Re: [ccp4bb] Call for Proposals: IMAGINE, a New Neutron Crystallography Diffractometer

2013-05-23 Thread Jacob Keller
Is this Laue diffraction in the sense that the neutrons are a spectrum of energies, or does Laue mean something else here? Jacob On Thu, May 23, 2013 at 3:53 PM, Meilleur, Flora meille...@ornl.gov wrote: IMAGINE, Neutron Crystallography Diffractometer High Flux Isotope Reactor (HFIR),

Re: [ccp4bb] a new version of XDS

2013-05-29 Thread Jacob Keller
Any thoughts of making a Windows executable? Might help a lot of users JPK On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: ... is available for academic users at http://homes.mpimf-heidelberg.** mpg.de/~kabsch/xds/

Re: [ccp4bb] a new version of XDS

2013-05-29 Thread Jacob Keller
, May 29, 2013 at 1:29 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Any thoughts of making a Windows executable? Might help a lot of users JPK On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: ... is available for academic users at http

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

2013-05-30 Thread Jacob Keller
Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically

Re: [ccp4bb] MAX IV Life Science Director position

2013-06-03 Thread Jacob Keller
Brighter than XFEL? Or is it going to be an XFEL? JPK On Mon, Jun 3, 2013 at 10:36 AM, Derek Logan derek.lo...@biochemistry.lu.se wrote: Hi, If anyone fancies becoming Life Science Director at the world's brightest light source, look no further than here:

Re: [ccp4bb] negative difference density around sulphur and oxygen atoms

2012-04-04 Thread Jacob Keller
I look forward to hearing from others how best to handle this in refinement. Dose-dependent occupancies (tau of an exponential decay function?) refined against unmerged data JPK *** Jacob Pearson Keller Northwestern University Medical Scientist

Re: [ccp4bb] iMosflm version 1.0.6 Mosflm version 7.0.8

2012-04-16 Thread Jacob Keller
Where can one find a discussion of the differences between Aimless and Scala? JPK On Mon, Apr 16, 2012 at 8:28 AM, Harry Powell ha...@mrc-lmb.cam.ac.ukwrote: Dear all We are pleased to announce the public release of new versions of iMosflm and Mosflm. We have addressed many bugs and

Re: [ccp4bb] resolution on PDB web page

2012-04-25 Thread Jacob Keller
I had heard that there was a world-wide Tungsten shortage, but this is ridiculous! JPK On Wed, Apr 25, 2012 at 1:29 PM, H. Raaijmakers hraaijmak...@xs4all.nlwrote: That's nothing. Once someone wrote me because the tungsten atom of my Tungsten containing formate dehydrogenase had dissapeared.

Re: [ccp4bb] detergent crystal?

2012-04-26 Thread Jacob Keller
Those don't look like DDM crystals I've seen, but the diffraction pattern does not look much like protein diffraction either. Which things from the picture did you shoot--the rods/needles? Jacob On Fri, Apr 27, 2012 at 5:07 AM, 于洪军 hongju...@moon.ibp.ac.cn wrote: Hi, I am trying to screen

Re: [ccp4bb] detergent crystal?

2012-04-27 Thread Jacob Keller
Wouldn't the lack of solubility of the alpha form of DDM suggest an easy purification protocol for the beta form? JPK On Fri, Apr 27, 2012 at 8:40 AM, R. M. Garavito rmgarav...@gmail.comwrote: Hongjun, I am in agreement with Bert as DDM is exceedingly difficult to crystallize, even in

Re: [ccp4bb] Suggestions for solving a structure with 8-10 copies per asymmetric unit

2012-04-30 Thread Jacob Keller
Why not run a number of jobs in parallel with varying numbers of monomers/asu? JPK On Mon, Apr 30, 2012 at 4:20 PM, mjvdwo...@netscape.net wrote: Provided that you guess the number of copies and your guess is reasonably close, my experience is that Phaser will do the job. But you have to tell

Re: [ccp4bb] effective iodide conc. for SAD data

2012-05-03 Thread Jacob Keller
I have wondered for a long time now why it is not standard practice for all crystallization protein stocks to contain either Br- or I- ions instead of Cl-, even for cationic buffers like TRIS, which could be titrated with HBr or HI to get in the 10+ mM range. Also, one could use Cs or Rb for the

Re: [ccp4bb] saxs on xtals

2012-05-07 Thread Jacob Keller
It might be that the bulk solvent correction is nullifying the interior of the ferritin structure, and there should be a way to tell the refinement software not to treat the interior as solvent. Perhaps then you might find your Fe? Also, I would think there should be some powder-like diffraction

Re: [ccp4bb] P21221 to P21212 conversion

2012-05-07 Thread Jacob Keller
Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt

Re: [ccp4bb] P21221 to P21212 conversion

2012-05-07 Thread Jacob Keller
affected is quite small, of course. Phil Jeffrey Princeton On 5/7/12 4:48 PM, Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output

Re: [ccp4bb] saxs on xtals

2012-05-08 Thread Jacob Keller
Dear Colin, the table you gave seems to have been from Fe2+Fe3+2O4 or from Fe3-xTixO4. I am curious what the nature of the Fe inside the ferritin is (I don't think it has Ti in it, though...). Is it elemental iron? Also, to Anna: can you send a picture of that diffraction pattern with spot

[ccp4bb] Powder Rings in Single Crystals

2012-05-09 Thread Jacob Keller
Dear Crystallographers, the saxs on crystals thread reminded me of a question I have had for a while, and never having collected data better than ~1.6 Ang or so, cannot answer myself from experience: I would think that there might be powder-like diffraction rings at distances corresponding to the

Re: [ccp4bb] Postdoc postion at SLS

2012-05-09 Thread Jacob Keller
I saw something online about the EIGER 16M: 201 GB of data per second! Is that number correct? JPK On Wed, May 9, 2012 at 9:58 AM, Meitian Wang meitian.w...@psi.ch wrote: Postdoctoral Fello*Next Generation Detector for Protein Crystallography* Your tasks Built on the success of PILATUS

Re: [ccp4bb] Powder Rings in Single Crystals

2012-05-09 Thread Jacob Keller
interference. Tim On 05/09/12 16:16, Jacob Keller wrote: Dear Crystallographers, the saxs on crystals thread reminded me of a question I have had for a while, and never having collected data better than ~1.6 Ang or so, cannot answer myself from experience: I would think that there might

Re: [ccp4bb] Powder Rings in Single Crystals

2012-05-09 Thread Jacob Keller
Yes, I just looked up the paper--seems right on topic--a powder-type ring at ~4.2 Ang, corresponding to Calpha-Calpha distances! But no 1.2-1.5 Ang ring, from what I saw. Maybe it gets swamped out by other things. I am thinking that the variety/distribution of bonds/distances of length 1-3 Ang in

Re: [ccp4bb] Powder Rings in Single Crystals

2012-05-09 Thread Jacob Keller
It seems to me that spherical forms of Wilson plots could be used to determine how many bonds of what nature were oriented in which direction, and this may have been what Bricogne's micro molecular replacement technique was capitalizing on? For example, one might be able to orient a straight DNA

Re: [ccp4bb] zinc with HEPES

2012-05-11 Thread Jacob Keller
Try adding water first, so that you are not mixing concentrated Zn with concentrated HEPES. Also it depends what else is in your cocktail. JPK On Fri, May 11, 2012 at 11:26 AM, Rajesh Kumar ccp4...@hotmail.com wrote: Dear All, This question sounds simple but I dont know the answer. I was

Re: [ccp4bb] zinc with HEPES

2012-05-11 Thread Jacob Keller
Just to make sure I understand pH correctly: isn't it true that the [OH-] should always be the same at a given pH (by definition)? JPK On Fri, May 11, 2012 at 11:48 AM, Katherine Sippel katherine.sip...@gmail.com wrote: That is probably because you pH Tris with HCl rather than HEPES with

Re: [ccp4bb] zinc with HEPES/seeding

2012-05-11 Thread Jacob Keller
mitegen loops might help, particularly micromesh... JPK On Fri, May 11, 2012 at 12:35 PM, Rajesh Kumar ccp4...@hotmail.com wrote: Dear Patrick, You along with others had made some suggestions last time. May be its a good time to update. With classical screening, I got a crystal like

Re: [ccp4bb] Strange Density

2012-05-16 Thread Jacob Keller
How about chloride? I know, there are negative electrostatics, but I think such is seen sometimes for halides. Or, is it possible that there is a side chain flipped? Jacob On Tue, May 15, 2012 at 9:51 AM, RHYS GRINTER r.grinte...@research.gla.ac.uk wrote: Dear Community, As I'm a relatively

Re: [ccp4bb] completeness in scala

2012-05-17 Thread Jacob Keller
Maybe it's including covert structure factors? See recent ccp4bb post subject... JPK On Tue, May 15, 2012 at 4:28 PM, case c...@biomaps.rutgers.edu wrote: On Tue, May 15, 2012, Toth, Eric wrote: In sports, maximal effort is considered to be 110%, so you're actually 9.9% short of getting

Re: [ccp4bb] Serine

2012-05-21 Thread Jacob Keller
I believe that's an alternative conformationtry modeling as such and see what happens. Jacob On Mon, May 21, 2012 at 3:57 PM, Uma Ratu rosiso2...@gmail.com wrote: Dear All: Some of serine residues in my model have extra positive Fo-Fc density at the edge of side chain. Some don't have.

Re: [ccp4bb] Propane still?

2012-05-21 Thread Jacob Keller
So much easier is to simply loop your favorite tubing a couple of times through a small N2 dewar, then direct the output into a 15mL tube immersed in same. Or, simply point the tubing directly into the immersed tube, and flow slowly. In both cases, the cold N2 will condense the propane. Of course,

Re: [ccp4bb] Propane still?

2012-05-21 Thread Jacob Keller
Well, not to be a downer, but wikipedia has some comments on the hazards... Environmental effects Tetrafluoromethane is a potent greenhouse gashttp://en.wikipedia.org/wiki/Greenhouse_gas that contributes to the greenhouse effecthttp://en.wikipedia.org/wiki/Greenhouse_effect. It is very stable,

Re: [ccp4bb] Death of Rmerge

2012-05-31 Thread Jacob Keller
Meant to include the following link in the previous message: http://www.youtube.com/watch?v=9Jn8K8EA7-Q JPK On Thu, May 31, 2012 at 1:20 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, in case you have not heard, it would appear that the Rmerge statistic has

[ccp4bb] Fwd: [ccp4bb] Death of Rmerge

2012-05-31 Thread Jacob Keller
of this program RESCUT. REMARK 200  R SYM FOR SHELL            (I) : 1.21700 I noticed structure 3RKO reported Rmerge in the last shell greater than 1, suggesting the police who were defending R-merge were fighting a losing battle. And this provides a lot of ammunition to those they are fighting. Jacob

Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge

2012-05-31 Thread Jacob Keller
Good idea, but how to get it to catch on without publishing in Science? JPK On Thu, May 31, 2012 at 4:21 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote: On 05/31/12 12:07, Jacob Keller wrote: Alas, how many lines like the following from a recent Science paper (PMID: 22605777), probably

Re: [ccp4bb] Death of Rmerge

2012-06-01 Thread Jacob Keller
I don't think any data should be discarded, and I think that although we are not there yet, refinement should work directly with the images, iterating back and forth through all the various levels of data processing. As I think was pointed out by Wang, even an intensity of 0 provides information

Re: [ccp4bb] Death of Rmerge

2012-06-01 Thread Jacob Keller
Let's say you collect data (or rather indices) to 1.4 Ang but the real resolution is 2.8 Ang and you use all the data in refinement with no resolution cut-off, so there are 8 times as many data.  Then your 15 mins becomes 2 hours - is that still acceptable?  It's unlikely that you'll see any

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Jacob Keller
I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless.

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Jacob Keller
I think some have used anomalous signals since the 1930s-40s, e.g., Bijvoet! JPK On Wed, Jun 6, 2012 at 10:23 AM, Ronald E Stenkamp stenk...@u.washington.edu wrote: There were a number of labs using anomalous dispersion for phasing 40 years ago.  The theory for using it dates from the 60s.  

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Jacob Keller
...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Jacob Keller
) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) .      With best wishes,           Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Jacob Keller
- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, June 06, 2012 11:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No offense taken (we all have our dour moments

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller
Wow, that's very cool! Can you divulge what the function of the protein is? One thinks of some kind of mechanical spring... JPK On Mon, Jun 18, 2012 at 8:49 AM, anna anna marmottalb...@gmail.com wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller
I have been curious and suspicious for a long time about multimer: I always assumed it to be a more homey substitute for oligomer, as there seems to me to be no difference in usage, and certainly not in the etymological sense. I have often heard it used by non-experts who don't know exactly the

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller
I love myriomer, but what's wrong with boring old polymer? JPK On Mon, Jun 18, 2012 at 10:27 AM, Emmanuel Saridakis esari...@chem.demokritos.gr wrote: Of course, oligomer (pure Greek) usually does that kind of job, but not in this specific case, since oligo means few and in this case we have

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller
at 10:37 AM, David Schuller dj...@cornell.edu wrote: On 06/18/12 11:17, Jacob Keller wrote:  But anyway, what is wrong with calling her structures polymers? Is there a subtle covalent insinuation to polymer? subtle? No, it's not subtle

Re: [ccp4bb] Model submission

2012-06-19 Thread Jacob Keller
What extra insight does the full-length protein give, i.e., why not just chuck it? JPK On Tue, Jun 19, 2012 at 10:35 AM, RHYS GRINTER r.grinte...@research.gla.ac.uk wrote: Dear All, I'm working out the finer details on a structural paper for submission to JBC. I'm having a slight problem

Re: [ccp4bb] Tool for calculating RMSD

2012-06-19 Thread Jacob Keller
Is part of your question based there being many ways to superimpose structures, which there are? JPK On Tue, Jun 19, 2012 at 5:34 PM, Petr Leiman petr.lei...@epfl.ch wrote: Would anyone be kind enough to explain what kind of information does the RMSD for two not-yet-superimposed structures

Re: [ccp4bb] estimate of effective concentration

2012-06-20 Thread Jacob Keller
It seems to me that concentration is a statistical, macroscopically-derived concept like temperature or pressure which gets exceedingly weird when applied to microscopic phenomena. One weirdness is, I guess, that the somewhat arbitrary size of the box you mentioned makes a huge difference in the

Re: [ccp4bb] Detergent and protein oligomerization

2012-06-21 Thread Jacob Keller
First of all, isn't the choice either dimer or trimer, and second, as a protein-detergent complex (PDC), it would be very unlikely that a trimer of 99 kD would run at 100 kD, although all is fair in love, war, and membrane proteins. JPK On Thu, Jun 21, 2012 at 10:50 AM, Raji Edayathumangalam

Re: [ccp4bb] Detergent and protein oligomerization

2012-06-21 Thread Jacob Keller
): 01235 778664 -- From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller [j-kell...@fsm.northwestern.edu] Sent: 21 June 2012 17:11 To: ccp4bb Subject: Re

Re: [ccp4bb] information received through the AFC: iycr2014

2012-07-05 Thread Jacob Keller
On Thu, Jul 5, 2012 at 1:44 PM, Eric Williams ericwilli...@pobox.comwrote: I'm guessing disorder is a major limiting factor on effective resolutions. ;) Now *that's* good... JPK On Thu, Jul 5, 2012 at 2:36 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: **Ø

Re: [ccp4bb] Crystal Optimization

2012-07-10 Thread Jacob Keller
Give a list of all you have tried? JPK On Tue, Jul 10, 2012 at 12:22 PM, Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at wrote: Dear All; Could somebody give a nice suggestion how the following type crystal could be optimized, I almost tried everything. Crystal Image is attached

Re: [ccp4bb] harvesting in cold room (was: cryo for high salt crystal)

2012-07-13 Thread Jacob Keller
You probably already know this, but nitrogen is not at all poisonous--about 78% of the air is nitrogen. I guess you were probably worried about asphyxiation? JPK On Fri, Jul 13, 2012 at 4:19 PM, Radisky, Evette S., Ph.D. radisky.eve...@mayo.edu wrote: Several have mentioned harvesting in

Re: [ccp4bb] harvesting in cold room

2012-07-13 Thread Jacob Keller
How frequently do the sensors go off? JPK On Fri, Jul 13, 2012 at 4:37 PM, David Schuller dj...@cornell.edu wrote: On 07/13/12 17:29, Jacob Keller wrote: You probably already know this, but nitrogen is not at all poisonous--about 78% of the air is nitrogen. I guess you were probably

Re: [ccp4bb] Regarding refinement in Refmac5

2012-07-18 Thread Jacob Keller
How about trying some ARP/WARP? JPK On Wed, Jul 18, 2012 at 11:54 AM, Pavel Afonine pafon...@gmail.com wrote: What happens if you do a round of refinement in phenix.refine after you have done the mutations? Note: Phenix Autobuild is a tool to build your model, not refine it (though it does

Re: [ccp4bb] resolution limit

2012-07-18 Thread Jacob Keller
I was [too] obliquely alluding to this thread... http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27056.html JPK On Wed, Jul 18, 2012 at 12:32 PM, Edwin Pozharski epozh...@umaryland.eduwrote: http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html Rsym...what's that? JPK On

Re: [ccp4bb] How to identify unknow heavy atom??

2012-07-24 Thread Jacob Keller
Perhaps also exafs should be mentioned--I believe the various ion species, redox states, and even binding geometry can be determined. JPK On Tue, Jul 24, 2012 at 12:37 PM, Roberts, Sue A - (suer) s...@email.arizona.edu wrote: Hello Actually, if the home source uses a copper tube, neither

Re: [ccp4bb] How to identify unknow heavy atom??

2012-07-24 Thread Jacob Keller
I think it's done on a crystal itself, but others who know better than I can comment. JPK On Tue, Jul 24, 2012 at 1:02 PM, Theresa Hsu theresah...@live.com wrote: Does EXAFS requires same amount of samples as ICP-MS/ICP-AES? Theresa On Tue, 24 Jul 2012 12:55:31 -0500, Jacob Keller j-kell

Re: [ccp4bb] ADP binds to the protein in solution but not show up in the structure

2012-07-27 Thread Jacob Keller
Or similarly, the conditions in the crystallization drop (pH, ions, etc.) may kick out the ligand. JPK On Fri, Jul 27, 2012 at 3:34 AM, herman.schreu...@sanofi.com wrote: ** Dear Ni Shi, Did you test a crystal, or uncrystallized protein? It may be that due to crystal packing effects, only

Re: [ccp4bb] dumb software question

2012-08-07 Thread Jacob Keller
You mean cell in terms of a living cell, not a unit cell, right? JPK On Tue, Aug 7, 2012 at 10:24 AM, Paul Kraft haresea...@yahoo.com wrote: Hi guys, is there a program similar to ccp4/coot that allows one to visuallize an ideal cell (either prokaryote or eukaryote) in 3D with semi accurate

[ccp4bb] Various OSes and Crystallography

2012-08-09 Thread Jacob Keller
Dear List, I guess this is somewhat of a perennial issue, but I am faced with choosing an OS for a new computer, and am curious about benefits and drawbacks with regard to crystallography. So far, I have been using windows, and have found no limitations whatsoever, but then again, maybe I don't

Re: [ccp4bb] Calculating I/sig when sig = 0

2012-08-23 Thread Jacob Keller
if the X-ray background is exactly zero and the observed (sic) intensity is exactly zero. -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller [j-kell...@fsm.northwestern.edu] *Sent:* Thursday, August 23, 2012 12:36 PM *To:* CCP4BB

Re: [ccp4bb] Off-topic: Duet vectors with C-terminal GST tag

2012-08-27 Thread Jacob Keller
How about just co-transfecting with two different plasmids which have different selection markers? I've done it a lot, and it seems to work fine... JPK On Fri, Aug 24, 2012 at 10:39 PM, Lye, Ming ming_...@hms.harvard.eduwrote: Dear CCP4bb, We would like to co-express proteins under Se-Met

Re: [ccp4bb] protein interactions

2012-09-06 Thread Jacob Keller
I know this isn't exactly your question, but it doesn't really take that long to clone, express, and purify things nowadays--a few days, even? Also, won't you be doing this anyway? So why not cut out the middle-man? Or, better still, in your cloning downtime, do the software stuff. JPK On Thu,

Re: [ccp4bb] the lysozyme of membrane proteins?

2012-09-11 Thread Jacob Keller
Wouldn't bacteriorhodopsin be a good choice, especially since it's colored and easy to express? Seems pretty expensive for a class, though, with all the detergents involved... JPK On Tue, Sep 11, 2012 at 4:18 PM, Ho Leung Ng h...@hawaii.edu wrote: Hello, I am developing an

[ccp4bb] Off-topic: Best Scripting Language

2012-09-12 Thread Jacob Keller
Dear List, since this probably comes up a lot in manipulation of pdb/reflection files and so on, I was curious what people thought would be the best language for the following: I have some huge (100s MB) tables of tab-delimited data on which I would like to do some math (averaging, sigmas, simple

Re: [ccp4bb] Off-topic: Best Scripting Language

2012-09-12 Thread Jacob Keller
For the specific purpose you list - input from tab-delimited data output to simple statisitical summaries and (I assume) plots - it sounds like gnuplot could do the job nicely. I wasn't aware that gnuplot can do calculations--can it? I was probably going to use it somewhere as a plotting

Re: [ccp4bb] Off-topic: Best Scripting Language

2012-09-13 Thread Jacob Keller
It turns out that the syntax and semantics of all reasonable programming languages are very similar, or fall into only a few classes (e.g. C-like, S-expressions, etc.), so once you are fluent in one from a class, it's easy to pick up the others. This can't be said of natural languages, which

Re: [ccp4bb] off topic: protein peptide binding

2012-09-14 Thread Jacob Keller
For the gel, it might be really hard to see the peptide as small things tend to blur terribly--better to look for shifts in the protein band. If I were you, I would do serial dilutions of the peptide at some constant, very visible protein concentration. Also you have to be sure that the

[ccp4bb] Off-topic: Pore-forming Substances

2012-09-24 Thread Jacob Keller
Dear Crystallographers: #off topic I am trying to calibrate some microscopic imaging intracellular pH measurements, but the usual nigericin (small pore-forming K+/H+ exchanger) technique does not seem to be working well. Maybe it actually never works well? Anyway, I was think of trying to use

Re: [ccp4bb] Direct crystallization of Lysozyme from eggs

2012-09-25 Thread Jacob Keller
Alhtough perhaps a little more macabre--maybe you could crystallize hemoglobin or myoglobin from blood or muscle (meat?). I recollect some story of whale myo- or hemo-globin crystallizing on the salty decks of a whaling ship... Jacob On Tue, Sep 25, 2012 at 11:59 AM, David Smith

Re: [ccp4bb] On maps and doubts

2012-10-10 Thread Jacob Keller
btw, this thread has one of my favorite titles ever... JPK On Tue, Oct 9, 2012 at 4:11 AM, Eleanor Dodson eleanor.dod...@york.ac.ukwrote: This is interesting. In principle m and D should provide an optimum map, and at high resolution they do a reasonable job. The answer about occupancy is a

[ccp4bb] Script for removing/gathering select rows of data

2012-11-07 Thread Jacob Keller
it should be a very generally useful script to have around, and I need such right now... Thanks very much, Jacob Keller

Re: [ccp4bb] Script for removing/gathering select rows of data

2012-11-09 Thread Jacob Keller
Dear all, thanks for your help--I made a very simple little script using awk, and it works excellently (anyone is welcome to it, of course). Thanks so much for taking the time. Jacob On Wed, Nov 7, 2012 at 9:49 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers

Re: [ccp4bb] Expert opinion for optimizing ethylene glycol crystallization condition

2013-01-05 Thread Jacob Keller
aided crystallization, so maybe it's not so bad. Also, proteins often have salt in the protein stock as well. Bottom line is that I wonder whether in Cale's case it might have been the Na or the Cl that was the key, and perhaps not the hepes/tris. Jacob Keller

Re: [ccp4bb] Golden Jubilee of Ramachandran Plot

2013-01-19 Thread Jacob Keller
Were there really no computers in 1963? JPK On Fri, Jan 18, 2013 at 9:51 AM, David Schuller dj...@cornell.edu wrote: http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Golden Jubilee of Ramachandran

[ccp4bb] Crystallography Near Absolute Zero?

2013-01-23 Thread Jacob Keller
Is anyone aware of any datasets taken at near absolute zero? I was wondering what would happen... Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu

Re: [ccp4bb] Off Topic- Cystine Detection

2013-02-06 Thread Jacob Keller
Couldn't you just run reducing/non-reducing SDS-PAGE lanes and see the difference? JPK On Wed, Feb 6, 2013 at 11:10 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote: Dear All, I am trying to probe the existence of a disulfide bond on the surface of my protein. I have attempted Ellman´s and my

Re: [ccp4bb] need some suggestions for crystallization

2013-02-06 Thread Jacob Keller
Does that CA have a metal center (I think they all do)? If so, doesn't the citrate compete for the metal? JPK On Mon, Feb 4, 2013 at 2:25 PM, Roger Rowlett rrowl...@colgate.edu wrote: Human carbonic anhdyrase II can be easily crystallized from 1.3 M sodium citrate/0.1 M TrisCl pH 8.5 at 10

Re: [ccp4bb] Off Topic- Cystine Detection

2013-02-07 Thread Jacob Keller
...@ufl.edu wrote: ** The disulfide bond is intramolecular. I do not have reasons to believe it is cross linking my protein On Wed, 6 Feb 2013 22:16:36 -0500, Jacob Keller wrote: Couldn't you just run reducing/non-reducing SDS-PAGE lanes and see the difference? JPK On Wed, Feb 6, 2013

Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Jacob Keller
I'd have to disagree on that. Protein crystals are fragile but not soft. If your crystals are like gelatine it's unusual. It has been demonstrated that elastic properties of protein crystals are similar to organic solids Interesting--do you have a reference quickly on hand for those

[ccp4bb] Improving Homology Models

2013-02-20 Thread Jacob Keller
Dear Crystallographers, it has been my experience that homology modelling programs get folds pretty well, but sometimes the details are pretty obviously bad, like too-close contacts. One might think that the modelling software would put in a sort of polishing step, but they don't seem to. Is

Re: [ccp4bb] How to compare B-factors between structures?

2013-02-25 Thread Jacob Keller
Why not normalize each to its average b-factor? And...maybe they are not significantly different in the first place? JPK On Mon, Feb 25, 2013 at 3:08 PM, Yarrow Madrona amadr...@uci.edu wrote: Hello, Does anyone know a good method to compare B-factors between structures? I would like to

Re: [ccp4bb] disulfide engineering

2013-02-28 Thread Jacob Keller
Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55

Re: [ccp4bb] How to compare B-factors between structures?

2013-03-04 Thread Jacob Keller
You only entertain addition+subtraction--why not use multiplication/division to normalize the b-factors? JPK On Mon, Mar 4, 2013 at 2:04 PM, James Holton jmhol...@lbl.gov wrote: Formally, the best way to compare B factors in two structures with different average B is to add a constant to all

[ccp4bb] Way off topic: Donate V. Cholera Genomic DNA?

2013-03-05 Thread Jacob Keller
Dear List, please pardon the major off-topicity, but I need a trace amount of V cholera genomic DNA to PCR from, and it just kills me to spend ~$300 to order it for this one and only use. Is anyone in the DC/Baltimore area willing and able to donate this? I travel on the capitol beltway daily, so

Re: [ccp4bb] Way off topic: Donate V. Cholera Genomic DNA?

2013-03-06 Thread Jacob Keller
reasons for going for the gDNA. Thanks again, Jacob On Tue, Mar 5, 2013 at 1:07 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear List, please pardon the major off-topicity, but I need a trace amount of V cholera genomic DNA to PCR from, and it just kills me to spend ~$300

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Jacob Keller
One final quote that is not in the twilight paper summarizes it nicely: The scientist must be the judge of his own hypotheses, not the statistician. A.F.W. Edwards (1992) in Likelihood - An account of the statistical concept of likelihood and its application to scientific inference , p.

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Jacob Keller
bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Jacob Keller *Sent:* Tuesday, March 12, 2013 3:44 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] validating ligand density One final quote that is not in the twilight paper summarizes it nicely: The scientist must

Re: [ccp4bb] first use of synchrotron radiation in PX

2013-03-13 Thread Jacob Keller
Did anyone see this prescient line in the PNAS paper? Seems that the MAD concept was suggested way back then... JPK While the enhancement of anomalous scattering has not yet been examined in detail, it is in principle possible to use data collected at three wavelengths (15) to completely solve

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

2013-03-15 Thread Jacob Keller
Well, wouldn't NCS be a parallel situation? I have heard, for example, that the maps of viruses are considerably better at a given resolution than monomeric proteins. So I would guess that someone has looked at this topic in the case of NCS. Maybe high solvent content would be equivalent to

[ccp4bb] Most Abundant Eukaryotic Membrane Protein List?

2013-03-18 Thread Jacob Keller
Dear List, Does anyone know of a source of quantification of membrane proteins in garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally, it just occurred to me that probably all HeLa cells are XX--seems right, no?) I am looking for the highest-expressed, particularly, and

Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List?

2013-03-18 Thread Jacob Keller
. pdb1OKC). Single chain or homodimer, but apparently its not very easy to crystallize. Jacob Keller wrote: Dear List, Does anyone know of a source of quantification of membrane proteins in garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally, it just occurred to me

Re: [ccp4bb] Philosophical question

2013-03-19 Thread Jacob Keller
Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident--or is there some more beautiful reason? One might argue that since basically all organisms share the convention (are there

Re: [ccp4bb] Philosophical question

2013-03-19 Thread Jacob Keller
keyboard configuration. I am dubious whether this model, however, would apply to the codon conventions. Jacob On Tue, Mar 19, 2013 at 10:44 AM, David Schuller dj...@cornell.edu wrote: On 03/19/13 10:34, Jacob Keller wrote: Never one to shrink from philosophizing, I wonder generally why

Re: [ccp4bb] Strange density in solvent channel and high Rfree

2013-03-19 Thread Jacob Keller
Isn't lowering the symmetry equivalent to using multiple models/conformations for one map? I remember seeing this done with the infamous MSBA structure from a few years ago, so caveat emptor I guess. And further, wouldn't using strict NCS make things equivalent to the higher-symmetry space group?

Re: [ccp4bb] Philosophical question

2013-03-19 Thread Jacob Keller
that it is the best possible system, or indeed should continue to be selected for (except that mutations to this machinery tend to be very much deleterious). -- David On 19 March 2013 14:34, Jacob Keller j-kell...@fsm.northwestern.eduwrote: Never one to shrink from philosophizing, I wonder

Re: [ccp4bb] Philosophical question

2013-03-19 Thread Jacob Keller
I don't understand this argument, as it would apply equally to all features of the theoretical LUCA No it won't. Different features would have different tolerance levels to modifications. Yes, this tolerance is the second (hidden or implicit) principle I referred to. So you'd have to explain

Re: [ccp4bb] Why the name aimless

2013-05-02 Thread Jacob Keller
Moreorless? Dolores? JPK On Thu, May 2, 2013 at 12:22 PM, Eric Williams ericwilli...@pobox.comwrote: I've always thought gormless is a woefully underused word. Eric On Thu, May 2, 2013 at 11:53 AM, Mark van Raaij mjvanra...@cnb.csic.eswrote: i.e. the next program will be Graceless or

Re: [ccp4bb] Why the name aimless

2013-05-02 Thread Jacob Keller
Nevertheless? JPK On Thu, May 2, 2013 at 2:18 PM, Roger Rowlett rrowl...@colgate.edu wrote: Some of my undergraduate students need the CCP4 program feckless. :) ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate

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

2007-05-30 Thread Jacob Keller
==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 from the regular

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

2007-05-31 Thread Jacob Keller
-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, as it produces MAD and SAD and not MRD and SRD

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