Re: [ccp4bb] [off topic] Recovering pET expression plasmid from BL21 strain

Hi Javier, For a few years (during an industry job) we regularly cloned directly into BL21 (we made our own high competency cells) and confirmed via expression before plasmid sequencing. Only after sequencing did we transform into a cloning strain for miniprep and “long term storage”. We didn’t

Re: [ccp4bb] [External] [ccp4bb] Off topic : plasmid expression vector for E.Coli with a cleavable his-tag at the c-ter

recommended by another. Others may have further suggestions for Flavio. *From: *CCP4 bulletin board on behalf of Karla J. F. Satchell *Date: *Friday, February 16, 2024 at 7:13 AM *To: *CCP4BB@JISCMAIL.AC.UK *Subject: *Re: [ccp4bb] [External] [ccp4bb] Off topic : plasmid expression vector

Re: [ccp4bb] [off topic] Recovering pET expression plasmid from BL21 strain

This should all go fine. You can maxi- or mini-prep the plasmid DNA from the expression strain and transform it back into a cloning strain for sequencing, etc. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 19 Feb 2024,

[ccp4bb] [off topic] Recovering pET expression plasmid from BL21 strain

Dear all, I'm sure this issue comes up very often, but for the first time in our lab we need to recover a pET-type expression plasmid from a BL21-like E. coli strain (NEB's T7 Express). I know a RecA+ strain is not suitable for plasmid production, but the basic plan is to grow and mini-prep the

Re: [ccp4bb] [External] [ccp4bb] Off topic : plasmid expression vector for E.Coli with a cleavable his-tag at the c-ter

Date: Friday, February 16, 2024 at 7:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [External] [ccp4bb] Off topic : plasmid expression vector for E.Coli with a cleavable his-tag at the c-ter Hi everyone— Thought I might chime in. This technology was developed in my lab based on our studies

Re: [ccp4bb] [External] [ccp4bb] Off topic : plasmid expression vector for E.Coli with a cleavable his-tag at the c-ter

Satchell From: CCP4 bulletin board on behalf of Srivastava, Dhiraj <bda2be8a675a-dmarc-requ...@jiscmail.ac.uk> Date: Friday, February 16, 2024 at 6:42 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [External] [ccp4bb] Off topic : plasmid expression vector for E.Coli with a cleavab

Re: [ccp4bb] [External] [ccp4bb] Off topic : plasmid expression vector for E.Coli with a cleavable his-tag at the c-ter

sequence, it may leave either no extra residues or only one or two residues. Dhiraj From: CCP4 bulletin board on behalf of Flavio Di Pisa Sent: Friday, February 16, 2024 3:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [External] [ccp4bb] Off topic : plasmid expression

[ccp4bb] Off topic : plasmid expression vector for E.Coli with a cleavable his-tag at the c-ter

Dear community, I'm looking for a commercial expression vector for E.Coli with a cleavable his-tag at the c-ter. Anyone can help me? Thank you in advance, Flavio. To unsubscribe from the CCP4BB list, click the

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

ck! Irwin From: CCP4 bulletin board on behalf of Hughes, Jonathan Sent: 02 November 2023 09:17:30 To: CCP4BB@JISCMAIL.AC.UK Subject: [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 s

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

:53 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] [OFF TOPIC] On Ni-NTA resin TEV cleavage I have always performed TEV cleavage after eluting my protein from the Ni-NTA column (TEV cleavage performed during overnight dialysis in imidazole free buffer as imidazole inhibits TEV activity at high

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

I have always performed TEV cleavage after eluting my protein from the Ni-NTA column (TEV cleavage performed during overnight dialysis in imidazole free buffer as imidazole inhibits TEV activity at high concentrations). I use TCEP as reducing agent and have never included EDTA, by this method I've

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

Hi Rafael, In this case I recommend the use of Zn-charged Chelating Sepharose™ Fast Flow (Cytiva), as we have established it in the early days when first applying IMAC to the purification of native antibody fragments (see PMID: 1367302 and PMID: 8163179). While the Zn-IDA matrix has

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

Dear Rafael In addition to the excellent suggestions already offered by previous responders, I can attest that Ni-penta resin (sold among others by a company with an odd name Marvelgent) is resistant to EDTA and DTT, and it leaks very little Ni (almost none). Plus, it elutes with low inidazole,

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

Hi Rafael, Dom et al, Indeed nickel eluted with imidazole stays on all your proteins with a His tag, and addition of DTT will make almost all proteins go brown and crap out at this point. But, as Dom says, addition of EDTA before the DTT will solve the problem. Most of the time… If your

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

== about.me/david_briggs<http://about.me/david_briggs> From: CCP4 bulletin board on behalf of Rafael Marques Sent: Tuesday, October 31, 2023 7:21:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [OFF TOPIC] On Ni-NTA resin TEV cleavage External Sender: Use c

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

Hi Rafael, Once I inherited a protocol with a problem similar to yours and they told me that the precipitation was caused by nickel leaking out during the elution with 250 mM imidazole. I am not sure whether this was true, however, their fix was to place something like 20 ul of 200 mM EDTA at

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

Hi Rafael, the simple answer is that the EDTA and DTT( or any other reducing agent) is not required for the TEV activity. You can have your TEV protease in 20 mM Tris pH 7.5 (RT) and 150 mM NaCl, plus either 10% Glycerol or 50% glycerol depending on storage conditions preference - 80 or -20C

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

Hi everyone, I have been looking on this bb and other websites as well but I could not find a veredict. We are suspecting that when I elute my sample from my Ni-NTA column, the imidazole concentration (250 mM) is making it to precipitate. Once my sample has a cleavable TEV site, I was planning

[ccp4bb] [Off-topic] Research Coordinator position available immediately

There is a Research coordinator position available immediately at University of Oklahoma. *Research Coordinator* *-* *Job Number:* *230192* *Organization:* Chemistry/Biochemistry *Job Location:* Oklahoma-Norman-Norman Campus *Schedule:* Full-time *Work Schedule:* 8 AM - 5 PM Monday -

[ccp4bb] [Off-topic] NMR manager position available

There is a NMR manager position available at University of Oklahoma. *NMR Manager position at University of Oklahoma * *Organization:* Chemistry/Biochemistry *Job Location:* Oklahoma-Norman-Norman Campus *Schedule:* Full-time *Work Schedule:* Monday - Friday 8-5 *Salary Range:* Target

Re: [ccp4bb] Off topic - 3D models demonstrating drug binding to students

These magnetically-linking atomically accurate single-atom models look interesting - but I understand they might be too detailed or might shift around inadvertently :Snatoms Online Store - Magnetic Molecular Models for Educationsnatoms.comI also cannot say I used them (but I am always looking for

Re: [ccp4bb] Off topic - 3D models demonstrating drug binding to students

] Off topic - 3D models demonstrating drug binding to students Dear CCP4, I apologize if this is off topic but I thought this may be a good community to ask. Before we re-invent the wheel this end, we are looking for any commercial source of three-dimensional macromolecular models that can

[ccp4bb] Off topic - 3D models demonstrating drug binding to students

Dear CCP4, I apologize if this is off topic but I thought this may be a good community to ask. Before we re-invent the wheel this end, we are looking for any commercial source of three-dimensional macromolecular models that can be used to teach how drugs are designed to fit to protein targets.

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hi Oleksiy, If the Akta Start is just for loading affinity columns (without air sensor or software), why not to get a Cyvita peristaltic pump for £3k rather than £9k? They

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

.jpg@01D73AFE.96DB0800] From: CCP4 bulletin board On Behalf Of Kovtun, Oleksiy Sent: Friday, September 16, 2022 8:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure Hi Eike, Instead of AKTA Pure I purchased a combo of AKTA Go (€24k with air sensor

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hi Eike, Instead of AKTA Pure I purchased a combo of AKTA Go (€24k with air sensor) and AKta start (€9k with frac collector). It provides two parallel workstations with AKTA start handling the dirty job of loading lysates onto affinity cartridges and the GO doing clean SEC stages. For multiple

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hi Stephan, You’re mostly correct, however, gradients made on instrument with one pump are less reliable. Thank you. Vaheh From: CCP4 bulletin board On Behalf Of Stephan Rempel Sent: Friday, September 16, 2022 7:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off-topic: experience

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hi Eike, we bought a Biorad back in 2005 or so, an Akta Purifier in 2011 and recently an Akta Go (2020). All work(ed) well, the latter two are in use. Don't know about the Biorad, it's in Santiago de Compostela. Both the Biorad and Purifier have been used a lot, the Akta Go not that much so

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

mber 2022 13:17 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure Hello Eike, A couple of comments on the AKTA Pures (while I have not experience with the BioRad systems). We have a couple of AKTA Pures and we (and another lab close to us) had a

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

ry soon. Hth, Marko Marko Hyvonen Department of Biochemistry University of Cambridge https://hyvonen.bioc.cam.ac.uk @HyvonenGroup mh...@cam.ac.uk<mailto:mh...@cam.ac.uk> From: CCP4 bulletin board On Behalf Of Schulz, Eike-Christian Sent: 16 September 2022 08:40 To: CCP4BB@JISCMAIL.A

[ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Dear all, I am considering to purchase a chromatography system for routine protein purification. The device is supposed to be used in a multi-user environment, hence ease of use, ease of training and ease of maintenance is important. I am rather looking for a robust system people like to use

Re: [ccp4bb] Off-topic question related to ITC binding studies

Hi Gergő, Thank you for discussing it in detail. It is a great help. Based on the curve fit, we also believe that the two proteins bind independently to the DNA duplex with the same affinity. The DNA indeed contains 2 sites for protein binding. As far as the dimerization of protein is concerned,

[ccp4bb] RES: [ccp4bb] Off-topic question related to ITC binding studies

16 de agosto de 2022 14:41 Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Assunto: [ccp4bb] Off-topic question related to ITC binding studies Hello everyone! Hope this email finds you well. I have an off-topic question regarding ITC binding studies, which was asked by a reviewer

[ccp4bb] Off-topic question related to ITC binding studies

Hello everyone! Hope this email finds you well. I have an off-topic question regarding ITC binding studies, which was asked by a reviewer. We performed an ITC binding study (using Affinity ITC, TA Instruments) to evaluate protein-DNA interaction which resulted in a perfect sigmoidal curve.

Re: [ccp4bb] Off topic: Are all storage dewars equal?

Hi Carmien, It appears to me that the dewars in your first link are those made by Taylor Wharton. You can do a search with that name and hopefully find less expensive options. We've used them for many years and they are good. Another one, you could try, is VME https://mvebio.com/aluminum-dewars/

[ccp4bb] Off topic: Are all storage dewars equal?

Hello everyone, We want to buy a storage dewar that can house seven unipucks. I have seen dewars on the website of the crystallography suppliers (such as the HC35 https://www.moleculardimensions.com/products/high-capacity-cryogenic-refrigerators), which is significantly more expensive than the

Re: [ccp4bb] Off-topic: Mol* Viewer re-centring hack

Hi Jon, Glad to see you are making use of the Mol* viewer. I am also replying on-list as others will hopefully find my response useful. For your specific case, I would recommend using the 'selection mode' - activated by clicking the cursor icon at the top right of the viewport. This mode

[ccp4bb] Off-topic: Mol* Viewer re-centring hack

I have been using Mol* recently which looks like a really nice tool for basic model viewing. When you click off an atom (which is the normal action for clearing a selection in model viewers), it changes the zoom, orientation and re-slabs it. Has anyone found a hack to stop it

[ccp4bb] Off-topic - Cryojet5 - boiloff heater spare

Dear, My apologies for the off-topic post. Our (11-years old) Oxford Instruments Cryojet5 LN2 cryocooling has broken down and to repair this, we are looking to purchase a simple ‘boiloff heater’ element for the shield flow dewar leg. Oxford Instruments informed us that this product was

[ccp4bb] Off topic: docking for biological insight

Dear ccp4 community, When I see the (improving) accuracy of docking in generating drug like leads, I see predominantly synthetic compounds used. It occurred to me that it might be informative to use docking of naturally occurring compounds (amino acids, sugars, lipids, factors etc) to find

Re: [ccp4bb] off topic -- pymol error message

; To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] off topic -- pymol error message > > Hi all, > > What does this message means when loading a pdb file in pymol: > > 'utf-8' codec can't decode byte 0xd6 in position 37: invalid continuation byte > > Thank you! > > Chen > &g

[ccp4bb] off topic -- pymol error message

Hi all, What does this message means when loading a pdb file in pymol: 'utf-8' codec can't decode byte 0xd6 in position 37: invalid continuation byte Thank you! Chen -- Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin University No.92 Weijin Road, Nankai

Re: [ccp4bb] Off topic - gene toxic for expression strains

Hi there, Somehow I've missed the original email :) Sorry! There are options for expressing really toxic genes, some of which have already been mentioned and others perhaps not: 1. tight regulation of expression (promoter, repressor, other regulatory elements, or a combination thereof). Beyond

Re: [ccp4bb] Off topic - gene toxic for expression strains

Hi Andy, just to follow up on Christian suggestion, which is exactly the way to go. In case you are using an already pET based vector, simply try BL21-AI (https://www.thermofisher.com/order/catalog/product/C607003), which has the T7 RNA polymerase under arabinose promoter should do the trick.

Re: [ccp4bb] Off topic - gene toxic for expression strains

Hi Andy, have you tried another promotor? Arabinose is much tighter, just to be sure that it is really not leaking. Cheers Christian On Mon, Apr 4, 2022 at 10:20 AM Andrew Lovering wrote: > Dear Board, > > > > Perhaps off-topic, but in the wider scope it’s relevant to many on here. > > > > We

[ccp4bb] Off topic - gene toxic for expression strains

Dear Board, Perhaps off-topic, but in the wider scope it's relevant to many on here. We have a gene that we are able to clone, and propagate in DH5a etc non-expression cells (hence nucleotide sequence is non-toxic) But, when we attempt to transfer to an expression strain we get no colonies We

[ccp4bb] Off-topic: Replacement CCD camera for Rigaku Dekstop Minstrel UV imager

Hi, I know the chance is low, but in a desperate try to fix our long-serving Rigaku crystal imager I'm wondering whether anyone is aware of any decommissioned (Desktop) Minstrel systems around which could provide spare sparts. Unfortunately Rigaku crystal automation systems are no longer

Re: [ccp4bb] Off-topic: happy 2022

For those who want to riddle it out (and as structural biologists hopefully don’t come across mirror and glide planes) a ppt where you can take the International Tables and superimpose the tetragonal PG diagrams on the Kaleidoscope. Find the unit cell first, and then ferret out the rest.

Re: [ccp4bb] Off-topic: happy 2022

Looks like no. 12 p4g to me: http://www2.clarku.edu/faculty/djoyce/wallpaper/wall12.html Happy New Year. On Sat, 1 Jan 2022 at 20:52, Bernhard Rupp wrote: > ..and which one of the 17 plane groups do we see here? > > Cherrs br > > On Sat, Jan 1, 2022, 12:47 Phoebe A. Rice wrote: > >> Apologies

Re: [ccp4bb] Off Topic: CCP4MG Help

M > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Off Topic: CCP4MG Help > > CAUTION: This email comes from an external source; the attachments and/or > links may compromise our secure environment. Do not open or click on > suspicious emails. Please click on the “Phish Alert

Re: [ccp4bb] Off Topic: CCP4MG Help

@JISCMAIL.AC.UK Subject: [ccp4bb] Off Topic: CCP4MG Help CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook

[ccp4bb] Off Topic: CCP4MG Help

Hello all, Looking for advice from any CCP4MG users. I am making some structural figures and have run into a problem. I posted a question to the CCP4MG-specific email list quite a while ago but received no responses, so I don't know if that list is still active. Essentially, I want to change

[ccp4bb] (off topic) Job posting - Associate Director, Protein Science

https://boards.greenhouse.io/roivantsciences/jobs/3549863 Finally posted! Thank you for looking. Artem - Cosmic Cats approve of this message To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] off-topic: pH meters

The meter doesn't matter so much as the electrode. For the meter, anything with at least 3 pH multipoint calibration is sufficient for most purposes. I usually bought something from our preferred university vendor a with very large LCD displays for my aging eyes. For protein work, and especially

[ccp4bb] off-topic: pH meters

Fellow protein biochemists: My ~30 year-old Beckman pH meter is finally showing its age, and I’m looking for a high-quality replacement that doesn’t cost insane amounts of money. My initial thoughts gravitate toward Mettler (it’s a name I trust, and some of their low-end instruments aren’t

Re: [ccp4bb] Off topic, protein characterization and binding job opportunity in Boston area

Here is the right link - https://www.linkedin.com/jobs/view/2662640332/?refId=cCDvahCrRPGWslMQWMgEOQ%3D%3D Thank you everyone for pointing this out. On Mon, Aug 23, 2021 at 4:18 PM Yanfeng Zhou wrote: > Hi, > > Sorry for the off topic post. If anyone is passionate about working in an >

[ccp4bb] Off topic, protein characterization and binding job opportunity in Boston area

Hi, Sorry for the off topic post. If anyone is passionate about working in an exciting biotech powered by machine learning, structural biology, and protein engineering, around Boston in the US, please check the link below.

Re: [ccp4bb] off-topic: structural motif / domain comparison

sday, August 5, 2021 23:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off-topic: structural motif / domain comparison Dear all Sorry for an off-topic question here. I wonder if anyone may be aware of any search program which allows one to 'blast' a protein domain just like we 'blast' a pro

Re: [ccp4bb] off-topic: structural motif / domain comparison

You might also find use in databases such as pfam, ecod, cath, scop. Orly On Fri, Aug 6, 2021, 09:43 Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain just like > we 'blast'

Re: [ccp4bb] off-topic: structural motif / domain comparison

Perhaps DALI can be of use http://ekhidna2.biocenter.helsinki.fi/dali/ Dal. pá 6. 8. 2021 v 8:42 odesílatel Sam Tang napsal: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain just like > we

Re: [ccp4bb] off-topic: structural motif / domain comparison

Hi Sam, Perhaps the Modeller service is what you’re looking for? https://salilab.org/modeller/ Best wishes, Chris On Fri, 6 Aug 2021 at 07:42 Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to

Re: [ccp4bb] off-topic: structural motif / domain comparison

Like PDBeFOLD search? https://www.ebi.ac.uk/msd-srv/ssm/ Jan On Fri, Aug 6, 2021 at 8:43 AM Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain just like > we 'blast' a

[ccp4bb] off-topic: structural motif / domain comparison

Dear all Sorry for an off-topic question here. I wonder if anyone may be aware of any search program which allows one to 'blast' a protein domain just like we 'blast' a protein sequence? For example I have an epitope in hand and would like to find out whether this also exists in other proteins.

Re: [ccp4bb] off-topic: glycans

> *From:* CCP4 bulletin board on behalf of Sam Tang > > *Sent:* 29 June 2021 06:12 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] off-topic: glycans > > > *External Sender:* Use caution. > > Dear community > > Sorry for an off-topic question here

Re: [ccp4bb] off-topic: glycans

== about.me/david_briggs From: CCP4 bulletin board on behalf of Sam Tang Sent: 29 June 2021 06:12 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off-topic: glycans External Sender: Use caution. Dear community Sorry for an off-topic question here. I wonder

[ccp4bb] off-topic: glycans

Dear community Sorry for an off-topic question here. I wonder if anyone may be aware of any glycan modification database where we can predict what is what. For example, if I got a mass difference of m/z X on LC-MS, and I would like to have a rough idea what it might be, where should I go for?

[ccp4bb] Off-topic: research associate job posting

Dear CCP4 friends We are looking for fresh talent :) please see the posting below or directly at MassBio.

Re: [ccp4bb] OFF TOPIC question

nt: Thursday, November 26, 2020 8:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] OFF TOPIC question Hi all, I have two constructs having different ori, p15ori and M13 ori, different promoters araC and LacI, and different antibiotic resistance chloramphenicol and Ampicillin respectively. I would

Re: [ccp4bb] OFF TOPIC question

, November 26, 2020 2:48:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [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

[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

Re: [ccp4bb] OFF TOPIC question

*One correction to the previous question:* I have two constructs having different ori, p15ori and M13 ori, different promoters *araBAD promoter* and LacI, and different antibiotic resistance chloramphenicol and Ampicillin respectively. I would like to know which E. coli host cells will be good for

[ccp4bb] OFF TOPIC question

Hi all, I have two constructs having different ori, p15ori and M13 ori, different promoters araC and LacI, and different antibiotic resistance chloramphenicol and Ampicillin respectively. I would like to know which *expressing E. coli host cells* will be good for the co-transformation of these

Re: [ccp4bb] (off-topic) beamline for XAFS

Dear Banu, I would recommend looking also at SSRL beam line 7-3 and 9-3 as they are well set up for protein EXAFS. Greetings, Jan On Tue, Nov 10, 2020 at 11:03 AM PULSARSTRIAN wrote: > Dear all, > Sorry for the off topic. > Looking for suggestions on beamlines for XAFS on proteins

[ccp4bb] (off-topic) beamline for XAFS

Dear all, Sorry for the off topic. Looking for suggestions on beamlines for XAFS on proteins with [4Fe-4S] clusters: I have two options, one at BNL and another at APS@ANL. At BNL, I think 6-BM (BMM) seems to be more for biological samples on metalloproteins on the other hand, ANL has

Re: [ccp4bb] Off-topic: Mild cross-linking protocol

If you have hopes for cysteine residues in reasonable proximity, then bis-iodoacetamide (with a suitable spacer, commercially available is the ethylenediamine spacer). Any reasonable chemist can make you other spacer lengths to order. Homobifunctional PEG with maleimide, N-hydroxy succinimide

[ccp4bb] Off-topic: Mild cross-linking protocol

Dear all, Sorry for the off-topic question. I need to prepare an heterodimeric protein complex for an immunisation, and I would like to make sure that the dimer will be stable and it won't dissociate after injection. I am wondering if any of you has a mild cross-linking protocol (and

[ccp4bb] Off-topic: amphipathic polymer NV-10

Dear all,Sorry for an extremely off-topic question. We are looking for an amphipathic polymer, NV-10. It used to be made by Expedeon and has been used for assisting proper protein folding as latest as in 2019 as gathered from the literature. Now in the year 2020, it seems to have disappeared

[ccp4bb] [OFF TOPIC] Cell biology bb

Hi Folks, how are you doing? Hope everyone is safe! I was wondering if there is a bulletin board email group like this one concerning Cell Biology, where we could find not only discussions about related topics but also post-doc opportunities. I would be very glad if you guys know any and could

[ccp4bb] off-topic: coronavirus test summaries

Just FYI, here are two useful links for those who would like to see what's being used to test for coronavirus: https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf

[ccp4bb] off-topic: work opportunities at Enko

Hello! Sorry (not sorry) for the off-topic post. We have a few jobs posted and I'd like to re-post them here. Please see the link for full descriptions >>> https://www.enkochem.com/careers-enko -Scientist, Structural Biology & Protein Chemistry -Senior Scientist, Protein Target Discovery

Re: [ccp4bb] Off-topic: (micro)array image analysis software

Hello, You could run Image Quant TL in a VM (parallels, vmware or virtual box). https://bmi.cchmc.org/resources/software/imagequant-tl For this appliation (arrays), we use an old program called VisualGrid that is no longer available and run it an isolated XP VM via virtual box (in linux).

[ccp4bb] Off-topic: (micro)array image analysis software

Hello, clearly off-topic but maybe someone here is experienced in the analysis of array scans and can offer some advice? That would be beautiful. Here’s the problem: I want to test an ELISA-based HT array for phosphorylation profiling of a whole pathway, with almost 200 antibodies at once.

Re: [ccp4bb] Off-topic (somewhat): Call for papers on structure-guided kinase drug discovery

Dear Isabel, I strongly support and **heartily thankyou** for your email below in support of IUCr Journals. A wide range of readerships are covered, now also including IUCrJ with its articles describing results aimed at highly diverse readerships ie well beyond crystallography. I would also add

Re: [ccp4bb] Off-topic (somewhat): Call for papers on structure-guided kinase drug discovery

Yes, this issue will definitely compete with IUCr's many journals dedicated to kinase drug discovery. /sarcasm On a more serious note: nobody should be "loyal" to a journal or scientific society; both are servants of the scientific community, not the other way around. If they stop supporting

Re: [ccp4bb] Off-topic (somewhat): Call for papers on structure-guided kinase drug discovery

Dear Julie and Mathew, I feel advertisement on behalf of professional publishers is not appropriate for the bulletin board. MDPI should pay for its advertisements, rather than get them for free. (Being a for-profit firm, they should also pay for, rather than invite editing, but this is of course

[ccp4bb] Off-topic (somewhat): Call for papers on structure-guided kinase drug discovery

Dear colleagues, Mathew Martin and I would very much appreciate your contributions on the topic of "Recent Advances in Structure-Guided Kinase Drug Discovery" for a special issue of the International Journal of Molecular Sciences (IJMS, ISSN 1422-0067, Current

[ccp4bb] (off-topic) fundraising campaign - EMERGENCY VENICE

Dear All, On behalf of Elisa Moretti (in Cc.) I share this fundraising initiative for Venice that was recently damaged by flooding: Dear all, I am sharing with you the news about the initiatives launched by Ca' Foscari University of Venice (Italy) in support of Venice and its citizens, hit

[ccp4bb] Off topic: 384 well stamper

Colleagues I have a quick question for you: we are in need of a small footprint 384 well plate stamper with dilution (optional but desired) capability. We are already evaluating Integra, Jena Analytic, and Apricot models but we are curious if there are other companies who sell this sort of

Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

Thanks to everyone who gave helpful suggestions; I now have stereo working on Ubuntu 18.04. To help anyone who comes across this in the CCP4 archives in the future, it was necessary to: 1) Install lightdm and set it as the default display manager. Other display managers that don't do

Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

I used to use Ubuntu Mate OS to get 3D work for coot and pymol. I am not sure if the latest version still works. Regards Xiao On Fri, Nov 8, 2019, 7:19 AM Chris Richardson wrote: > Apologies for the only slightly relevant question. > > Does anyone know the correct incantations to get nVidia

Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

Hi Chris We have it working with the Mate desktop. Composite disabled. Let me know if you would like more details Regards Christine. Sent from my iPad > On Nov 8, 2019, at 4:18 AM, Chris Richardson > wrote: > > Apologies for the only slightly relevant question. > > Does anyone know the

Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

CCP4BB" Envoyé: Vendredi 8 Novembre 2019 13:18:44 Objet: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04 Apologies for the only slightly relevant question. Does anyone know the correct incantations to get nVidia 3D Vision glasses and emitter working with Ubuntu 18.04? None of

[ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

Apologies for the only slightly relevant question. Does anyone know the correct incantations to get nVidia 3D Vision glasses and emitter working with Ubuntu 18.04? None of the tricks that work with 16.04 are helping with the new release. In particular, disabling composite in the extensions

[ccp4bb] Summary: [ccp4bb] off topic: microscope in glove box

Dear Artem, Marta, Arwen, Robin, thank you all for the detailed info. We had a try today and it worked smoothly. Thanks again and best regards, Guenter Short version: It should be OK, especially since the vacuum is transient and not particularly 'strong*' :) Long version: if this is an

Re: [ccp4bb] off topic: microscope in glove box

Short version: It should be OK, especially since the vacuum is transient and not particularly 'strong*' :) Long version: if this is an older microscope there may be further delamination of optically bonded components if air is already admitted between glass planes (i.e. the optical cement is worn

[ccp4bb] off topic: microscope in glove box

Dear all, I want to put one of our microscopes into the glove box. Does anybody know whether some parts of the microscope optics do not like vacuum in the air lock ? Thanks and best regards, Guenter To unsubscribe

[ccp4bb] off topic: job posting

Good morning, We have two relevant job postingings that I would like to share. Thank you for your attention :) Artem https://careers.massbio.org/job/sr-scientistprincipal-scientist-computational-chemistry/49455467/ and

Re: [ccp4bb] Off-topic question

Hi, there is a guide here, but you should get the proper script for Pymol from the Consurf server. http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/consurf.php Jan On 6/22/19 10:24 PM, khaja faisal tarique wrote: > Hi everyone, > > I was wondering can anyone suggest

[ccp4bb] Off-topic question

Hi everyone, I was wondering can anyone suggest me how to project the primary sequence conservation calculated through the Consurf server. Any help or suggestion will be appreciated. I have pasted a figure from an article just for reference. Best Khaja [image: image.png]

[ccp4bb] Off topic: room temp FPLC column cooling

Hi Michael, besides the very valuable suggestion of Gianluca, which worked well in my PhD lab, more recently I had very good results using silica gel. You can find desiccant beads of different diameter and pore size (for absorbing water normally around 2.5 nm). Self-indicating ones help you

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