Re: [ccp4bb] Off topic: Water system sanitization

., 10 sty 2025 o 18:22 Patrick Loll <pjl...@gmail.com> napisał(a):Happy New Year, Everyone, I have a question about the “cleaning syringe” that is sold for DI water systems such as the Barnstead Nanopure (when one replaces the cartridge, one injects the contents of this 60-mL syringe in

Re: [ccp4bb] SUMO and SUMO protease

Hi Gloria! What’s the point of publishing a nice paper if nobody reads it? *Sigh* (see reference below, we’re happy to share vectors). So yes, SUMO fusions have definitely worked for us; this strategy is our first choice for expressing any new soluble protein, and we use it for a lot of membra

[ccp4bb] CCP4 installer on Sequoia

Hi all, I’m encountering problems installing CCP4 9.0 on a brand-new MacBook Pro (M4 chip, OS 15.1.1). Specifically, when I try to launch the Package Manager (cntrl-click-open, ccp4sm-uni), the icon does that brief “zoom out” thing, but then nothing else happens. I’ve worked my way down from

[ccp4bb] Apple M4 chip

I’m thinking about getting a new laptop before the imbeciles in the new US administration impose massive tariffs on anything made abroad. This would likely involve getting an Apple machine with the new M4 chip. These are only just being released, so it’s obviously too early for people to have

Re: [ccp4bb] Off topic: Nobel prize stats

gt; > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 Patrick Loll pjl...@gmail.com To unsubscribe from the CCP4BB list, click th

[ccp4bb] Microscope camera

Greetings, hive mind, We have an old (but still useful) Nikon SMZ stereomicroscope that we use for mounting crystals. I’d like to attach a digital camera to the phototube, both to capture crystal images for archival purposes, and also to live-stream as a teaching tool. I’d be grateful for any

Re: [ccp4bb] Database for submitting unprocessed diffraction data

We’ve used Zenodo. It’s not dedicated solely to diffraction data, but it does check the “freely available” box. > On Oct 18, 2023, at 12:23 PM, JEROME JOHNSON > wrote: > > Hello all, > > As the subject says, I am looking for an open online datab

[ccp4bb] PyMol tutorials: Summary

Thanks to everyone who responded to my query about PyMol tutorials. Several people evinced interest in seeing a summary of the results, so I’m attaching one below: YouTube tutorials for PyMol: = 1) Molecular Memory got a number of mentions: https://www.youtube.com/@Molec

[ccp4bb] PyMol tutorials?

Hi everyone, Can the hive mind recommend particular video tutorials that introduce PyMol? I’m looking for a beginner-level introduction, suitable for undergrads or early-career grad students. My hope is that some kind soul(s) can save me from slogging through hours on YouTube in order to find

[ccp4bb] Coot (& phenix) on Ventura

Hi everyone, I’ve been putting off upgrading to Mac OS 13 Ventura, but my computer is getting more and more pushy in its demands for a new OS. Hence I ask, What’s the current status of coot running on Ventura? I’m aware of the issues that have been discussed in this forum, but that thread seems

[ccp4bb] direct-to-video screen camera for xtal mounting

Does anyone have any experience with a setup in which the output from a camera on a microscope goes straight to a video display? I.e., not to a computer and thence to a display? I’m considering putting a crystal-mounting microscope into a glove box, and this kind of setup strikes me as simpler

Re: [ccp4bb] Solubility of Aluminum Fluoride

Kevin and Guillaume said it all quite well. I just want to stress one thing, namely that these solutions are metastable, and will eventually precipitate (hours to days). In the case of the beryllium salts, the precipitation is due to slow formation of metal hydroxide species. I have no direct

Re: [ccp4bb] Eiger images and XDS

. > > Could you try durin-plugin.so ? > > Possibly your machine has a problem; could you try a different Mac? > If all fails, send me a link to the data. > > Best wishes, > Kay > > On Tue, 31 May 2022 15:18:23 -0400, Patrick Loll wrote: > >> Hi all, >> >>

[ccp4bb] Eiger images and XDS

Hi all, Apologies for the non-CCP4 question: I’m attempting to use XDS to process some data from the Eiger detector at the AMX beamline (NSLS-2 17-ID-1). To read in the Neggia library, my XDS.INP contains the line “LIB=/…path.../dectris-neggia-mac.so" I’ve successfully used the same dectris

[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 absu

Re: [ccp4bb] Phosphatase enzymatic assay

g link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/

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

Transglutaminase, also known in some circles as “meat glue." > On 17 Jun 2021, at 11:50 AM, Bryan Lepore wrote: > > Greetings > > This enzyme meets none of the stipulations, but I will point out as it is > somewhat unusual to find in a grocery store : > > A food product called Just Egg contai

Re: [ccp4bb] Design of SUMO fusion proteins

> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > Patrick Loll pjl...@gmail.com To unsubscribe from

Re: [ccp4bb] Fluka-branded PEG 3000

I don’t think we have any of that PEG lying around (sorry), but you might also consider that PEGs are notorious for impurities of various types; perhaps the Fluka reagent has less of an impurity that is particularly vexing for your specific protein. Of course, I suppose it might have more of a

Re: [ccp4bb] The weekly nonsense

- > Many plausible ideas vanish > at the presence of thought > -- > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&a

[ccp4bb] Stabilizing Mitegen reusable bases/mounts

Hi everyone, I’ve become very fond of the Mitegen reusable bases for mounting crystals, since the reusable aspect savse me from having to discard the base every time I break a microloop. However, once the crystals arrive at the synchroteon, I observe motions of the loops (some gradual, some spo

[ccp4bb] Fwd: [ccp4bb] AW: Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

reserved=0, >> terms & conditions are available at >> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=02%7C01%7CHerman.Schreuder%40SANOFI.COM%7Cf86f5afb3c3d4664586e08d87502dc60%7Caca3c8d6aa714e1aa10e03572

[ccp4bb] CCwork/CCfree

, I mean the peaks of the histograms (phenix.r_factor_statistics suggests R ~ 0.15-0.18, Rfree ~ 0.19-0.22) I realize that I could probably dig up this information on my own, but I’m (feeling lazy)/(desirous of the community’s wisdom). Thanks, Pat Patrick Loll pjl...@gmail.com

[ccp4bb] flow rate for cooling stream?

Sorry, way off topic: Does anyone have an estimate for the flow rate one would typically use for the cold nitrogen stream passing over a protein crystal in a standard data collection? Background: Our nitrogen “generator” has gone belly-up and the vendor no longer services it, so I’m testing th

[ccp4bb] dewar horror stories

Hello community, We recently had a dry shipping dewar fail catastrophically (while en route to the beam line, so, major trauma). I sent it to a company that specializes in repair and refurbishing of cryogenic tanks, and they told me it has an internal leak, and hence is not reparable. I was exp

Re: [ccp4bb] Space group/Unit cell

This reminds me of something that we crystallized a few years back. It indexed as I222 (or I2(1)2(1)2(1)) and the cell was quite small; too small for the protein of interest. Almost certainly a contaminant, but it didn’t show up in Contaminer. Diffracted like gangbusters, but we never figured ou

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

The idea of contacting the editor (and/or author) is an excellent one, and indeed the correct thing to do scientifically. However, I’m disillusioned: I’ve been down this path before with a high-profile vanity journal, and while the editors paid lip service to the notion that the record should be

Re: [ccp4bb] A Question about crystal packing

Best regard > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > <https://ww

[ccp4bb] Fwd: [ccp4bb] SO4 or PO4

S has about 0.56 anomalous electrons at 8 keV, whereas P has about 0.44. This is a small difference between two weak signals—unlikely to give a clear result. If you could get to the sulfur & phosphorus edges, then you could (in principle) answer this, but that’s a very hard experiment to accompl

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

Fig. 2.13 in Gale Rhodes’ “Crystallography Made Crystal Clear” touches on rabbit heads and diffraction, and is one of my favorite cartoons (sadly it doesn’t directly address your problem). > On 2 Nov 2018, at 5:14 PM, Deborah Harrus wrote: > > Dear all, > > I came across an unidentified rabbi

Re: [ccp4bb] nonenzymatic removal of His tag?

1) Use a different protease, e.g. SUMO protease, which is sufficiently specific that it’s unlikely to cause any problems even if a little bit is carried along. See, for example (shameless plug #1): DOI: 10.1016/j.pep.2006.12.006 2) Use intein cleavage. NEB sells a vector that lets you fuse an in

Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

I second (third?) what Tommi and Kevin said about using an oil to cover the drop to slow evaporation (I like paraffin for this—not too viscous). Here’s an additional nuance: Saturate the oil with the alcohol first, before using it to cover the drop. > On 14 Aug 2018, at 2:58 PM, Thomas Krey w

Re: [ccp4bb] [ccp4bb] Oxford University Press

> I think what we should do is not publish in journal families where the profit > is above 10 per cent. Elsevier is the place to start as their profit margins > are like those of Apple, and of competition there is none. Elsevier: Like Apple, but without the design sense. But seriously, Adria

Re: [ccp4bb] Unknown density

Calcium likes to form octahedral complexes with water (or other oxygen-containing) ligands. This looks like a classic example. After you model and refine this, you’ll want to check water-metal distances, to make sure they are appropriate for calcium. There is a nice literature on such things,

[ccp4bb] ample

I’m intrigued by the prospect of using AMPLE to test multiple distant homologs in a MR problem. I’ve used HHPRED to identify about 20 high-probability homologs of known structure, each of which has about 20-25% identity with the unknown protein. However, it’s not clear to me from the documentati

[ccp4bb] comfortable OS X level

I’m still running Yosemite on my Macs, both because I’m change-averse and because folks reported problems with some crystallographic software upon upgrading the OS. These reports have now faded into the haze of the past, and so I ask, have the issues been resolved? Is it safe to move to Sierra?

Re: [ccp4bb] Off topic instrumentation

I’m looking at my copy of Terrance Cooper’s ‘The Tools of Biochemistry’ (Wiley, 1977). It identifies two approaches to fractionating gradients. The first is the one Michael describes (allowing the liquid to drip out of the bottom). The other is to pierce the bottom of the tube, and then pump a v

[ccp4bb] Off-topic x 2: Chaperone co-expression AND Bac-Mam contract work

Hello everyone, Please allow me to kill two off-topic birds with one email ‘stone’: 1) Can anyone suggest where I can lay hands on the pREP4-GroESL plasmid for bacterial co-expression of GroEL and GroES? I’ve checked with the original author (Philip Cole), but it’s been decades since he publi

Re: [ccp4bb] Crystal with ZERO diffraction

Sadly, I have seen numerous examples of reasonably-sized crystals that give no observable ordered diffraction (I shot a few this weekend, in fact). I can’t give you evidence for what is happening, but I guess that you can build a macroscopic assembly using lattice interactions that are only mode

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

Ave atque vale. The EDS was hugely useful (and will continue to be so in its new manifestation, we hope)—thanks to everyone who made it happen! Pat > On 13 Dec 2016, at 12:51 PM, Gerard DVD Kleywegt > wrote: > > Hi all, > > After tirelessly serving the scientific community with (mostly)

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

How about the ability to compile code? Are there decent compilers readily available for Windows? I like being able to write & compile the occasional fortran program {hic sunt dinosaurs}, and it’s easy to do this on a unix-based platform like OSX. If your reasoned arguments fail, I have found th

[ccp4bb] XDS.INP for X25

Hi, I'm trying to help a colleague process some data collected at beamline X25 of the late, lamented NSLS. Does anyone have an XDS.INP file that they know works for such data (this is for the Pilatus detector)? I have kludged together a file that looks right, but the processing still doesn't fee

Re: [ccp4bb] software/web server to determine ligand volume

VOIDOO will do this On 13 Aug 2014, at 2:06 AM, sreetama das wrote: > Dear all, > Is there any software or web server available to calculate the volume of a > ligand if the ligand coordinates are provided? > Google seems to come up only with options to calculate protein cavity volume. > > Than

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

You can cut a small piece of sponge and put that into the reservoir; this prevents the reservoir buffer from splashing up into the drop. The sitting drops should be reasonably safe, but the 10 uL hanging drops are big; they'll be vulnerable to falling off if the tray is jarred. Good luck! Pat

[ccp4bb] Fwd: [ccp4bb] : MTZ for a protein fragment and R factors, Masking and Maps

George, Remember that scattering from every point in the cell contributes to every reflection; the R-value is a global metric of agreement between the model and the data. Hence, calculating the R-value for a few selected residues is not a sensible thing to do, unless you want to ask how well yo

Re: [ccp4bb] question on charge charge interactions

Two Arg side chains stack next to each other in ferritin and in GST (see, for example, Arg-59 and its symmetry mate in 3F33). I expect there are other examples, but these two come readily to mind. Cheers, Pat On 27 Mar 2014, at 7:11 PM, Tom Peat wrote: > Hello All, > > I am appealing to th

Re: [ccp4bb] Determining concentration of membrane protein

No, because Bradford is based on the increase in absorbance when the dye moves from a hydrophilic environment to a hydrophobic one (like the protein interior, or like the interior of a micelle). When detergents are present in excess of their CMC, the change in absorbance from partitioning into t

Re: [ccp4bb] off-topic: bug busting

I'm joining the pig-pile on the Emulsiflex. I like it because: a. The folks at Avestin are very helpful (they're Canadian--just naturally nice) b. It'll break yeast as well as E coli c. It seems pretty gentle to me (we pack it in ice, so there's negligible sample heating)

Re: [ccp4bb] Puzzling observation about size exclusion chromatography

If your protein elutes very late, that means it's binding to the column matrix (so all estimates of size go into the trash). Check to see that the ionic strength of buffer is reasonable (equivalent to, say, 150 mM NaCl). If so, then the only solution is to go to a different matrix type. Pat On

Re: [ccp4bb] Calcium ions in enzymes

staph nuclease On 31 May 2013, at 6:25 AM, Wei Liu wrote: > Dear all, > > As we all know, many proteins contain calcium ions. Does anyone know if there > are reported cases where calcium ions play a catalytic role rather than a > structural role in enzymes? > > Best > Wei Liu -

Re: [ccp4bb] refinement hanging--what am I missing?

> Hi Pat, > > Your stats aren't all that bad, but I share your discomfort. > > Do the solvent regions retain any significant features? Have you tried > flipping those features? Have you applied NCS? What does the Fo - Fc map look > like? > > Charlie > > O

[ccp4bb] refinement hanging--what am I missing?

Hi all, Here is a problem that's been annoying me, and demanding levels of thought all out of proportion with the importance of the project: I have two related crystal forms of the same small protein. In both cases, the data look quite decent, and extend beyond 2 A, but the refinement stalls wi

Re: [ccp4bb] Convert cbf to png/tiff?

adxv reads cbf images, and can save them as postscript (actually, it's supposed to be able to save the image as tiff as well, but at least on my version of the program that feature doesn't work). Pat On 10 Jan 2013, at 3:36 PM, Frank von Delft wrote: > Hello all - anybody know an easy way to co

Re: [ccp4bb] vitrification vs freezing

There are implications of ice formation associated with the verb "to freeze" (the OED, for example, includes the following among several definitions of this verb: " Of a liquid, or liquid particles: To be converted into ice." Because the "to make cold" definition that Tim mentioned is also used

Re: [ccp4bb] Phaser MR with partial solution, 8 molecules/ASU

Are you sure that there are actually 8 molecules in the AU? I have on more than one occasion calculated the expected number of protomers based on Matthews' coefficient, only to find the solvent content is higher than I bargained for. This thought is stimulated by the fact that the solvent conten

Re: [ccp4bb] OFF TOPIC: recommendations for High Pressure Homogenizers

We have an Avestin C5 that's about 10 yrs old, and pretty much everything that Bert said is also true for us. The instrument works great for bacteria; it can also break yeast, but the pressures required are at the upper limit of its capabilities, so everything needs to be in tip-top condition. T

Re: [ccp4bb] Mercury phenylglyoxal

I second the mythical conclusion. We also tried to make it and failed 10-15 yrs ago (we came up with the di-iodo compound, if I recall). Many of these organomercurials are really tough to handle; I suspect that even if we had succeeded in making the desired compound, it would have been as solubl

Re: [ccp4bb] selective protection of C-terminal carboxylate

If you express the protein as an intein fusion you can make a C-terminal thioester, which you can then modify quite specifically with various reagents . Pat On 25 May 2012, at 10:00 AM, Sebastiano Pasqualato wrote: > > Dear all, > is anyone aware of a way to selectively protect the carboxylate

Re: [ccp4bb] Anaerobic glovebox crystal cryo-cooling

Think about "hyperquenching" (a high-falluting name meaning to use a stream of gas to blow off the cold layer that accumulates above the surface of the liquid nitrogen). We just blow some nitrogen at the surface of the dewar, very low tech...but it works. Importantly, you can use a more leisurel

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

> > Well, it is clear from this comment that in different fields there are > different rules... . In macromolecular Xtallolgraphy, where some people deal > with biologists from biomedical sciences, the impact of journals is an > important aspect during evaluation and, unfortunately, pre-publica

Re: [ccp4bb] very informative - Trends in Data Fabrication

Ron makes an excellent point. Many institutions devote far more energy to limiting risk than to doing the right thing. This leads administrators to a frightening, but logical conclusion: The less science we do, the less chance of our doing something that could invite a penalty on the university.

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

Hear, hear! I'm glad to know I'm not the last grump left standing. When I raise this point every year, my students regard me with bemused stares, as though they've just seen a coelacanth swim past their window... On 1 Apr 2012, at 10:18 AM, Gerard Bricogne wrote: > Dear Paul, > > May I jo

[ccp4bb] old-school stereo and Lion

The imminent replacement of Mobile-Me by iCloud provides an impetus for me to upgrade to Lion; but I'm currently happily using old-school stereo (i.e., a CRT monitor + Crystal-Eyes LCD glasses) under Snow Leopard. Can anyone attest to being able to use such equipment with Coot/PyMol under LIon?

[ccp4bb] synchrotron X-ray picture

Hi all, I have a vague memory of having a picture in someone's presentation once, showing a smoking hot X-ray beam emerging from the beam pipe in a hutch at a synchrotron. I think the picture might have been a double exposure, with a long exposure that captured air ionization superimposed on a

[ccp4bb] DDM crystals

Does anyone have any experience with formation of crystals of dodecyl maltoside in the presence of PEG? Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Gradu

[ccp4bb] Beckman Biosys 2000

I was just contacted by a group looking for install disks for the Biosys program used to run the old Biosys2000 FPLC from Beckman. I don't have the install disks anymore (we eventually bludgeoned our Biosys to death, and then set it on fire, if I recall--it was always very unreliable). However

Re: [ccp4bb] sealing slides on VDX plates?

Haven't done this for a while, but what we used to do was mix Vaseline plus mineral oil (both purchased for cheap at the local drugstore), and then apply it using a 10 ml syringe with a pipet tip attached. We used the mixture of Vaseline + mineral oil because Vaseline alone is too viscous (unle

[ccp4bb] is codon optimization worth it?

Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat --

Re: [ccp4bb] Rigaku high voltage tank

Bill, What do you mean by "high voltage tank"? When I hear this term, I think of the oil- (and PCB-) filled tank housing the transformer on an old generator; but there's nothing like that on the R-Axis. Do you mean the blue box housing the detector controller? If so, then I can tell you that we

Re: [ccp4bb] Mac OSX 10.7 Lion

Still doesn't beat my all-time favorite, an early Microsoft spell-checker that changed "diffract" to "defrocked." > > I forgot to mention how delightful the spelling auto-"correction" feature > can be. (It should have read "nothing unusual in and of itself"). > > That, at least, can be turne

Re: [ccp4bb] Protein preps become a jelly

Certainly not unprecedented, or even that unusual (I remember making gels from BSA and IgG solutions during grad school rotations). Gel formation usually requires crosslinking, so consider whether you might be getting adventitious disulfide bond formation. Pat On 30 Aug 2011, at 11:31 AM, aido

[ccp4bb] off-topic: Small molecule service MS

Can anyone recommend a good fee-for-service facility that does routine high-res mass spec on small molecules? Probably best to reply off-line; and I'd ask you to limit suggestions to facilities within the continental US (for reasons of convenience, rather than chauvinism). Thanks, Pat -

[ccp4bb] MS sequencing of Fab

We've crystallized a complex of an Fab bound to a protein. We have the hybridomas from which the Fab was prepared, but no protein sequence for the antibody. We're trying to plot the easiest course to get the sequence (since the crystals, alas, do not diffract to sufficiently high resolution so a

[ccp4bb] xds question: inverse beam, lots of wedges

We've just collected a number of inverse beam data sets. It turns out the crystals showed little radiation damage, so we have a lot of data: 2 x 360 deg for each crystal, broken up into 30 deg wedges. The collection order went like this: 0-30 deg, 180-210, 30-60, 210-240, etc. Now, assuming no

Re: [ccp4bb] Freezing crystals in a contained system

How low? Back in the old days when we mounted xtals in capillaries, you could sometimes see significant reduction in radiation damage by data collection temperature from room temp to ca. 0 deg C (zero is generally safe, since the PEGS/salts in your mother liquor will depress the freezing point).

[ccp4bb] tRNA expression

Here's an ignorant question: When people express an exogenous tRNA in E coli (to overcome rare codon issues, for example, or to supply a cognate tRNA for an orthogonal synthetase), what sorts of promoters are used? My (ignorant) guess is that something as potent as the T7 promoter might be a

Re: [ccp4bb] problem in heavy metal soaking

On 26 Sep 2010, at 9:00 AM, Seema Nath wrote: > I'm working with a protein which crystallizes in a mixture of PEG6K with 0.2M > AmSO4,my question is if there's any problem if I want to soak heavy metal > derivatives in this crystallizing condition? Does AmSO4 interfere in > heavy-metal soaking

[ccp4bb] waaay off-topic: P-1 pumps

Does anyone know how to disassemble a P-1 peristaltic pump from Pharmacia/Amersham/GE? We have a couple that need simple repairs to either a switch or a rheostat on the control panel, but I'm stumped as to how to actually get the damn thing open. If you've succeeded in doing this, I'd be grate

Re: [ccp4bb] Beginning crystallography text

At the risk of appearing immodest: http://www.amazon.com/Protein-Crystallography-Eaton-E-Lattman/dp/0801888069/ref=sr_1_10?ie=UTF8&s=books&qid=1278618335&sr=1-10 On 8 Jul 2010, at 3:35 PM, Peter Hsu wrote: > Hi all, > > I haven't gotten past the phase of growing the crystal, but I'd certainly

[ccp4bb] refrigerated shakers, redux

Hi all, Here is a summary of the responses to my inquiry about refrigerated shakers: Virtually all respondents advocated shakers manufactured by New Brunswick Scientific. I have rarely encountered such unanimity in this forum. The only exceptions were three votes for shakers of Swiss manufactur

[ccp4bb] off-topic--refrigerated shakers

Any recommendations for WELL-MADE refrigerated shakers? Our 1980-vintage New Brunswick Psycrotherm* is getting creaky, and the repair people claim that parts are not available. Hence, we're looking at the cost-effectiveness of replacing it with a new one. Probably best to reply off-list, and

Re: [ccp4bb] chiral volumes--2nd try

Joel, Agh. I can honestly say that this explanation never occurred to me, even though it is consistent with the data (But come on, any introductory organic chem text explains the R/S rules by moving from atom 2 to 3 to 4, and not by jumping from 2 to 4...surely you would follow the s

[ccp4bb] chiral volumes--2nd try

Sorry, the original post looks garbled (mirroring my internal state, no doubt). I'm trying again, sending as plain text: Friends, A question about the definition of chiral volumes: I'm looking for the definition of the SIGN of a chiral volume. The only ccp4 reference I can find (readily) i

[ccp4bb] chiral volumes--losing it

Friends, A question about the definition of chiral volumes: I'm looking for the definition of the SIGN of a chiral volume. The only ccp4 reference I can find (readily) is this: http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html This page gives an algorithm for determini

[ccp4bb] python install issues?

Hi, I'm simultaneously installing ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard. On both machines, the command: source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5) gives the error: ***

[ccp4bb] 3D search for peptide conformers?

I have a 10-residue stretch of a protein that adopts an interesting conformation; I'd like to know if this conformation occurs in other proteins. I'd welcome suggestions for tools that will allow me to to search for this peptide conformation in the PDB. I naturally thought of DALI, but it s

[ccp4bb] Postdoctoral position in anesthetic discovery

We seek a structurally-oriented post-doctoral fellow to participate in a general anesthetic discovery program consisting of high through-put approaches, coupled to medium through-put secondary screens, to include x-ray crystallography, isothermal titration calorimetry and in vivo assays. T

[ccp4bb] Postdoctoral position in DUB structural biology

A postdoctoral position is available to study the structures and functions of a novel class of human deubiquitinating enzymes involved in neurodegeneration. An NIH-funded position is available immediately to study the structure, catalytic function, and ligand-binding properties of the hum

[ccp4bb] off topic--Torrey Pines equipment

Does anyone have any experience with equipment from Torrey Pines Scientific (incubators, constant temperature circulators)? Probably best to reply off-line; if there's a groundswell of interest I can post a summary. Thanks, Pat -

Re: [ccp4bb] measure detergent concentration

I'll second this. We've done this as an exercise in NSLS Membrane Protein Crystallization workshop for a few years, and it works like a charm. You can stain in a warm iodine chamber and visualize by scanning the TLC plate on a garden variety scanner (we use an inexpensive Canon LIDE that p

Re: [ccp4bb] Sumo protease (Ulp) expression vector

Try PubMed, rather than Google: Weeks SD, Drinker M, Loll PJ (2007) "Ligation independent cloning vectors for expression of SUMO fusions." Protein Expr Purif. 2007 May; 53(1):40-50. We express the Ud1 domain of the yeast hydrolase. Contact me off-line if you're interested. Pat On 12

[ccp4bb] alternative graphics programs for OS X--summary

Hi, Thanks to the many replies to my queries about cheap/easy alternatives to Photoshop and CorelDraw on OS X. In a rare display of unanimity, the bulletin board spoke with essentially one voice: ALTERNATIVE TO PHOTOSHOP: Gimp (not gimpshop) http://www.gimp.org/ As one sage respon

[ccp4bb] cheap/useful alternatives to bloatware

Hi, This is off-topic in the sense that it's not about reciprocal space, but graphics ARE an integral part of publishing and teaching... I just upgraded to Leopard*, and find that my versions of Photoshop & CorelDraw no longer work. I can't stomach spending big bucks for the new version

Re: [ccp4bb] low UV reading on AKTA prime

I second Scott's post. About the only problem we've had with our Akta instruments is this type of degradation of the filter. I'm not sure what the mechanism is, but the filters do seem to crap out after a while, at least in the cold room (oxidation? I have no idea of what the filter is mad

Re: [ccp4bb] fortran format descriptor help

I get this: read(5,100)xinten,siginten,fobs,sigfobs,itest 100 format(6x,3i5,3(6x,f10.3),/,25x,f10.3,6x,i10) On 17 Jun 2009, at 4:18 PM, Francis E Reyes wrote: INDE 00 -9 IOBS= 9062.000 SIGI= 200.300 FOBS=95.190 SIGMA= 1.060 TEST= 0

Re: [ccp4bb] TEV nucleotude sequence with restriction site

You seem to be describing the MCS found in many TEV-site-containing expression plasmids (am I missing something?) E.g., look at the sequences in Sheffield et al., Protein Expression and Purification 15, 34 –39 (1999) (let me know if you want a PDF, I don't want to send it to the whole bb)

[ccp4bb] coupling between occupancy and b-values in refinement

Hi all, I'm looking for a reference to bolster my response to a referee, in which I defend my decision not to refine the occupancy of a ligand in structure refined at around 2 A resolution (note the ligand binding slte lies on a two-fold crystallographic axis, so the maximum occupancy is

Re: [ccp4bb] phasing with se-met at low resolution

Greg Petsko's group did something like this about a billion years ago (yet, strangely, I remember the paper, even though I'd be stumped if you asked me what I had for breakfast...) They covered the range from room temp down to very cold, using different cryoprotectants (importantly, they we

[ccp4bb] anode lifetime?

Does anyone have a reasonable estimate for the expected working lifetime of a copper anode on a MicroMax007? (Yes, I'm thinking about stimulus funding...). Thanks, Pat --- Patrick J. Loll, Ph. D.

[ccp4bb] Postdoctoral position available: Protein recognition of anesthetics

A postdoctoral position will be available Fall 2009 in Philadelphia, PA, USA. The successful candidate will join a collaborative research effort between the Eckenhoff laboratory at the University of Pennsylvania and the Loll laboratory at the Drexel University College of Medicine. This coll

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