Re: [ccp4bb] PDB redo R free

Dear Robbie and Tim， Thanks a lot for your reply. I just do not understand that if we can change the R free set during different rounds of refinement, the gap between Rwork and Rfree would be small, and Rfree would be meaningless, as R-free set is not "free". Best regards, Qixu Cai Email:

Re: [ccp4bb] PDB redo R free

Hi Qixu,PDB-REDO tries to have a minimum number test set reflections to reduce the error margin in R-free. As Tim says this is not a problem but if you reach out privately we can change your calculation to use your current testset. That is not recommended though.Cheers,RobbieOn 28 Apr 2023 04:51,

[ccp4bb] isopeptide bond and shelx topology file

Hello, Can you suggest how to make isopeptide bond in coot and generate .cif file to refine the structure in phenix? Also need suggestions to create shelxl topology file for non standard amino acids. I used PRODGR before but seems like the sever is down last couple of months. Any alternatives?

Re: [ccp4bb] happy/sad maps

Hi James! I’m not sure exactly what cpp4, coot and phenix do for their FFT’s, but I’m assuming they must mask off the ‘corners’ of the 3D FFT data cube transform (where the frequency is greater than the Nyquist) during the forwards transform. If you take your Cheshire map and do the FFT in

Re: [ccp4bb] happy/sad maps

what about if you run a 2-D FFT rather than 2-D FFT, if your hand drawing map in on a 2-D paper? > On Apr 28, 2023, at 10:48 AM, James Holton wrote: > > Its still April, but this one isn't a joke. > > The smiley-face electron density in the left panel of the attached image has > the

[ccp4bb] happy/sad maps

Its still April, but this one isn't a joke. The smiley-face electron density in the left panel of the attached image has the remarkable property that any attempt to sharpen or blur the map turns it into the frowny-face on the right.  If you'd like to try this yourself, the hidden_frown.map

[ccp4bb] Isopeptide and shelxl topology file

Hello, Can you suggest how to make isopeptide bond in coot and generate .cif file to refine the structure in phenix? Also need suggestions to create shelxl topology file for non standard amino acids. I used PRODGR before but seems like the sever is down last couple of months. Any alternatives?

Re: [ccp4bb] PDB redo R free

Dear Qixu Cai, it is a misconception that Rfree was not free anymore. The gap does not close when you swap the reflections in Rfree set. The 'free' reflections are freed when you do proper refinement, i.e., when the value of the target function becomes stationary. See

[ccp4bb] Registration open: Structure Meets Function Webinar #26 - New Technologies in Instruct

Dear all, Registration is open for the 26th edition of the Structure Meets Function webinar from Instruct-ERIC. The webinar

Re: [ccp4bb] PDB redo R free

To add to Tim's references, the algorithms that pdb-redo uses to deal with Rfree and possible bias are described here: https://journals.iucr.org/d/issues/2012/04/00/ba5174/index.htmlIf you happen to have a very small dataset (< 5000 reflections) pdb-redo does 10-fold cross validation and returns

[ccp4bb] Academic position openings in Exeter, UK

Dear all, The Living Systems Institute in Exeter, south-west England, is advertising eight new academic positions at all levels. The details are available at https://www.exeter.ac.uk/research/livingsystems/joinus/lsirecruitment2023/. Most of the positions can be in any topic relevant to the