Re: [ccp4bb] Ligand superposition!

Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il <mailto:bshaa...@bgu.ac.il> > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 > >

[ccp4bb] Ligand superposition!

Hi All, I have over 50 pdb files that I have downloaded from PDB that all have the same ligand bound. I wamt to superpose the ligands (and move the protein coordinates using that matrix). The goal is for me to see how difference in ligand environments in different complexes. Is there an

Re: [ccp4bb] Structure prediction - waiting to happen

or a reference in your grant application: https://www.biorxiv.org/content/10.1101/2022.03.08.483439v2 . Cheers -- Ian On Sat, 1 Apr 2023 at 13:06, Subramanian, Ramaswamy mailto:subra...@purdue.edu>> wrote: Dear All, I am unsure if all other groups will get it - but I am sure this group w

[ccp4bb] Structure prediction - waiting to happen

Dear All, I am unsure if all other groups will get it - but I am sure this group will understand the frustration. My NIH grant did not get funded. A few genuine comments - they make excellent sense. We will fix that. One major comment is, “Structures can be predicted by alpfafold and other

Re: [ccp4bb] To Trim or Not to To Trim

Dear All, I am kind of in agreement with Manfred, but I also have concerns. The RCSB and the databases are public databases used by non-structural biology experts a lot. They take the model as if it is an experimental result - rather than it being a model. Example: I just got a paper with

Re: [ccp4bb] Lys-Arg crosslink?

Is there enough density for Glucosepane? Rams subra...@purdue.edu On Feb 25, 2023, at 1:42 PM, Celia Goulding wrote: External Email: Use caution with attachments, links, or sharing data In a recent structure we found strong electron density between a closely positioned Arginine

Re: [ccp4bb] Map superposition!

boxes (unit cells) and symmetry can be different, gridding can be different too. I can help off list should you need any assistance! Pavel On Wed, Jan 25, 2023 at 6:30 AM Subramanian, Ramaswamy mailto:subra...@purdue.edu>> wrote: Hi All, I have two maps - both cryo-EM. One with a

[ccp4bb] Map superposition!

Hi All, I have two maps - both cryo-EM. One with and one without ligand. I am trying to superpose them and I cannot seem to get ChimeraX to work. I then tried VESPER and that also does not work. The built models superpose very well. What is the best way to superpose maps. Thank you.

Re: [ccp4bb] CCP4i under M1Pro

Hi Kelvin, I have the same problem. Cheers! Rams subra...@purdue.edu On Jun 28, 2022, at 11:45 AM, Lau Kelvin <5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote: External Email: Use caution with