[ccp4bb] Why Do Phases Dominate?

ere be an alternative summation which emphasizes amplitudes? If so, that might be handy in our field, where we measure amplitudes... Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Se

Re: [ccp4bb] Why Do Phases Dominate?

Perhaps this was really my question: Do phases *necessarily* dominate a reconstruction of an entity from phases and amplitudes, or are we stuck in a Fourier-based world-view? (Lijun pointed out that the Patterson function is an example of a reconstruction which ignores phases, although obvious

Re: [ccp4bb] Why Do Phases Dominate?

- Original Message - From: "Gerard Bricogne" To: Sent: Friday, March 19, 2010 2:32 PM Subject: Re: [ccp4bb] Why Do Phases Dominate? Dear Marius, Thank you for pointing this out - I was about to argue in the same direction, i.e. that the Fourier transform is at the heart of diffr

[ccp4bb] Peptide Binding Register Determination Software

, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***

[ccp4bb] Crystallography Near Venice/Padova Italy

Dear Crystallographers, is anyone here aware of structural biology or otherwise crystallography-intensive labs around the Venice/Padova region? Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program

[ccp4bb] Understanding Conformational Differences

automatically? Thanks for your consideration, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email

Re: [ccp4bb] Dissolving Hydrophobic ligands for co-crystallization and assays

, the monkeys' appetites increased, their eyes became watery, and they evinced a "pensive" disposition! Jacob Keller ps I always wondered whether this might have actually been due to proteins crystallizing in their veins... - Original Message - From: "Robert Immormi

[ccp4bb] Native Gel Theory and Practice

Dear Crystallographers, I am trying to optimize a native gel experiment of a two-protein complex, running the smallest-detectable amount of protein component A with varying amounts of component B. MWCharge MW/Charge A 22 -5-4308 B 17-24 -702 This experi

Re: [ccp4bb] monomeric coiled coil

e more readily-accessible experimentally? I am intrigued by the idea... Jacob Keller

Re: [ccp4bb] non-symmetric tetramer ?

I had a tetramer with 222 symmetry--1f38 and related entries. Is that what you mean? Jacob - Original Message - From: "Fred" To: Sent: Wednesday, July 28, 2010 1:31 PM Subject: [ccp4bb] non-symmetric tetramer ? Dear CCP4bb, Could someone please, point me to some references about

Re: [ccp4bb] I-TASSER predicts NADPH binding, need to confirm with experiment

I like nanodrop ultrafiltration: concentrate your protein to the highest stable concentration possible figure out what is the lowest possible robustly-detectable nadph signal on your nanodrop combine the two in such a way in the top of a microcon of appropriate MWCO to acheive the highest possib

Re: [ccp4bb] I-TASSER predicts NADPH binding, need to confirm with experiment

ultrafiltration sounds really fancy to me. I am afraid that I have no access to such equipment yet. Thanks for letting me know about this new technology. Sincerely, Xuan Yang 2010/8/4 Jacob Keller I like nanodrop ultrafiltration: concentrate your protein to the highest stable

Re: [ccp4bb] Unidentified density.

Could this be a metal cluster? Is your protein solution colored at all? Have you made an anomalous difference map? Is there reductant in the mix? What small molecules were in the mother liquor? JPK - Original Message - From: "" To: Sent: Thursday, August 12, 2010 10:24 AM Subject:

Re: [ccp4bb] Summary: I-TASSER predicts NADPH binding, need to confirm with experiment

e specific absoption at 340nm, UV spectrum was suggested as a nice way to check NADPH. Thanks to Vellieux Frederic. I recored the UV spectrum of freezed protein and fresh sample from 400nm to 240nm. The results were negative. No 340nm peak was observed at all (attachment 1 series). Jacob Kelle

Re: [ccp4bb] Heavy atom sites?

> > > MAD and SIRAS will in general behave like SAD. However if your isomorphous > difference is large and the anomalous signal is lost in the noise, they > might be dominated by it and so tend to behave more like SIR. > > I thought that MAD and SIRAS had no hand ambiguity--not true? Jacob Keller

[ccp4bb] Disulfide Designer Program

Dear Crystallographers, I remember having heard of a program which takes a given oligomeric assembly, and suggests optimum disulfides to stablize the complex. Can someone refresh my memory which program that is, and where it is available? Best Regards, Jacob Keller

Re: [ccp4bb] Local real-space refinement by phenix

But there is no better way to accumulate wisdom than having children...And certain types of wisdom are *only* accessible through having children! Then again, I have always wondered why most of the authors of the western classics were bachelors--weren't they missing a whole, major facet of life expe

Re: [ccp4bb] Disulfide Designer Program--Summary

Dear Crystallographers, Here is a summary of the methods for oligomeric stablization through structure-informed engineered disulfide bonds (thanks to all who responded): = SSBOND: Although the Google-accesible server seems to be down currently, it can still be a

Re: [ccp4bb] how to optimize crystallization of a membrane proteinf

I have to say that in my limited experience with membrane protein crystallization, these liquid crystal / spherulite type things are very common, and seldom turn into anything useful. Perhaps others on the list more experienced than I can corroborate or refute this. I just don't want this guy to ge

Re: [ccp4bb] Confirming expression of a GPCR in HEK293

If I were you, I would just make a gfp-tagged construct--this is an easy way to make sure that the protein is there, and made it to the membrane. If necessary, you can blot for gfp, or add other tags in the process for alternative blotting (one on each side to make sure it is not cleaved, for ex

[ccp4bb] Reverse Translatase

it would seem to me conceptually almost impossible that it *not* exist. Best Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208

Re: [ccp4bb] Reverse Translatase

ilar to gapped gene assembly from short synthetic fragments (that first protease better be *really* non-specific!). At the end one could sequence the resulting long DNA to see what the original protein was like. A. On Tue, Sep 7, 2010 at 8:35 AM, David Schuller wrote: On 09/06/10 21:36, Jacob

Re: [ccp4bb] Reverse Translatase

Just as a thought exercise or challenge--can you provide an algorithm or rule that will be able to distinguish in all cases what is a "design" and what is an "illusion of one's instinct for conveying selective advantage?" What would such a criterion be? And how about this side-question: do lower

Re: [ccp4bb] Radiation damage with crystals containing metal centers (TaBr people chime in?)

llected at high energy. Also, I think the decay function itself is steeper at the peak wavelength, leading to a less-internally-consistent data set at the peak. Does this argument hold water? Jacob Keller

[ccp4bb] Molecular Replacement of a Known Anomalous Substructure

be the best way to implement this idea in the given software? All the best, Jacob Keller *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)467-4049 [EMAIL PROTECTED] ***

Re: [ccp4bb] C-termini in protein-protein interaction

Hi Oleg, I solved a structure that uses a c-terminal beta hairpin to tetramerize the protein. See 1F38. All the best, Jacob Keller ==Original message text=== On Wed, 30 May 2007 5:01:09 pm CDT olegchem wrote: Dear all, I am looking for examples of protein-protein

[ccp4bb] Is anomalous signal a different wavelength?

exactly the same. Does anybody know here for sure, or at least where to look or whom to ask? All the best, Jacob Keller *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)467-4049 [EMAIL PROTECTED] ***

Re: [ccp4bb] Is anomalous signal a different wavelength?

==Original message text=== On Wed, 30 May 2007 6:51:09 pm CDT Ethan Merritt wrote: On Wednesday 30 May 2007 16:24, Jacob Keller wrote: > I have been wondering recently whether the anomalous component of a > diffraction pattern is of a > different wavelength

Re: [ccp4bb] Is anomalous signal a different wavelength?

ft which is little shifted from the Compton-scattered wave, although it might be even a few periods behind. I will try to look into this, and see if the observations and equations agree with what I am saying. All the best, Jacob Keller ps perhaps "anomalous" is better than "resonant,&

Re: [ccp4bb] Double conformations of cysteine !

with two conformations. Therefore, if there is not an easy way to do this now, we should try to implement a good way to do this in the future. All the best, Jacob Keller ==Original message text=== On Fri, 06 Jul 2007 12:46:29 pm CDT Prasenjit Bhaumik wrote: Hello, W

[ccp4bb] Oligomer which lacks conformational cooperativity

, and the subunits do not exhibit crosstalk, what on earth is the reason for their oligomerization? All hypotheses and especially references would be greatly appreciated, Jacob Keller *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645

Re: [ccp4bb] Oligomer which lacks conformational cooperativity

I forgot to mention we also tried urea, at various concentrations. JPK ==Original message text=== On Wed, 15 Aug 2007 11:39:14 am CDT Jacob Keller wrote: Sorry about this not being exactly CCP4 related, but I think it is still of general interest to the structural

Re: [ccp4bb] The importance of USING our validation tools

Hello All, This debacle is actually quite reminiscent of a similar incident that Wayne Hendrickson caught in the 1970's concerning purported "tRNA crystals." Turned out to be completely fabricated, and the guy's career went down the drain, I think. A good example to tell y

Re: [ccp4bb] Wasp web server

el: +44-(0)1223-766 044 / 760 468, fax: 766 002 ___ ===End of original message text======= *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)467-4049 [EMAIL PROTECTED] ***

Re: [ccp4bb] Questions about diffraction

omething which it seems would be necessary to produce interference. NB this issue came up in a crystallography class several years ago, and I have been ruminating on it, on and off, since then. JPK ******* Jacob Keller Northwestern University 6541 N. Francisco #3 Chica

[ccp4bb] Strange diffraction images

ou put on the web. I would shudder to think of indexing it, however. All the best, Jacob Keller ps I wonder whether a crystal was ever solved which had two interpenetrating, non-commensurable lattices in it. That would be pretty fantastic. ==Original message text=== On Mon,

Re: [ccp4bb] Strange diffraction images

s probably commensurate. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Mon, 27 Aug 2007, Jacob Keller wrote: > What a beautiful and interesting diffra

Re: [ccp4bb] Strange diffraction images

rick FRS >Dept. Structural Chemistry, >University of Goettingen, >Tammannstr. 4, >D37077 Goettingen, Germany >Tel. +49-551-39-3021 or -3068 >Fax. +49-551-39-2582 > > >On Mon, 27 Aug 2007, Jacob Keller wrote: > >> What a beautiful and interesting diffraction

Re: [ccp4bb] Strange diffraction images

u can check the paper describing a single domain of this protein complex or contact one of its authors. Bart J Mol Biol. 1998 May 15;278(4):855-70. Crystal structure of a functional unit from Octopus hemocyanin. Cuff ME, Miller KI, van Holde KE, Hendrickson WA. Jacob Keller wrote: > I am stil

[ccp4bb] How many twinned crystals?

a ref about this? I always thought it was an anomaly, but All the best, Jacob Keller

Re: [ccp4bb] MS for verification of protein constructs

I second Dr. Loll's question, and would like to be CC'd in whatever MS tips, including service-providers, are sent. I have been having a bit of a debacle with a certain MS service provider. Jacob Keller ==Original message text=== On Wed, 05 Sep 2007 11:41

[ccp4bb] Statistics differences

program last, right before composing "Table I" for publication? That seems suspicious... Jacob Keller ==Original message text=== On Fri, 07 Sep 2007 3:39:27 am CDT Andreas Kohl wrote: Dear all, we have currently two open postdoctoral positions in our department

[ccp4bb] MS method reference

unlabelled. Those bands with a shift would have been exposed to the reagent in that experiment, indicating that fragment/lysine's location with respect to the cell membrane. I suspect that somebody must have thought of this previously...there is nothing new under the sun. Jacob Keller

Re: [ccp4bb] Thermal melt and heme in the protein

en. BE A BETTER WELTENBUMMLER!===End of original message text=== ******* Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)491-2438 [EMAIL PROTECTED] ***

Re: [ccp4bb] "Quick soak" method

/ Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile) ===End of original message text=== *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)491-2438 [EMAIL PROTECTED] ***

Re: [ccp4bb] His tag does not bind.

, was successfully purified. Of course this makes complete biochemical sense, but nevertheless I am very glad I checked the pH. Jacob Keller On Wed, 10 Oct 2007 8:12:46 pm CDT changrui lu wrote: Dear all, I am trying to express a 150 kd protein in E coli. I have it in two constructs, one with

[ccp4bb] Primary source for detergent properties

Dear CCP4BB, Although this is not exactly CCP4-related, I thought somebody here might know whether there is somewhere a definitive list or tabulation of detergent properties which are not simply copied out of catalogs, but have been traceably experimentally determined. In particular, it would

Re: [ccp4bb] Primary source for detergent properties

(517) 353-9125/ /FAX: (517) 353-9334Email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>/ /****/ On Oct 22, 2007, at 5:48 PM, Jacob Keller wrote: Dear CCP4BB, Although this is not exactly CCP4-related, I thought somebody here might know whether there is somewhe

[ccp4bb] Sliding window net charge program?

Hello all, does anybody know of a program which calculates net charge within a sliding window of user-defined size? Hydropathy programs are almost this, but not quite--they use absolute values rather than the signed ones (what is the opposite of an absolute value called? the relative value?).

[ccp4bb] Protein Charge in a Moving Window

Does anyone have or know of a program to calculate net charge of a protein sequence in a user-defined sliding window? Somewhat like a hydropathy plot, but with positive and negative values instead of absolutes. It should be out there, I would think. Jacob *

Re: [ccp4bb] protein degradation?

inding in the mortar, but for me, it is still better than shivering in the cold room by the sonicator. Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Camp

Re: [ccp4bb] Dissolving s-adenosylhomocysteine

I solved a structure in the presence of SAM, which is the same as SAH but with a donor methyl group, and saw clear density for SAH, and not SAM, so it seems that the SAM was either spontaneously de-methylated in solution, or the protein which bound the SAM spontaneously demethylated it. In any c

Re: [ccp4bb] The importance of USING our validation tools

Does anyone here know what, if anything, happened with the whole Ajees et al. debacle? Just swept under the carpet, lost in the mists of time? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos

[ccp4bb] Solubilities Database

Hi All, Sorry for the non-ccp4 question, but it is of general crystallographic interest, and I believe this list may be the best place to ask, as we all need to know about solubilities almost all of the time, so... Does anybody know of a good online database of solubilities of common compoun

Re: [ccp4bb] DTT sensitive?

Did you check the pH of your DTT and the protein solution before and after? I have had some experience with DTT changing pH (as might well be expected...). Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos L

[ccp4bb] Malonate Crystals?

Dear Crystallographers, I have just found some crystals in a 1 year old screen, and, having been repeatedly trained to be very skeptical, think that probably they are salt. So the question: has anybody seen malonate crystals before? I was wondering whether they could possibly be birefringent, g

[ccp4bb] Protein-detergent micelle sizes

were given in one recent BB posting, but I was looking for a more systematic tabulation... Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston

Re: [ccp4bb] To bathe or not to bathe.

. Enjoying the debate, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.467.4049 cel: 773.608.9185 email: [EMAIL PROTECTED

[ccp4bb] Off topic, but am desparate...

at I want is a ~1500 x 1500 grid with boxes color-coded by their z values. I cannot figure out how to do this in gnuplot or anywhere, despite efforts to learn gnuplot and other programs. Any suggestions? Best regards, Jacob Keller *** Jacob Pearson

[ccp4bb] Off topic, but am desparate...Ah, a solution!

Hi All, Thanks for all of the great suggestions--it was actually Ethan Merritt's suggestions and pointing to the right Gnuplot documentation that really worked for me. Gnuplot is actually pretty powerful, and can make quite nice images. Again, thanks a million for the help. Jacob K

[ccp4bb] CCP4 for bioinformatics?

, and I was imagining a "moleman" homolog for bioinformatics (perhaps seqman?). Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive E

Re: [ccp4bb] FW: [ccp4bb] salt sensitive complex

Hi Jerry, I believe that if you make your cuvette and sample buffers exactly the same, you would really cut down on noise, and get an accurate reading. Did you do that, or is it possible? Jacob *** Jacob Pearson Keller Northwestern University Medical Sci

[ccp4bb] NCS-related: Parameter for map/structure quality?

other, because there are about twenty times the number of reflections to describe the same underlying structure, all other things (e.g., solvent content) being equal. Is there a indication of this in the statistical measures usually reported in Tables I*, or anywhere else? Regards, Jacob

[ccp4bb] Side chain chemical modifiers

Dear Crystallographers, I am looking for a way to modify any specific set of sidechains in my protein (e.g., all K's, or all D's and E's, etc.). A few requirements: 1. Relatively cheap 2. Definitely non-cell-membrane-crossing 3. Specific 4. Any reasonable amount of change in mass (+ 5-5000 Da?

Re: [ccp4bb] significant drop in Rfree ?

There was once a fellow named Zeno who made a similar argument. Aristotle was not convinced. Dr. Merritt, are you bringing a proof from Aristotle? But he believed in intelligent design (see below for his argument), and therefore would be shunned and blacklisted these days from any scientific

[ccp4bb] Copper Staining

Dear Crystallographers: just to share something I found out recently, that is really helpful to know: 5 min Copper Stain protocol Normal SDS-PAGE gels can be stained in 5 min with 300mM CuCl2. Simply remove the gel, rinse ~10s in water, place 5 min in CuCl2, and the gel is negatively staine

Re: [ccp4bb] Copper Staining

ECTED] *** - Original Message - From: "Artem Evdokimov" <[EMAIL PROTECTED]> To: "'Jacob Keller'" <[EMAIL PROTECTED]>; Sent: Monday, March 03, 2008 6:31 PM Subject: RE: [ccp4bb] Copper Staining There's an even faster reagen

[ccp4bb] ecoli outer membrane / yeast cell wall permeability

Dear Crystallographers, does anybody know the extent to which the outer membranes of e. coli and/or the cell walls of s. cerevisiae are permeable to various solutes? In particular, I was thinking of small, hydrophilic molecules. References would be great as well--I am not sure where to look...

[ccp4bb] Coomassie-bound structure?

Dear crystallographers, has anybody here ever heard of a protein structure with coomassie dye bound? Seems like it would be easy enough to do, but a search of the PDB did not yield anything. Surely somebody must have done this...? Jacob *** Jacob Pear

[ccp4bb] Ajees et al denouement?

Has anybody heard about what happened in the end with the Ajees et al debacle which raised so much dander? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus

[ccp4bb] Concatenated Crystal Screen Database

Dear Crystallographers, does anybody have an nicely-formatted excel file with all or several of the commonly-used crystal screens in it? That would be quite helpful for me. Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical

Re: [ccp4bb] Mosflm : data process of crystal with huge unit cell

Perhaps it should also be noted here that the long crystal axis should be oriented close to parallel to phi, in order to minimize overlaps. I have heard anecdotal evidence (anyone else?) that this long axis, in plate crystals, is usually normal to the surface of the plates. Perpendicularly-bent

[ccp4bb] DDM artifacts?

between salt, temp, cmc, and cloud points, but nothing on precisely this topic (detergent-related crystallization artifacts). Best Regards, Jacob Keller ps. in passing, it seems like it would be a great idea to get together an excel database of all false-positive results (e.g. phosphate salt

[ccp4bb] Crystals grown directly on loop?

about for more conventional, known crystallization conditions? It seems that this would be a spectacular way to decrease damages/stresses caused by handling... Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program

[ccp4bb] birefringent spacegroups

Dear Crystallographers, is there a list somewhere of spacegroups which can and cannot be birefringent? Upon what feature of the spacegroup does this depend? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training

[ccp4bb] Small lysozyme crystals protocol

Dear Crystallogrphers, does anybody here know a protocol to get consistently well-diffracting but smaller, ~50um, cryoprotect(ed/able) lysozyme crystals? Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training

[ccp4bb] DLS options?

background very clean, and one could see easily the degree of mono/polydispersity of the SEC peak(s). It was not, however, inexpensive. Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F

Re: [ccp4bb] Anion binding sites in proteins

I have been interested in this topic as well, so could any responses that are not also addressed to the BB be sent to me as well? Thanks very much, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos

Re: [ccp4bb] Advice for phasing

Wouldn't it make sense to do MIRAS with both the Se and Hg derivatives, and add in some multi-crystal averaging from the native set? You seem like you are almost there, though. I assume you have already tried DM and NCS averaging (if there is any)? Jacob ***

[ccp4bb] Imidazole's ability to chelate metal ions

assume that the affinity is weak, but at the concentrations at which we are wont to use it in our elutions (~100-500 mM), does it not seem likely that other metal ions are being competed away from our proteins as well? Jacob Keller *** Jacob Pearson Keller

Re: [ccp4bb] Imidazole's ability to chelate metal ions

s another reason I ask for the sources of the numbers quoted in a couple of the responses. Thanks for all of the helpful responses so far, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Se

Re: [ccp4bb] Using multiple crystals for structure solution in P1 using MAD/SAS/SAD

a of "the truth," as if taking many snapshots of the same object, and putting them together to form a three-dimensional object. In Hazes' language, don't all isomorphous crystals "draw from the same [underlying] distribution?" Jacob Keller ps admittedly if there is rad

[ccp4bb] light-zapped crystallization

Doesn't the technique in that paper seem like just a fancy way to elevate the temperature briefly? What else could zapping with a 780 nm laser do? Also, it seems that since N = 1, the technique is way too nascent (and it might be stillborn) to be applied. Jacob K

[ccp4bb] helix generator

Dear crystallographers, is there a program around, ccp4 or otherwise, into which one can input a sequence and get a .pdb of an ideal helix of the input sequence? Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist

Re: [ccp4bb] helix generator

/ Kristof On 31 Jul 2008, at 16:55, Jacob Keller wrote: Dear crystallographers, is there a program around, ccp4 or otherwise, into which one can input a sequence and get a .pdb of an ideal helix of the input sequence? Thanks, Jacob Keller

Re: [ccp4bb] helix generator

Hi all, thanks for being so helpful! I have gotten the job done, thanks to the many responses. with appreciation, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240

[ccp4bb] April fools hand issue solved

Dear crystallographers, although many laughed off one CCP4BB poster's comments several months ago as an April fools' trick (he had proposed that Bijvoet had actually botched the job, as I remember), there is now apparently experimental evidence against that trick: "Was Bijvoet right? Sodium

Re: [ccp4bb] truncate ignorance

Does somebody have a .pdf of that French and Wilson paper? Thanks in advance, Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438

Re: [ccp4bb] truncate ignorance

] *** - Original Message - From: "William Scott" <[EMAIL PROTECTED]> To: "Jacob Keller" <[EMAIL PROTECTED]> Cc: Sent: Monday, September 08, 2008 3:28 PM Subject: Re: [ccp4bb] truncate ignorance It is A34: 517 htt

[ccp4bb] Are cell parameter shifts real?

small that it would make no difference? The bottom line questions are: 1. given that there really are cases of cell shifts, and that there are also probably experimental artifactual changes, how is one to decide what to do? 2. Can there be (or what is?) a plausible mechanism for these shifts?

Re: [ccp4bb] Are cell parameter shifts real?

Jim -- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller Sent: Tuesday, September 09, 2008 3:08 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Are cell parameter shifts real? . The bottom line questions are: 1. given that th

[ccp4bb] Biochem off-topic--gently breaking protein-protein interaction

putative binding protein, so a western is out of the running, although we do have tons of both proteins, hence coomassie is IN the running. Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos

Re: [ccp4bb] Facebook for Neerds

RE: [ccp4bb] Facebook for NeerdsIf you would fourier transform the whole site, you could get myspace back, but where would you get the phases? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Sear

Re: [ccp4bb] Crystallogrphy today

clearly. Furthermore, one gets a sense of the excitement of discovery, and the unsurety about some new proposed hypothesis which has not yet become cannonized into fact. For this reason, it is sometimes even worthwhile to saunter down to the...library! Jacob Keller

Re: [ccp4bb] Crystallogrphy today

descending incredulity: "are you stupid? everybody knows that!". Jacob Keller ps I recognize that the above was probably not what you meant... *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory

Re: [ccp4bb] Crystallogrphy today

Germany. On Mon, Sep 22, 2008 at 5:52 PM, Jacob Keller <[EMAIL PROTECTED]> wrote: To understand the fundamentals of any discipline, I have always found it completely worthwhile to go back to the original source, where the idea was first discovered or presented. This is

Re: [ccp4bb] Crystallogrphy today

- From: "Marius Schmidt" <[EMAIL PROTECTED]> To: "Jacob Keller" <[EMAIL PROTECTED]>; Sent: Monday, September 22, 2008 8:42 PM Subject: Re: [ccp4bb] Crystallogrphy today i have a suggestion for a nice book for you, you will love it. it is in German, great!, has ove

Re: [ccp4bb] Quick-soak

MIRAS. Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROT

[ccp4bb] Off-topic: coomassie linearity?

, i.e. where and how extensive the linear range is, and 2. Can anybody suggest a more linear protein gel stain? Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 C

Re: [ccp4bb] Off-topic: coomassie linearity? SUMMARY

Biorad flamingo seem linear, and as sensitive as silver. But...for the fluorescent dyes, one optimally needs a fluorescence scanner. Thanks all, Jacob Keller ps The original coomassie reference seems to be S. Fazekas de St. Groth, R.G. Webster and A. Datyner, Two new staining procedures for

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