Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

Thanks for the quick responses!  I was looking for a command-line tool (should have said).  Here's the list: 1. phenix.pdb.biomt_reconstruction 2. Makemultimer.py: http://watcut.uwaterloo.ca/tools/makemultimer/docs 3. Quat in pymol: https://p

[ccp4bb] Postdoctoral position in structural biology of comammox in Vienna

*Postdoctoral position in structural biology of comammox in Vienna* For 120 years, microbiologists had strongly assumed that nitrification must be performed by two distinct groups of microorganisms (‘nitrifiers’) in cooperation: the ammonia oxidizers and the nitrite oxidizers, respectively. Th

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

Hi Frank, phenix.pdb.biomt_reconstruction command should do it. Pavel On Tue, May 25, 2021 at 12:44 PM Frank von Delft < frank.vonde...@cmd.ox.ac.uk> wrote: > Hello all - this presumably has a really simple solution: > > For a PDB file with a (correct) biomolecular assembly record (REMARK > 350

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

On Tue, 2021-05-25 at 20:04 +, Frank Von Delft wrote: > Yes I thought so too, but discovered I am too stupid to decode the highly > parsimonious manual on the ccp4 pages. > The first thing that I'd try (using Coot) is Calculate -> PISA -> Assemblies... #

[ccp4bb] deadline EXTENDED - speaker abstracts – cryo-EM software (ACA cryo-EM session talks)

Dear cryo-EM community, Co-chairs Peijun Zhang and I would like to invite abstracts for talks for an upcoming session on cryo-EM software at the annual meeting of the ACA (American Crystallographic Association). This is an excellent opportunity to highlight your latest and greatest image-proces

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

And to run it as a single command line option: http://legacy.ccp4.ac.uk/html/pisa.html On Tue, May 25, 2021 at 1:07 PM Debanu Das wrote: > Easy way to do it online: https://www.ebi.ac.uk/pdbe/pisa/ > or here: http://www.ccp4.ac.uk/pisa/ > > Best, > Debanu > > On Tue, May 25, 2021 at 1:04 PM Fran

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

Easy way to do it online: https://www.ebi.ac.uk/pdbe/pisa/ or here: http://www.ccp4.ac.uk/pisa/ Best, Debanu On Tue, May 25, 2021 at 1:04 PM Frank Von Delft wrote: > Yes I thought so too, but discovered I am too stupid to decode the highly > parsimonious manual on the ccp4 pages. > > What I nee

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

Yes I thought so too, but discovered I am too stupid to decode the highly parsimonious manual on the ccp4 pages. What I need is a command line that always works. Presumably that's a well defined problem...? Sent from tiny silly touch screen __

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

Hi Frank, PISA is your friend here. Thanks, Debanu On Tue, May 25, 2021 at 12:44 PM Frank von Delft < frank.vonde...@cmd.ox.ac.uk> wrote: > Hello all - this presumably has a really simple solution: > > For a PDB file with a (correct) biomolecular assembly record (REMARK > 350), what program do I

[ccp4bb] writing coordinates of full biomol into one (PDB) file

Hello all - this presumably has a really simple solution: For a PDB file with a (correct) biomolecular assembly record (REMARK 350), what program do I use to generate and write out the coordinates of the biomolecular assembly (or one of them). Thanks Frank ###

Re: [ccp4bb] [summary] Does anyone know of a "CHARMM bulletin board" ?

Hello, I am posting this summary in case anyone else encounters the same problem. Replies were received from David A. Case, Morpholino Peligro, Arunabh Athreya, Tushar R. and Walker Olivier (through Adriana Miele). The problem: how to get MD runs when you are not a specialist (first time you