[ccp4bb] PhD position at San Raffaele University, Milan, Italy

2023-06-22 Thread Degano Massimo
Dear All, one PhD Position is available in our lab (http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html) to use an integrated structural biology approach to study the role of B-cell receptors in different forms of leukaemia and lymphom

[ccp4bb] NCS restraints in Refmac5

2022-10-13 Thread Degano Massimo
Dear all, I have crystal with a protein homotetramer in the asymmetric unit, and I suspect from the electron density that the average B-factor of one chain may be substantially different than the others. Thus I would like to see the effect, if any, of changing the B-factor restraints between t

Re: [ccp4bb] Calculating RMSD of a loop

2019-09-17 Thread Degano Massimo
Hi, (good old) LSQMAN from the Uppsala Software Facotry will do this for you. First you align the structures based on the subset of atoms you want to match, then use the RMSD command to calculate the rmsd for the subset of atoms you are interested in. Best wishes, Massimo -- Dr. Massimo Degan

[ccp4bb] PhD Positions in Milan

2019-06-10 Thread Degano Massimo
Dear All, I would like to draw your attention to the PhD Course in Molecular Medicine at the San Raffaele Vita-Salute University, now open for applications (https://www.unisr.it/en/offerta-formativa/medicina-chirurgia/post-lauream/dottorato-medicina-molecolare). A total of 40 positions are avai

[ccp4bb] Fellowships available at Scientific Institute San Raffaele, Milan - Italy

2019-04-13 Thread Degano Massimo
The Biocrystallography Unit of the IRCCS Scientific Institute San Raffaele in Milan is looking for: - One junior research fellow to study the biochemical and structural features of a G-protein coupled receptor involved in the remyelination of the central nervous system, within the framework of

Re: [ccp4bb] Unknown density

2018-03-07 Thread Degano Massimo
I would not rely only on coordination numbers, since Ca2+ can be also hepta-coordinated. You can look at the high resolution structures of parvalbumin and nucleoside hydrolases. And, although not up to date, this site is also useful http://mespeus.bch.ed.ac.uk/tanna/ . The anomalous map sugges

Re: [ccp4bb] Antibody modelling software

2017-03-24 Thread Degano Massimo
Try also the LYRA server http://www.cbs.dtu.dk/services/LYRA/ In my experience, most programs do an excellent job with the canonical CDR loops, but care must be taken when looking at the CDR3s. Hope this helps, Massimo Sent from my iPhone On 24 Mar 2017, at 20:18, Hugh Morgan <1103e90ebb53