Re: [ccp4bb] C-terminal amide

2017-10-12 Thread Bernhard Lechtenberg
HI Abhisek, I had the same problem a few years back. Here is the solution I came up with thanks to help from the CCP4bb: 1) Add pointer atom in Coot NH2 and create link to C-terminal residue (Coot: Extensions -> Modeling -> Make link) 2) create cif file with correct link description (see below)

[ccp4bb] C-terminal amide

2017-10-12 Thread Abhishek Anan
Dear all, I am trying to solve the structure of a peptide with C-terminal amide. In order to add the amide group to the c-terminal TYR, I substituted TYR with TYC (tyrosinamide) and created a link between the preceding GLY and TYC. When refined in refmac, the pdb inserts a TER card between GLY and

Re: [ccp4bb] CCP4 series 7.0 update 045

2017-10-12 Thread Andrey Lebedev
Dear CCP4 users There were two mistakes in my previous e-mail announcing the update 7.0.045: - an incorrect list of platforms for which the new version of shelxe is provided and - an out-of-date reference to SHELX web-site. The correct statement is as follows: shelxe (Mac OS X, Linux 64 bits, Wi

Re: [ccp4bb] ccp4 website not secure

2017-10-12 Thread Ville Uski
Dear all yes, the cert should be valid, but let me know if some of you continue having problems with it. I had an error last week on Android, complaining about unknown certificate authority, but this error went away for some reason, possibly thanks to a system update. As Michael said, https is on

[ccp4bb] A clearer 3D view of sugars

2017-10-12 Thread John Berrisford
Dear CCP4BB Carbohydrates, even when formed from very few sugar units, can often be hard to interpret in three dimensions when all their atoms are shown. This week, PDBe have updated the 3D structure viewer (LiteMol) on our web pages to add a simpler representation of common pyranose sugars.

[ccp4bb] 2018 HERCULES School - Neutron & Synchrotron Radiation Science

2017-10-12 Thread Silvia Onesti
HERCULES 2018 - European School 28 Years of Neutron & Synchrotron Radiation Science 2018 session: 25 February-30 March, 2018 DEADLINE FOR APPLICATION: 25 October 2017 HERCULES is a European course for PhD students and young researchers using Neutrons and Synchrotron Radiation for applications

Re: [ccp4bb] areaimol missing symmetry mates

2017-10-12 Thread Eleanor Dodson
Eugene is away but I think the PISA symmetry checking only looks at 2 unit cells in all directions from the origin, so if the origin chain is far away you may lose contacts. .. As someone says - always try to place the molecule reasonably close to the origin. There is an old program pdbset xyzin