[ccp4bb] Data Fitting for protein-ligand interaction.

2013-09-12 Thread Matthias Barone
Dear All I've been reading several mails that adress the problem of acetylated N-termini when refining peptide ligands with refmac. I managed to include LINKR records after running refmacs review restraints as suggested by Eleanor Dodson in one of the mails I found: LINKRC ACE I 0

[ccp4bb] Antw: Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

2015-03-18 Thread Matthias Barone
Hi, I just checked the PIC sever tim suggested. very nice indeed. If you only want to map different interfaces and the amino acids involved in, I suggest to run the pisa server, too. http://www.ebi.ac.uk/pdbe/pisa/ . I used it extensively to find out whether a certain set of crystal contacs

[ccp4bb] Antw: Re: [ccp4bb] High B factor

2016-10-14 Thread Matthias Barone
Picking up the mail of Pavel, Phenix refines occupancies.. If you expect the loops to be disordered, did you try to lower the occupancy of these residues, following Ethan Merritt statement that "general uncertainty [...] is represented better by occupancy <1 rather than an arbitrary large B

[ccp4bb] Antw: Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

2016-10-17 Thread Matthias Barone
ors to get a feel > > for which bits are wiggly, but they'll never think to color it by > > occupancy. > > Let them fly ... at least for protein atoms ... > > Carlos > > > ---- > > *From:*

[ccp4bb] Antw: Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Matthias Barone
Dear Rohit Additionally to the very good suggestions, I'd feed the structure into the PDB_REDO server. Its a fast and easy way to detect if the refinement strategy is correct. The server gives you a good feeling how tight the x-ray weights need to be. If however PDB_REDO does not manage to

[ccp4bb] Antw: Re: [ccp4bb] When should one add solvents

2017-04-19 Thread Matthias Barone
Hi Abhishek Im by far not as experienced as others in the bulletin board, but I made the experience that automated water update with Phenix leads to an aggressive placement of solvent molecules, which can be damped a bit by restricting H-bond distances of newly placed waters. As Robbie and

[ccp4bb] Antw: Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

2017-07-02 Thread Matthias Barone
Beside the good propositions of fixing the environment, flip the peptide, or using PDB_REDO, I would suggest the following additional attempts: Try 1) setting the OCC of the sidechain (CG and further) below 0.3 or mutate directly to Ala. See which ones remain visible in a diff map and bring

Re: [ccp4bb] "reset" a structure before re-refinement

2017-08-20 Thread Matthias Barone
Thanks James for your reply. I my naive way, I thought that when doing paired refinement, it would be sufficient to run several cycles of refinement with simulated annealing followed by a thorough real space rebuilding. What is your thought about using the "jiggling" of additional cartesian

[ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

2017-06-14 Thread Matthias Barone
If you dont use Phenix, print the figures of https://doi.org/10.1016/S0969-2126(02)00743-8 and use them beside your screen. Helps a lot if you wanna have a quick look at Rfact distributions.. >>> Paul Emsley 14.06.17 15.25 Uhr >>> On 14/06/2017 14:09, Khoa Pham