[ccp4bb] Regarding RNA AMBER OL3 Force field

Hello!! If anyone is using the AMBER OL3 force field kindly send it to me. I am working on RNA str prediction. It would be a great help if you can send me this. Thank you Sincerely To unsubscribe from the CCP4BB list, clic

[ccp4bb] Forthcoming RSC meeting

A reminder that the registration deadline for the free one-day RSC meeting on British X-ray Crystallographers is fast approaching. More details can be found here: https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent w

Re: [ccp4bb] Outlawed PDB files, what should a muggle do

Thanks David (and others who replied the same off list) Yes, this is exactly what I wanted thank you Agree that dimple should probably accept mmCIF, but for the moment I have the capacity to compute maps so jobsagoodun All the best Graeme From: David Waterman S

Re: [ccp4bb] Outlawed PDB files, what should a muggle do

Of course the proper answer should be to fix dimple to read mmCIF (for which I would also recommend gemmi) -- David On Wed, 20 Sept 2023 at 16:35, David Waterman wrote: > gemmi convert --shorten 7qgf.cif foo.pdb > > ? > -- David > > > On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,L

Re: [ccp4bb] Outlawed PDB files, what should a muggle do

gemmi convert --shorten 7qgf.cif foo.pdb ? -- David On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > Looks like PDB files have been outlawed because mmCIF > > But dimple needs PDB files > > cif2pdb says nope > > Grey-Area

Re: [ccp4bb] wwPDB NEWS - Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

I'm using a similar scheme for converting mmCIF to PDB with 'gemmi convert'. 1. Long CCD codes are replaced with 3-character codes that end with a tilde (ABCDE -> AB~) 2. The HETNAM record is used to store the original CCD codes (in columns 72-79). HETNAM AB~

[ccp4bb] Outlawed PDB files, what should a muggle do

Looks like PDB files have been outlawed because mmCIF But dimple needs PDB files cif2pdb says nope Grey-Area work :( $ cif2pdb --help * ERROR * No cif file read on input Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif * ERROR * No cif file read on input Grey-Area

[ccp4bb] 3 Year Structural Biologist Position in Australia

An opportunity exists for Postdoctoral Fellow (Structural Biologist) to join the research laboratory of Professor Wai-Hong Tham in the Department of Biomedical Sciences and Biochemistry, Research School of Biology at the Australian National University. The Tham Laboratory works on infectious d

Re: [ccp4bb] the structures of Nucleic acid

Hi I am also reminded that I was involved in the data collection but not structure solution of a DNA cyclic octamer from a single wavelength dataset collected to atomic resolution (on image plate…), which was solved after locating a Ba (which turned out to be one of several with partial occupan

Re: [ccp4bb] the structures of Nucleic acid

Hi folks just my two ha’porth. Back in the mid 1990s, when MAD was becoming common and tunable beamlines were being installed at every synchrotron you could shake a stick at, I was involved in several successful projects involving 5-Br-U in oligo-DNA crystallography. In my (very, very) naïve h