Re: [ccp4bb] replacing B-factor column and color accordingly

Hi Yahui, There are definitely some old python scripts floating around online to help with this sort of thing. pdb-tools · PyPI GitHub - harmslab/pdbtools: A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

Re: [ccp4bb] Tools for identifying possible contaminants

I think this may do the contaminant search you are looking for. ContaMiner (kaust.edu.sa) Best, Mike On Wed, Jul 3, 2024 at 12:04 PM Kyle Gregory < 3632

Re: [ccp4bb] nearestcell

Hi Kay, http://flops.arcib.org:8084/sauc-1.1.1/ similar to the nearest-cell server, which seems to change its link and is harder to find (or stale link) https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi HTH, Mike On Wed, Dec 27, 2023 at 1:39 PM Kay Diederichs < kay.diederi...@uni-konsta

Re: [ccp4bb] binding pockets...

Have you tried P2Rank? It is quite fast, and there is a standalone version that has command line options to run against all coordinate files in a directory using batch mode. https://prankweb.cz/ https://prankweb.cz/about https://github.com/rdk/p2rank You can try the web version to see how it per

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

Since we've already gone down this rabbit hole (pun intended), there's been quite a bit written in the last year about the 'value of a statistical life' and pandemic insurance. https://www.forbes.com/sites/theapothecary/2020/03/27/how-economists-calculate-the-costs-and-benefits-of-covid-19-lockdow

[ccp4bb] Position available: Protein biochemist at Civetta Therapeutics

https://careers-civetta.icims.com/jobs/1395/job Overview Civetta Therapeutics (Cambridge, MA) is recruiting a Scientist to Senior Scientist level position in Protein Sciences. Civetta is a cutting-edge biotechnology company, backed by Deerfield Management, and recently launched from the Broad Ins

[ccp4bb] Job Posting: Director, Structural Biology and Biophysics - Takeda Pharmaceuticals

*Job Description: * Director - Structural Biology and Biophysics Job ID 1602180 Location San Diego, California, United States; *OBJECTIVES:* The Director of Structural Biology and Biophysics leads all activities in the Structural Biology and Biophysics group at TCAL, including Molecular

Re: [ccp4bb] Sister CCPs

I'm sorry, but did you just use the words "crystallographers" and "modest" in the same sentence? :-) On Thu, Feb 13, 2014 at 6:41 AM, Eleanor Dodson wrote: > I agree with Frank - it keeps crystallographers modest to know how > challenging wet lab stuff still is.. > Eleanor > > On 12 February 201

[ccp4bb] Postdoc Position at Millennium Pharmaceuticals

Post-Doctoral Program: Structural Biology (protein crystallography) for more details and to submit an application, see http://www.millennium.com/careers/ requisition 6606 Happy Holidays.

Re: [ccp4bb] real-space vs. reciprocal space refinement

Thanks to everyone who has responded so far. I'd like to provide a few more details since I'm also interested in the practical ramifications of the theoretical arguments presented thus far. 1. density map at 3.2 A resolution was used to refine a model that had already been built and refined at 2.

[ccp4bb] real-space vs. reciprocal space refinement

Dear CCP4 experts, Recently, I was debating a colleague on the pros/cons of refinement done in reciprocal space compared to refinement in real space. I always thought reciprocal space refinement was preferable since measured amplitudes will be more accurate than calculated phases (unless good exp

[ccp4bb] disorder, solvent content, and diffraction limit

Greetings, I've taken a protein (structure known) with some disordered termini and created a new truncated construct that lacks these disordered bits (approx. 5% by mass of the total protein). To my delight, the new construct crystallizes much more readily than the full-length one (more hits in