Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Dear Rafael, do you know if your protein interacts with another protein? This could be critical. I have been studying proteins that require a protein partner to be expressed as soluble protein. Co-expressing both proteins in E. coli shifts the expression from insoluble to soluble. Hope this h

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Hello Rafael, I would give one more by reducing the temperature for the expression.  I am assuming that you did the expression at 37 oC. I would start expression at 30 oC and reduce it further after induction to 25 oC or so and let it grow longer.  But refolding the protein is also possible.  T

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Hi Dave, I should have mentioned that, but yes, I tried 16 degrees overnight and even up to 40 hours. The _expression_ level is great, majority is in the pellet though and the elution fraction is far from desirable for my kinetic assays. Best wishes _

Re: [ccp4bb] off-topic: Synergy Finder

Dear all Many thanks for all the responses this afternoon. Turns out if I am lucky enough then I may be able to link up in 10-15 refreshes. And only on Microsoft Edge not Chrome or Safari. Apparently the server is there but the connection from my place is not quite stable -- and that's why my neig

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Dear Rafael, I agree with the previous answers, decreasing the temperature to 16-18°C overnight during protein expression really helps with folding. It works wells with BL21(DE3) and Rosetta cells. I think there is even a E.coli strain for lower temperature but I have never used them myself. A

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Hi Rafael, We have had great success across many projects using Arctic Express with induction at as low as 4C, often getting high level soluble expression rather than insoluble lumps. https://www.agilent.com/en/product/protein-expression/competent-cells-for-difficult-protein-expression/insoluble

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Refolding protocol is often specific to the protein. As a rule of thumb, consider exploring refolding in large dilution regime as well as dialysis and on-column methods. As far as refolding GST fusions, I personally recommend re-cloning without GST and refolding the guest proteins by itself. This c

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Very interesting--I’d like to hear more about this heat-shock idea. First, am I understanding correctly? Grow at 37 deg to desired OD; heat shock 20 min; then chill and induce/express at desired temperature (e.g., 20 deg)? Second, what sorts of problems did this help with? E.g., a lack of high-l

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Hello, we found that a short (20 min?) heat shock to 42 degrees C followed by cooling on ice prior to induction and growth at lower temp, as suggested by David, worked for several proteins, but not all. Best wishes, Jon Cooper. Emeritus at UCL. jon.b.coo...@protonmail.com Sent from Proton Mail

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

Hi Rafael, I have you tried reducing the temperature post-induction? You can grow the cells to OD600 , reduce the temperature (I have gone as low as 16ºC), add IPTG and harvest the cells the following morning. The reduction in temperature can slow down the rate of protein production allowing t

Re: [ccp4bb] Off topic: Water system sanitization

Thank you! I’m an idiot for not thinking of the MSDS. Sent from my iPhone, pls excuse typosOn Jan 11, 2025, at 3:30 AM, Michał Taube wrote:Hi Patric, it seems that this is water solution of 0-2% chloramine-T , trihydrate.https://www.barnstead-water.com/images/CMX25-msds.pdfBest MichalW dniu pt.,

Re: [ccp4bb] Off topic: Water system sanitization

Hi Patric, it seems that this is water solution of 0-2% chloramine-T , trihydrate. https://www.barnstead-water.com/images/CMX25-msds.pdf Best Michal W dniu pt., 10 sty 2025 o 18:22 Patrick Loll napisał(a): > Happy New Year, Everyone, > > I have a question about the “cleaning syringe” that is s

Re: [ccp4bb] [OFF-TOPIC] Dissolving DMPC/ Na Cholate in buffer for nanodisc assembly

Dear Rafael, What final concentration of DMPC are you trying to achieve? Or are you more concerned with a ratio? For example, 20 mg/ml DMPC is nicely soluble in 50-100 mM sodium cholate (TRIS 7.8, 20-100 mM NaCl), and for preparation of micelles one can then suck the cholate out with bio-beads...

Re: [ccp4bb] [OFF-TOPIC] Dissolving DMPC/ Na Cholate in buffer for nanodisc assembly

inada" De: Artem Evdokimov Enviado: segunda-feira, 2 de dezembro de 2024 17:17 Para: Rafael Marques Cc: CCP4BB@jiscmail.ac.uk Assunto: Re: [ccp4bb] [OFF-TOPIC] Dissolving DMPC/ Na Cholate in buffer for nanodisc assembly Dear Rafael, What final concentration of DM

Re: [ccp4bb] Off topic: Nobel prize stats

Forgot to credit the Nobel Prize website :The Nobel Prize in Chemistry 1946nobelprize.org-BWL To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Off topic: Nobel prize stats

The Nobel Prize in Chemistry 1946 James Batcheller Sumner “for his discovery that enzymes can be crystallized” Prize share: 1/2 John Howard Northrop and Wendell Meredith Stanley "for their preparation of enzymes and virus proteins in a pure form" Prize share 1/2 jointly Thought it might be w

Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

Dear Markus, I've had to solve this exact issue in the past. Putting a 'simple' (nothing is simple these days, everything has some kind of AI or other evil gnomes in it) spectrofluorimeter into the cold room *should* be OK. Caveat #1: I don't know if this will work with your specific device Cavea

Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

I think you are right, in the final equilibrium all the moisture would condense on the (evaporator?) coils, and there should be provision for them to drip into a reservoir outside. However each time the door opens and humid air is admitted, there will be condensation everywhere. If you leave th

Re: [ccp4bb] Off topic: Nobel prize stats

Thank you all for useful links, slides and thoughtful comments. I completely agree with Mark's comment that it is difficult to quote a single number. Precisely for the reasons he mentioned. The link to PDB, https://pdb101.rcsb.org/learn/other-resources/structural-biology-and-nobel-prizes seems the

Re: [ccp4bb] Off topic: Nobel prize stats

x27; ; 'CCP4BB@JISCMAIL.AC.UK' Asunto: RE: [ccp4bb] Off topic: Nobel prize stats This is not the same, but it may help... https://www.xtal.iqf.csic.es/Cristalografia/index-en.html Martin _ Dr. Martin Martinez-Ripoll Research Professor Emeritus mart

Re: [ccp4bb] Off topic: Nobel prize stats

You may want to add Kavli Prize laureates as well. -Lisa Keefe IMCA-CAT > On Jul 22, 2024, at 8:59 PM, Joel Sussman wrote: > >  > 22-Jul-2024 22:00 > Dear Nukri, > Please see: > https://proteopedia.org/w/Nobel_Prizes_for_3D_Molecular_Structure > best regards > Joel > > --

Re: [ccp4bb] Off topic: Nobel prize stats

22-Jul-2024 22:00 Dear Nukri, Please see: https://proteopedia.org/w/Nobel_Prizes_for_3D_Molecular_Structure best regards Joel Prof. Joel L. Sussman joel.suss...@weizmann.ac.il Dept. of

Re: [ccp4bb] Off topic: Nobel prize stats

I prepared this slide for a course (it only goes back to 1962, and some more recent awards should be added; but it’s a start). I looked at the PDB website and I think it would be a stretch to say that some of these were awarded for structural biology; the PDB puts in a link that relates the aw

Re: [ccp4bb] Off topic: Nobel prize stats

Nice, AI failed yet again to produce a comprehensive list of awardees. Some of the names match up with your link but it is very incomplete. Jürgen > On Jul 22, 2024, at 2:47 PM, William Scott > <2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote: > > https://pdb101.rcsb.org/learn/other-reso

Re: [ccp4bb] Off topic: Nobel prize stats

https://pdb101.rcsb.org/learn/other-resources/structural-biology-and-nobel-prizes > On Jul 22, 2024, at 11:41 AM, Nukri Sanishvili wrote: > > Dear All, > Does anyone know the number of Nobel Prizes awarded for macromolecular > structures? > This would be a very effective way to explain the imp

Re: [ccp4bb] Off topic ; how to remove fluorescein from superdex increase

Have you tried Guanidinium chloride? Jürgen > On Jul 3, 2024, at 1:22 PM, Daniele de Sanctis wrote: > > Hi Flavio > > I’d suggest to contact Regenfix > https://www.regenfix.eu/ > > Usually they give you back a column better than the original one completed > with an experimental calibration

Re: [ccp4bb] Off topic ; how to remove fluorescein from superdex increase

Hi Flavio I’d suggest to contact Regenfix https://www.regenfix.eu/ Usually they give you back a column better than the original one completed with an experimental calibration curve. Cheers Daniele On Wed 3 Jul 2024 at 18:56, Nicholas Clark < b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wro

Re: [ccp4bb] Off topic ; how to remove fluorescein from superdex increase

Hi Flavio, I’d recommend reaching out to Cytiva directly ( scientificsupport...@cytiva.com). We had an issue with oxidized metal on our S200 and they were able to provide useful suggestions (plus side is, you know what they suggest won’t ruin the resin). Best, Nick Clark Nicholas D. Clark, PhD

Re: [ccp4bb] Off-topic: UCSF Chimera Download

I realised i have its chimeraX, not the old chimera. Sorry. O. On 18. Jun 2024, at 18:21, Kovtun, Oleksiy mailto:oleksiy.kov...@mpinat.mpg.de>> wrote: I dug out a MacOS dmg file, too. I will DM you a link. O. On 18. Jun 2024, at 18:09, Nicholas Clark mailto:ndcla...@buffalo.edu>> wrote: Tha

Re: [ccp4bb] Off-topic: UCSF Chimera Download

I dug out a MacOS dmg file, too. I will DM you a link. O. On 18. Jun 2024, at 18:09, Nicholas Clark mailto:ndcla...@buffalo.edu>> wrote: Thanks for the responses. I’ve made multiple attempts over the last few days which is why I reached out. Maybe it’s just high traffic and I’ll have to keep

Re: [ccp4bb] Off-topic: UCSF Chimera Download

Hi Nick, their web site goes offline from time to time. If you are on linux, I can share recent binaries. Best, Oleksiy On 18. Jun 2024, at 17:53, Nicholas Clark > wrote: I’m trying to navig

Re: [ccp4bb] Off-topic: UCSF Chimera Download

upgrades. Hope this helps. Andy From: CCP4 bulletin board on behalf of Nicholas Clark <b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> Sent: 18 June 2024 17:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: UCSF Chimera Download External Sende

Re: [ccp4bb] Off-topic: UCSF Chimera Download

Thanks for the responses. I’ve made multiple attempts over the last few days which is why I reached out. Maybe it’s just high traffic and I’ll have to keep trying. Oleksiy, thanks for the offer but I’m on MacOS. Best, Nick On Tue, Jun 18, 2024 at 12:07 PM Kovtun, Oleksiy < oleksiy.kov...@mpina

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 s

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, 0

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

ly 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 19:53 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re:

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 slightly

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, ow

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 protei

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

Hi Rafael, For completeness - there are alternatives to imidazole for eluting proteins from Ni-NTA resins: EDTA - (strips Ni2+, and therefore everything bound to the Ni2+) - 50mM should be sufficient, in your favourite buffer/salt system. Obviously not appropriate for metalloproteins. You'll

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 t

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 respec

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 a

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

Hi Ed, The future is already here... and virtual reality is your friend. This is a field that will likely be revolutionized in the near future, and your students would get an advantage by being exposed to these new technologies. You could check the following: https://www.labcompare.com/10-Featured

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 far.

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

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 catastrophic failure of the 3-wavelength detector "block". Price tag for the replacement part (apparently a black

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, w

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/ We

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 cha

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

This means that you have an O-umlaut in your PDB file. That should never happen! PDB files should only have basic ASCII characters, not UTF-8. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of 陈成 > Sent: Tuesday, April 5, 2022 13:12 > To: CCP4BB@JISCMAIL.AC.U

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 u

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. Al

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

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. htt

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

Hi Or make your first object residues 1-50 & 60-100 and the second object 50-60 (i.e. don't leave a gap between them). ISTR there's a way to join two atoms, but I can't remember off-hand. Harry -- Dr Harry Powell > On 5 Nov 2021, at 19:10, Denis Rousseau > wrote: > > Hi Matthew > > Try mak

Re: [ccp4bb] Off Topic: CCP4MG Help

Hi Matthew Try making one set from 1-100 and a separate set from 50-60. Then change the color of the 50-60. It worked on my computer. Best Denis From: CCP4 bulletin board on behalf of Whitley, Matthew J Sent: Friday, November 5, 2021 2:21 PM To: CCP4BB@JISC

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 i

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 > excit

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

A lesser known service with very powerful search across domains and chains is TopSearch by Manfred Sippl & Cie.: https://topsearch.services.came.sbg.ac.at/ Its training set includes PDB entries up to 2018. Best, BR From: CCP4 bulletin board On Behalf Of Sam Tang Sent: Thursday, Augu

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' a

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 'blas

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 protein

Re: [ccp4bb] off-topic: glycans

Thanks David! This is exactly what I am looking for. Sam On Tue, 29 Jun 2021 at 19:35, David Briggs wrote: > Hi Sam, > > GlycoMod from Expasy sounds like it might do what you want to do. > > https://web.expasy.org/glycomod/ > > D > > -- > > *Dr David C. Briggs* > > Senior Laboratory Research S

Re: [ccp4bb] off-topic: glycans

Hi Sam, GlycoMod from Expasy sounds like it might do what you want to do. https://web.expasy.org/glycomod/ D -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == Diamond User Committee (MX) CCP4 WG2

Re: [ccp4bb] OFF TOPIC question

Hello Anamika, >From the information you gave, you have two different promoters- araC and the >lac promoter. LacI is the lac inhibitor. The lac promoter is a two part >system- when lactose is not present, the inhibitor sits near the promoter and >blocks transcription of genes downstream. Almost

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

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

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

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 este

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). D

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 sc

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 p

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 composit

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 3D

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 corr

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

Hello, The desktop changed in the passage from Ubuntu16 to Ubuntu18. I think Nvidia stereo now works only with a xfce desktop. The passage from debian 8 to debian 9 was not a problem as long as xfce is kept. Best regards Wim - Mail original - De: "Chris Richardson" À: "CCP4BB" Envoyé: V

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

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 me

Re: [ccp4bb] Off topic: room temp FPLC column cooling

Bear in mind that if you have cold buffers going into a room temperature (or warmer) pumps, you can get outgasing that will cause inaccurate flow or loss of priming for the pumps. You may be able to work around by using freshly degassed eluents, but the outgasing will still be a problem for long ru

Re: [ccp4bb] Off topic: room temp FPLC column cooling

Hi, a cheap solution would be to put buffers, fraction collector, and the column (if not too big) inside a cold cabinet, next to the FPLC. you probably need to use longer pipes but it works Best regards, GIA Le 07/06/2019 16:51, - - a écrit : Dear all, our cold cabinet FPLC is rotting a

Re: [ccp4bb] off topic: Membrane protein "into" soluble protein

In theory yes, you can fuse the termini to restrain the protein. You could use T4 lysozyme and insert in the loop which they use for crystallizing GPCRs (many references, including https://www.ncbi.nlm.nih.gov/pubmed/25450769). The potential problems are that you have no idea where the termini a

Re: [ccp4bb] Off topic question

Dear Reza, CD hit will do exactly that. Cheers, Georg Sent from my iPhone On Jan 3, 2019, at 2:41 PM, Reza Khayat mailto:rkha...@ccny.cuny.edu>> wrote: ​Hi, Happy new year to all! A bit of an off topic question. Does anyone know of a method/program to extract the most distinct "n" (n>2)

Re: [ccp4bb] Off topic question

Hi Reza, happy new year! The choice would depend on your alignment (aminoacid or nucleotides? are the sequences closely or distantly related? is it a large alignment? are there many gaps?)... Anyway, I think the safest, unbiased way to determine a group of outliers might be to compute a phylogeneti

Re: [ccp4bb] Off topic question

On Thursday, January 3, 2019 12:40:05 PM PST Reza Khayat wrote: > ?Hi, > > > Happy new year to all! A bit of an off topic question. Does anyone know of > a method/program to extract the most distinct "n" (n>2) sequences from a > sequence alignment? Thanks. If these putative "most distinct"

Re: [ccp4bb] Off topic question

PCA? On Jan 3, 2019, at 3:41 PM, Reza Khayat mailto:rkha...@ccny.cuny.edu>> wrote: ​Hi, Happy new year to all! A bit of an off topic question. Does anyone know of a method/program to extract the most distinct "n" (n>2) sequences from a sequence alignment? Thanks. Best wishes, Reza Re

Re: [ccp4bb] OFF TOPIC

Hi Anamika, As far as I understood, the biotin in the elution buffer is helping your protein to get stripped off from the Avidin column. So, maybe you dialyze your purified protein (or run FPLC) and get rid of biotin completely, before you load the protein on to strptavidin coa

Re: [ccp4bb] OFF TOPIC

Hi Anamika, - Have you double-checked that the sequence of your cDNA is correct and includes the biotin acceptor peptide tag (BAP tag aka AviTag; GLNDIFEAQKIEWHE in single-letter amino acid code)? - Are you using a dedicated bacterial strain that over-expresses BirA enzyme? This may not be str

Re: [ccp4bb] OFF TOPIC

You don’t say so, but one assumes that you have a BAP tag on the protein, and co-express a biotin ligase such as BirA? Ed T.A.Edwards Ph.D. Associate Professor of Biochemistry Deputy Head of School _ Astbury Centre for Structural Molecular Biology School of M

Re: [ccp4bb] OFF TOPIC

Hello, you probably purified a contaminant. Do a blot with an anti-biotin antibody or get electro-spray mass spectrometry done in order to confirm the identity of your protein. Wim On 13/11/2018 11:13, Anamika Singh wrote: Hi All,

Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice

r 27, 2018 5:41 AM To: Whitley, Matthew J Cc: ccp4bb Subject: Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice Dear Matthew, I am also late in responding to this, but as part of a Nature Protocols paper on iMosflm (Supplementary Informat

Re: [ccp4bb] Off-topic, protein in dye-front (ion front?) on native-PAGE

Hi All, Sorry to bring this old topic up again. I planned to run tricine gels but I found a possible error in table 2 (4% stacking gel formula) in Hermann Schägger protocol (Nature Protocols volume 1, pages 16–22 (2006), the author wrote 3ml 3X gel buffer in a total of 12 ml solution, it should b

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