independent of the software used. However, the residues being selected for the alignment can make a big difference and different

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Problem with structural alignment

Dear Ishan, A structural alignment should be independent of the software used. However, the residues being selected for the alignment can make a big difference and different programs have different selection criteria. There are two cases: 1. Different proteins. Here one needs to decide what

[ccp4bb] EMBL and Intruct-ERIC membership

We are delighted to announce that EMBL

Re: [ccp4bb] Problem with structural alignment

Well CCP4mg does this very nicely and it is easy to check the results - all displayed on the screen so you can pinpoint outliers.. Eleanor On Mon, 16 Dec 2019 at 06:38, Ishan Rathore wrote: > Hi, > > I am trying to compare multiple homologous structures of a protein, where > I am analysing the

[ccp4bb] Deadline extended: First CCP4 Study Weekend illustration competition

Dear colleagues, thanks to those of you who have sent entries for this CCP4 Study Weekend competition. As a number of people have requested it, we have decided to extend the deadline until Monday 23 December (one week from now). Looking forward to receiving your entries – see below for the

[ccp4bb] PhD studentships at University of Leicester, UK

Dear all, Could you please forward the following opportunities to suitable candidates? Applications are invited for BBSRC funded PhD studentships positions in the laboratory of Prof Daniel Panne. The group studies higher–order signalling complexes that are important in gene/chromatin regulation