Re: [ccp4bb] .cif file generator for compound stereochemical restraints

Thanks Paul for addressing my inquiry late hours. Kudos to your huge contributions to the vast crystallography community. All my best wishes, Jacob On Sun, Mar 22, 2020 at 11:15 PM Paul Emsley wrote: > On 23/03/2020 03:05, Jacob Wong wrote: > > I love the ccp4 suite. I'm interested in knowing if

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

On 23/03/2020 03:05, Jacob Wong wrote: I love the ccp4 suite. I'm interested in knowing if there is any other solution out there that may be more economical in licensing, especially if I only go as far as coot as a "commercial user". Are you suggesting that coot may not be a freeware anymore in

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

Thanks Paul - I love the ccp4 suite. I'm interested in knowing if there is any other solution out there that may be more economical in licensing, especially if I only go as far as coot as a "commercial user". Are you suggesting that coot may not be a freeware anymore in the near future? Yours, Ja

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

Just would love to know what else is out there in addition to ELBOW in Phenix? Acedrg is the modern dictionary generator distributed by CCP4. My utility is to generate the .pdb and .cif files from a SMILES string that would allow me to do compound fitting and real-space refinement in coot, I

[ccp4bb] .cif file generator for compound stereochemical restraints

Dear all, Just would love to know what else is out there in addition to ELBOW in Phenix? My utility is to generate the .pdb and .cif files from a SMILES string that would allow me to do compound fitting and real-space refinement in coot, and then reciprocal refinement elsewhere (assuming I won't

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

Guys, Thanks for all the help. I figured out what's wrong with the sequence file. I had accedently entered an "X' to one of the sub-chains. Cheeres ! Gihan To unsubscribe from the CCP4BB list, click the following link: h

Re: [ccp4bb] CCP4BB vs COVID19

Structure of 2019-nCov RNA polymerase: https://www.biorxiv.org/content/10.1101/2020.03.16.993386v1.full.pdf+html /Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex with cofactors nsp7 and nsp8 at a resolution of 2.9-Å...A comparative analysis to show how remdesivir

Re: [ccp4bb] CCP4BB vs COVID19

For what it’s worth, I’ve spent the last few days going over most of the existing COVID-19 related structures and rebuilding/re-refining wherever I considered necessary. The resulting models along with some basic explanatory notes are at https://drive.google.com/drive/folders/1S5qJtCnK00Nrcbww

Re: [ccp4bb] CCP4BB vs COVID19

James, there are lots of quite simple experiments that would be could be done, but I can't get anyone to think seriously about the problem - let alone do the experiments. The attitude seems to be, "it can't be as simple as you suggest - someone would have noticed it". * Has anyone measured virule

Re: [ccp4bb] CCP4BB vs COVID19

Dear all, I assume most of you are aware of the EMBL-EBI datahub which was set up in January to provide essential virus research data to all scientists, but in case someone missed it I would like to share the link: https://www.ebi.ac.uk/ena/pathogens/covid-19 (https://www.ebi.ac.uk/ena/pathogens

[ccp4bb] Urgent call for expression of interest in COVID-19 related access at DIAMOND LIGHT SOURCE

Dear users, RESPONSE TO COVID-19 EMERGENCY Diamond is offering, subject to light touch rapid review, free-at-the-point of use remote access to a range of facilities (see below) to help research aimed at combatting the COVID-19 outbreak. This applies equally to users from all countries. To hel

Re: [ccp4bb] CCP4BB vs COVID19

Relevant to the discussion: * Cell, Vol. 110, 551–561, September 6, 2002, Copyright 2002 by Cell Press An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes * Bacterial RNA thermometers: molecular zippers and switches Jens Kortmann and Franz Narberhaus NATURE

Re: [ccp4bb] CCP4BB vs COVID19

Thank you Patrick, RNA structure is still structural biology, so I think relevant here.  It seems to me that RNA as a thermometer would be an easy hypothesis to test?  Has anyone measured virulence vs temperature in cell culture? The 3D structure of the genome is no doublt important.  I would

Re: [ccp4bb] CCP4BB vs COVID19

Well, look at that!  I had missed that one.  Thank you Dan. Ahh, those Ig folds.  They are like dougnuts.  Is there anything they can't do? Interesting that Tan et al. arrived at their conclusions from a very different line of evidence.  They seem to have missed the covariance with the silen

Re: [ccp4bb] CCP4BB vs COVID19

hi There are developments in cyclic and constrained peptides see for example J Am Chem Soc. 2019 Mar 13;141(10):4167-4181. hope it helps On 22/3/2020 8:01 pm, Abhishek Anan wrote: Dear all, Not directly related to the discussion but does any

Re: [ccp4bb] CCP4BB vs COVID19

Dear all, Not directly related to the discussion but does anyone know of a antiretroviral protease inhibitor that is a peptide? I am new to the topic and read that peptides suffer from bioavailability issues. Are there any workarounds? best, Abhishek On 3/21/20, Rigden, Dan wrote: > Hi James >

Re: [ccp4bb] Error running Phaser-MR

Dear Gihan, The most likely thing I can think of is that the sequence contains a character not recognised as a legitimate one-letter code. This could happen if you use a special letter coding for an ambiguous residue, or if you say it’s a nucleic acid sequence instead of a protein sequence. S