[ccp4bb] 3D viewing on PC

I am looking for information on methods of stereoscopic (3D) viewing of macromolecular structures on the PC monitor (manufacturers, vendors, prices etc.). Thank you, Oliviero To unsubscribe from the CCP4BB list, click the

[ccp4bb] AI and cis-peptides

Does anybody know if cis-peptides are predicted by the AI tools (AlphaFold2, ColabFold, or ESM-2)? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB

Re: [ccp4bb] visualising anis B factors

You might be interested in Chimera too (--> Tools --> Structure Analysis --> Thermal ellipsoids) On 23.01.2019 16:17, Eleanor Dodson wrote: Is there any easy way to do this? Coot? ccp4mg? Eleanor Dodson - To unsubscribe from the CCP4BB list, click the following li

Re: [ccp4bb] high B factor

Dear Anandhi, you might be interested in PMID: 29752562. BW, Oliviero On 09.11.2018 01:30, Anandhi Anandan wrote: Hello everyone, I am trying to solve the structure of a protein with a bound ligand at 2.65 A resolution. XDS was used for data reduction, phaser-MR for molecular replacement a

Re: [ccp4bb] coiled-coil "degree"

Dear Jorge, recently I saw an interesting paper that might help you to do exactly what you need: Bioinformatics doi: 10.1093/bioinformatics/bty347. BW, Oliviero On 28.08.2018 15:03, Jorge Iulek wrote: Dear all,     I am working currently on a structure that, nicely, presents two differe

[ccp4bb] B-factor standardization

Dears, everybody knows that B-factors may change amongst different crystal structures and that they need to be standardized when different protein crystal structures are compared. If I am not wrong, I remember that someone proposed to standardize B-factors of protein atoms as “BS = B - Bave”

Re: [ccp4bb] looking for a link between diffraction resolution and order within the crystal

Dear Vincent, you might be interested in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314880/. Best, Oliviero On 28.11.2017 15:44, vincent Chaptal wrote: Hi, I've been searching but can't find what I am looking for so I thought I ask specialists. I am curious about the link between reso

[ccp4bb] mmCIF and CIF

Dears, does anybody know how to transform an mmCIF file of the Protein Data Bank into a CIF file (the slightly different format used in small molecule crystallography)? Thanks, Oliviero

Re: [ccp4bb] chloride or water

Hi Rohit, you might be interested in the following paper: Buried chloride stereochemistry in the Protein Data Bank BMC Structural Biology 2014, 14:19 doi:10.1186/s12900-014-0019-8 http://www.biomedcentral.com/1472-6807/14/19 Best, Oliviero On Tue, January 20, 2015 10:53, Eleanor Dodson wrote

Re: [ccp4bb] two identical proteins in one asymmetric unit

Dear SHJ, there is no reason to expect that the 3D structure of two molecules within the same asymmetric unit are identical even if their chemical formula is identical. These two molecules experience slightly different crystal packing contacts are are expected to be different. Obviously, in gener

Re: [ccp4bb] low B factor for water

Dear Simon, low B factors might indicate a higher number of electrons, i.e. an atom larger than oxygen, like for example a metal cation (calcium etc.) of an anion (chloride etc.). Take a look at the environment arounf the "strange" solvent molecule. Oliviero On Thu, December 13, 2007 22:36, Yue