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

hey presto! thanks doriano (it does run on windows, right?)... best jon -Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Doriano Lamba Gesendet: Montag, 13. Januar 2025 17:01 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] replacing B-factor column and color accordingly P

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

hi everyone, i know you're all busy doing experiments, writing papers, teaching and running the whole joint while being underpaid on fixed-period contracts, but wouldn't it be nice if someone were to put together a dedicated PDB screen editor? my pals in HH tell me to edit PDB files from the com

[ccp4bb] AW: [ccp4bb] Pipetting Robot

dear ulrike, we bought an oryx from douglas instruments https://www.douglas.co.uk and have been delighted with its performance for screening and in particular optimizing conditions. there are of course alternatives if you want to spend more money! best jon -- Prof. Dr. Jon Hughes Institute for Pl

[ccp4bb] AW: [ccp4bb] Commercial storage of biological samples

dear alexandra, DNA at least is extremely stable, so i'd just spot the plasmids onto filter paper (labelled with a pencil)... and send the spots to a trusted (young!) friend somewhere far away. at least i'd trust that more than any profit-oriented company. best jon -- Prof. Dr. Jon Hughes Depar

[ccp4bb] Protonation Dynamics in Protein Function: final symposium of SFB 1078, 1-3 Sep 2024 in Berlin

Hello everyone, We invite you to the final symposium of SFB 1078 in Berlin from 1 to 3 September. This meeting will be a celebration of twelve years of research into protonation dynamics in protein function and associated themes, marking the culmination of our journey. It will feature ten scien

[ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

hello CCP4 people, rather off-topic: is there a purpose-written windows editor for PDF files? with interleaved anisotropy lines, missing column delimiters etc., simply extracting the B-factors for Ca atoms is hard work using a standard character editor. would anyone think of working with DNA wit

[ccp4bb] AW: [ccp4bb] [OFF TOPIC] On Ni-NTA resin TEV cleavage

(this is from a different jon) if a chelator really is necessary at this stage (post AmS?), in any case use IDA instead of EDTA! that's pretty obvious from the affinities of EDTA/NTA/IDA. cheers jon Von: CCP4 bulletin board Im Auftrag von Jonathan Bailey Gesendet: Mittwoch, 1. November 2023 19:5

[ccp4bb] red mesh missing in raster screenshot

hallo everyone, in the latest COOT, draw/screenshot/Raster3D the screenshots look great, but the red mesh regions of 2Fo-Fc are missing. the green is fine, as is the e- density itself several of my pals find the same! is the red mesh switched off somewhere or is it a bug? best jon -- Jon Hu

[ccp4bb] AW: quantifying electron density

" try to fix the problem: https://bl831.als.lbl.gov/END/RAPID/end.rapid/Documentation/end.rapid.Manual.htm best jon -Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Hughes, Jonathan Gesendet: Mittwoch, 28. Juni 2023 18:16 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] q

[ccp4bb] quantifying electron density

hello everyone, is there software that can use an electron density map to quantify the number of electrons in a selected volume somewhere in a protein? cheers jon -- Professor Jon Hughes, BSc, PhD Department of Physics Free University of Berlin Arnimallee 14 14195 Berlin Germany mobile: 

[ccp4bb] AW: [ccp4bb] Crystallization Robots

hey shawn, we like our oryx4! it's pretty easy to program and use (after the very helpful intro from patrick / douglas instruments) - and it has helped our work enormously. it takes a while to do its job, but for us that is not relevant. it's more important that it can do all sorts of useful thi

[ccp4bb] 13CO2 cylinder for free

hello (mostly) NMR people! we inherited a cylinder containing ~3 litres of 13CO2 (originally from cambridge isotopes). you can have it for free best jon Von: CCP4 bulletin board Im Auftrag von Andres PALENCIA Gesendet: Mittwoch, 2. März 2022 11:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb]

[ccp4bb] AW: Phosphatase enzymatic assay

hey, my information is that detecting phosphorylation via ms is non-trivial because the P groups are lost during fragmentation and prior to detection. cheers jon -Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Wim Burmeister Gesendet: Mittwoch, 15. September 2021 14:47

[ccp4bb] AW: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

GFP:H6 is a nice place to start. it doesn't have enzymatic activity, but it expresses nicely in coli and is visible to the human eye during affinity-purification on NiNTA/imidazole (and the fluorescence is interesting too). the biochemistry dept. here uses it routinely with undergrads. cheers jo

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

s become exaggerated – which is another word for "misrepresented". cheers j Von: Ian Tickle Gesendet: Freitag, 28. Mai 2021 12:10 An: Hughes, Jonathan Cc: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS Hi Jonathan On Thu, 27 May 2021 at 18:34, Hughes, Jo

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

redit cards, beaches being what they are. they were a nice couple though. cheers j -Ursprüngliche Nachricht- Von: Gerard Bricogne Gesendet: Donnerstag, 27. Mai 2021 20:19 An: Hughes, Jonathan Cc: CCP4BB@jiscmail.ac.uk Betreff: Re: [ccp4bb] AW: [ccp4bb] (R)MS Dear Jonathan, You are rig

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

n a beach in sardinia. -Ursprüngliche Nachricht- Von: Gerard Bricogne Gesendet: Donnerstag, 27. Mai 2021 19:05 An: Hughes, Jonathan Cc: CCP4BB@jiscmail.ac.uk Betreff: Re: [ccp4bb] AW: [ccp4bb] (R)MS Dear Jonathan, Isn't it six of one and sqrt(36) of the other ? Best wishes

[ccp4bb] AW: [ccp4bb] (R)MS

ard deviation (RMSD) is a more appropriate parameter of variability than variance? or am i missing something? cheers j Von: Ian Tickle Gesendet: Donnerstag, 27. Mai 2021 18:32 An: Hughes, Jonathan Cc: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] (R)MS Hi Jonathan It's historical, it&

[ccp4bb] (R)MS

o yes! but maybe the crystal people could explain to me why the B factor is the variance (with units of Ų) rather than the standard deviation (i.e. RMS, with units of Å) when, to my simple mind, the latter would seem be the more appropriate description of variability in space? cheers jon Von:

[ccp4bb] AW: Fluka-branded PEG 3000

Good luck Mr. Hyde! jon Von: CCP4 bulletin board Im Auftrag von Correy, Galen Gesendet: Montag, 22. März 2021 18:01 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Fluka-branded PEG 3000 Dear all, I'm wondering if anyone could spare 50-100 g of Fluka branded PEG 3000 (see attached image)? We hav

[ccp4bb] AW: [ccp4bb] Open position - data management in biophysics

the translation is, of course, fake. jon Von: CCP4 bulletin board Im Auftrag von Jan Dohnalek Gesendet: Freitag, 22. Januar 2021 11:02 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Open position - data management in biophysics On Fri, Jan 22, 2021 at 10:54 AM Pearce, N.M. (Nick) mailto:n.m.pe

[ccp4bb] AW: [ccp4bb] Up-to-date 3D stereo solution

just cross your eyes. jon -Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Jan Stransky Gesendet: Samstag, 12. Dezember 2020 12:11 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Up-to-date 3D stereo solution Dear all, I am wondering, if anyone has experience with implement

[ccp4bb] AW: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

i think the answer to all these doubts and questions is quite simple: the AlphaFold2 people must make all details of their methods public (source code) and, as would probably be necessary, open their system for inspection and use by independent experts. isn't that what peer review and reproducib

[ccp4bb] AW: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

scientific research requires that experimental results must be testable, so you have to publish your methods too. if the alphafold2 people don't make their code accessible, they are playing a game with different rules. maybe it's called capitalism: i gather they're a private company best jon

[ccp4bb] AW: Tiny rocks on my CX100 shipping dewar

hey jack, our experience with these "logistics" people is that you'll probably need to buy a new dewar ;-) cheers jon Von: CCP4 bulletin board Im Auftrag von Tanner, John J. Gesendet: Freitag, 4. Dezember 2020 17:04 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Tiny rocks on my CX100 shipping dewa

[ccp4bb] AW: [ccp4bb] OFF TOPIC question

Bl21Pro j Von: CCP4 bulletin board Im Auftrag von Anamika Singh Gesendet: Donnerstag, 26. November 2020 11:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] OFF TOPIC question One correction to the previous question: I have two constructs having different ori, p15ori and M13 ori, different pro

[ccp4bb] AW: Re: [ccp4bb] short anti-parallel homodimerization motifs

llographic dimeric symmetry! Harder to dissect and isolate the dimerization element to my first look but I will look closer. yours, -yong On Thu, Sep 24, 2020 at 5:07 PM Yong Tang mailto:liutan...@gmail.com>> wrote: Thanks so much Jon - let me look into it. Yours, Yong On Sep 24, 2020, at

[ccp4bb] AW: Re: [ccp4bb] RES: [ccp4bb] Looking for suggestions with protein expression

Of course! Using a B strain for cloning is just asking for trouble. Manno... -- Jon Hughes Sent without the use of Apple products. Jon Cooper schrieb Re: "In our lab we generally use BL21 for plasmid replication." I am interested because on the occasions that I prepared plasmids in

[ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

hi ian, oh no! all those trump fans across the pond will love the "hypothesis of evolution" idea. they won't know the word "hypothesis" of course, but unfortunately you might get famous for it anyhow. cheers jon Von: CCP4 bulletin board Im Auftrag von Ian Tickle Gesendet: Mittwoch, 1. Juli 2020

[ccp4bb] AW: [ccp4bb] Cold cabinet recommendations for AKTA Pure

hi alan, why do you want to put the thing in a cold cabinet? if you have protease problems, there are better ways to get rid of them than exploiting Q10. on the other hand, you'll increase viscosity and thus slow down the flow rates. also, the high humidity will reduce the lifetime of your Äkta

[ccp4bb] totally off-topic: non-semester

hi everyone, warning this has NOTHING to do with structural biology or the rest of the world. there is a movement in germany to declare the university summer semester 2020 to be a "non-semester", see https://www.nichtsemester.de/cbxpetition/offener-brief/ it's in german and i don't think people ou