[ccp4bb] how to apply non-protein crystallographic symmetry

I have a pdb file for a non-protein having C 1 2/c symmetry. PyMol can't recognize the spacegroup. Can someone recommend software that can apply the crystallographic symmetry to give the full structure? Richard Gillilan MacCHESS Cornell University

Re: [ccp4bb] how to apply non-protein crystallographic symmetry

, available at http://ewald.ac.chemie.uni-goettingen.de/shelx/eingabe.php. Best, Tim On 07/14/2014 10:26 PM, Richard Gillilan wrote: I have a pdb file for a non-protein having C 1 2/c symmetry. PyMol can't recognize the spacegroup. Can someone recommend software that can apply

Re: [ccp4bb] I/sigmaI or I/sigmaI

/sigmaI Dear Qixu Cai, You can find information about where to find the archives here: http://www.ccp4.ac.uk/ccp4bb.php#archives Best regards, Folmer 2014-02-19 14:44 GMT+01:00 Cai Qixu caiq...@gmail.commailto:caiq...@gmail.com: Dear Richard Gillilan, Where to find the archives of Dec 2003? I

Re: [ccp4bb] I/sigmaI or I/sigmaI

There was an informative discussion on this very topic back in Dec 1-2, 2003 if you browse the CCP4BB archives. Richard Gillilan MacCHESS On Feb 12, 2014, at 6:43 AM, Cai Qixu wrote: Dear all, Does the I/sigmaI in “Table 1” mean for I/sigmaI or I/sigmaI ? Thanks for your answer. Best wishes

[ccp4bb] Summary: identifying protein crystals via visible light only

smb.slac.stanford.edu/news/Visex.pdf (their listed products seem to be UV-based, but apparently this one is visible.) Both of these are proprietary commercial products, so it is impossible to know exactly what they are doing. Richard Gillilan MacCHESS

Re: [ccp4bb] fluorescent pedal

in bright x-ray beams over time. Of course there is always cutting thin slivers of the plastic fluorescent sheet material everyone uses at beamlines. Not sure where they get that. Richard Gillilan MacCHESS On Feb 14, 2014, at 12:18 PM, Scott Classen wrote: Hi Ronnie, We use YAG discs

[ccp4bb] identifying protein crystals via visible light only?

of this? Richard Gillilan MacCHESS Cornell

Re: [ccp4bb] archival memory?

for heavy atom derivatives of Thermolysin written in VENUS format, I'm your man. On 12/12/2012 1:57 PM, Richard Gillilan wrote: Better option? Certainly not TAPE or electromechanical disk drive. CD's and DVD's don't last nearly that long and James Holton has pointed out. I suppose there might

[ccp4bb] archival memory?

will have no interest in private momets of Queen Elizabeth's life, no matter how amusing they might be. -artem On Dec 14, 2012 9:20 AM, Richard Gillilan r...@cornell.edumailto:r...@cornell.edu wrote: This is too funny. My wife's new job is scanning Sumerian clay tablets into computer. I kid

Re: [ccp4bb] archival memory?

University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Richard Gillilan

[ccp4bb] archival memory?

tab.). Has anyone here looked into this or seen similar products? Richard Gillilan MacCHESS

Re: [ccp4bb] archival memory?

at 3:02 PM, Richard Gillilan r...@cornell.edumailto:r...@cornell.edu wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check

Re: [ccp4bb] archival memory?

On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote: Good luck on your search in 100 years for a computer with a USB port. You will also need software that can read a FAT32 file system. Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud On 12/12/2012 1:02 PM, Richard Gillilan

Re: [ccp4bb] archival memory?

PM, Richard Gillilan r...@cornell.edumailto:r...@cornell.edu wrote: SanDisk advertises a Memory Vault disk for archival storage of photos that they claim will last 100 years. (note: they do have a scheme for estimating lifetime of the memory, Arrhenius Equation ... interesting. Check it out

Re: [ccp4bb] Izit dye stained crystal

think we gave the poster an award for that. I don't have my past notes handy to remember, but could look it up if you're interested. Richard Gillilan MacCHESS On Nov 30, 2012, at 4:19 PM, Sarathy Karunan Partha wrote: Dear all, We did some Izit dye staining to test our crystal (salt

Re: [ccp4bb] Izit dye stained crystal

or disclosure of the contents of this message is not permitted and may be unlawful. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Richard Gillilan Sent: Friday, November 30, 2012 5:21 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Izit dye

[ccp4bb] BioSAXS Postdoc position at CHESS

the position, contact Dr. Richard Gillilan at r...@cornell.edu. Cornell is an equal opportunity, affirmative action educator and employe

[ccp4bb] Fall BioSAXS beamtime available at MacCHESS

, or you think you may have a mixture, you may want to investigate on-site SEC. Fractions can be collected directly into the same 96-well plates used by the BioSAXS robot. I you are interested, contact me (Richard Gillilan) for details. -- Hope you can join us this Fall! Best Richard

[ccp4bb] Fwd: [ccp4bb] Do my SAXS data agree with the crystal structure?

In theory, there should be a simple way to calculate P(r) directly from the crystal structure rather than indirectly from the expected scattering curve. Distribution of pair distances, r^2 weighted. This would remove any ambiguity about choice of Dmax. ... but I can't think of any of the

[ccp4bb] BioSAXS and other postdoc positions open at CHESS

Note: CHESS has multiple postdoc positions open in various areas of x-ray science. I am posting the BioSAXS ad here, but applicants will automatically be considered for all the positions. Job opening: Postdoctoral

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

in reciprocal space and model features is not simple. Richard Gillilan MacCHESS

Re: [ccp4bb] SAXS workshop

LIKE to go ... but would you actually be able to go? I would also be interested in hearing from any interested potential organizers. (Please also keep in mind that SAS2012 is in Australia Nov 2012, so that may make a difference in your travel plans). Richard Gillilan chair-elect ACA SAXS SIG

[ccp4bb] BioSAXS beamtime available

an AKTA Purifier size-exclusion chromatography (SEC) system for use at the F2 beamline. If your samples seem to aggregate rapidly after preparation, or you think you may have a mixture, you may want to investigate on-site SEC. If you are interested, contact me (Richard Gillilan) directly for details

Re: [ccp4bb] IUCr committees, depositing images

For the record, the amount of disk storage space per unit cost has doubled every 14 months for the last 30 years. It's an exponential relationship: www.mkomo.com/cost-per-gigabyte So data generated at a very high rate today, will be trivial to store in the near future. That's not to say it is

Re: [ccp4bb] not so good news (Steve Jobs RIP)

Jobs and Apple not only deeply shaped my career, but also my son's path as well. I bought an Apple II+ with my first Summer's earnings as an undergraduate lab assistant in organic chemistry in the very early 80's. Spent winter break writing a printer driver in Apple 6502 code so I could plot

Re: [ccp4bb] Bicarb at low pH

Hi Jacob, high-pressure cryocrystallography methods may be useful in this case. I copied your question to Chae Un Kim here at MacCHESS and he forwards this suggestion: -- Hi Richard, I think pressure cryocooling might be useful. They may want to check

Re: [ccp4bb] Mac OSX 10.7 Lion

Listening to Jobs speak recently, I got the distinct impression that the end of the era of general desktop computers PC's may be on the horizon. Of course that's iPad sales rhetoric, but it may be that the public moves away from general computers and that surely will have implications for

Re: [ccp4bb] Off topic_protein degradation.

BioSAXS can also tell you if the protein is folded or not, but in either case, you may want to purify on site since degradation is so fast. Many BioSAXS beamlines (including ours at MacCHESS) now have SEC systems on site. Richard Gillilan MacCHESS Cornell University On Aug 19, 2011, at 3:55

[ccp4bb] Fwd: [ccp4bb] Blue color upon X-ray exposure?

north however, appears to be purely a light-scattering phenomenon and not a result of trapped electrons. Richard Gillilan MacCHESS -James Holton MAD Scientist Todd Geders wrote:

Re: [ccp4bb] decrease of background with distance?

David had developed an empirical theory to model the air, solvent, Compton acoustic contributions and correct the integrated data for these, without background correction of course since the optic DS background was ultimately to be our data! ... Hi Ian, did David publish this theory

Re: [ccp4bb] decrease of background with distance?

Thank you all for your informative responses! While examining the effects of unusual beam profiles on data collection due to capillary optics, I had collected a wedge of data on a large, high-quality lysozyme crystal at 8 different sample to detector distances. I restricted the analysis of

Re: [ccp4bb] Mosaicity beam divergence

Sorry, I meant to say does divergence add to the reported mosaicity value. If so, do actual mosaicity and divergence add in quadrature to give the reported value? On Aug 6, 2009, at 6:14 PM, Richard Gillilan wrote: Does anyone know if beam divergence gets included in the mosaicity values

[ccp4bb] Foils for energy calibration

pure elements)? I notice that a number of companies offer XRF standard kits. Richard Gillilan MacCHESS

Re: [ccp4bb] Scalepack error model?

and W ? - Thanks Richard Gillilan MacCHESS Some of the error model parameters are defined at the moment by user, they can be refined iteratively by experimenter by adjusting parameters in subsequent runs of scalepack, but most of the time it is not required. New version will adjust

[ccp4bb] Scalepack error model?

Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. Richard Gillilan MacCHESS

Re: [ccp4bb] Scalepack error model?

/Bayesian reasoning works? The scalepack manual has no equations for this. Richard Gillilan MacCHESS

[ccp4bb] Fwd: [ccp4bb] structure - function

Begin forwarded message: From: Richard Gillilan r...@cornell.edu Date: June 23, 2009 9:43:20 AM EDT To: Nadir T. Mrabet nadir.mra...@medecine.uhp-nancy.fr Subject: Re: [ccp4bb] structure - function A very interesting question. Stephan Jay Gould was well known for his argument that evolution

Re: [ccp4bb] Phantom Crystals - a recap

If I understand the idea correctly, I would still expect to see good Bragg spots, but the amplitudes would represent the rotationally averaged protein. This is like the hexagonal water lattice (Ih): there is disorder in how the water molecules are oriented at each lattice point (not really

Re: [ccp4bb] structure - function

Some years ago, I produced a short computer-animated video (complete with music and narration) for Jon Clardy's group on chorismate mutase. The e. coli and b. subtilis forms of chorismate mutase catalyze the same claisen rearrangement but have completely different folds and hydrogen bond

Re: [ccp4bb] Phantom Crystals

is distorted. Richard Gillilan MacCHESS BTW, I've also seen and harvested ghost crystals that were bubbles. Folds of skin can look like crystal edges sometimes. Speaking of ghosts, I had a dried out drop that looked just like a statue of Buddha I thought. One of my students came upon one

[ccp4bb] sharp beam focus and radiation damage?

I know that sometimes people like to defocus the x-ray beam at the sample so that the intensity profile is not sharply peaked. I think the rationale is that the sharp peak will cause damage, but contribute few photons to the overall diffraction pattern. Does anyone know of a reference

[ccp4bb] How small is a microbeam?

to hear people's opinion on the topic. Richard Gillilan MacCHESS

Re: [ccp4bb] long term data backup

$3M/TB clay tablets Probably the only medium that will still be practically readable a few decades from now! Having seen a few up close here on Cornell campus, I recommend you save the archeologists some headache and bake them. At least you can write on both sides. The unfortunate fact

[ccp4bb] Fwd: more about low order reflections

Since Sacha is having trouble posting directly the list I will forward his latest message since It addresses my second set of questions: Begin forwarded message: From: Alexandre OURJOUMTSEV sa...@igbmc.fr Thank you, Richard, for your questions ! Unfortunately, I failed to pass my mail to

[ccp4bb] Importance of low order reflections?

in these cases? Richard Gillilan MacCHESS

Re: [ccp4bb] Importance of low order reflections?

over- determined if one had access to the full molecular transform, so we are always only using bits and pieces of it in crystallography. But to what extent that can, in principle, be abused by leaving out low resolution I would like to know. Richard Gillilan MacCHESS

Re: [ccp4bb] definition of I Sigma I

There was a detailed and useful discussion of this on this list back around Dec 1, 2003. If you search in the archives for I on sig I you will find it. Best Richard On Dec 10, 2008, at 5:14 PM, ANDY DODDS wrote: Hi, does anyone have a definition of I Sigma I please. Any definitions

Re: [ccp4bb] Crystallogrphy today

is coherent diffraction imaging ... I think C. Riekel et. al. just published a Phys Rev Letter on this subject. Richard Gillilan MacCHESS

[ccp4bb] Fwd: [ccp4bb] Spooky, moving crystals

in confined spaces, weak magnets are a problem. Richard Gillilan MacCHESS On Jul 21, 2008, at 2:39 PM, Edward Snell wrote: This reminded me of a haunted beamline that removed crystals from the loop. You'd loop the crystals up nicely, block the stream, transfer the crystal fast to the goniometer

[ccp4bb] Structural importance of ordered water?

on water positions. Thanks Richard Gillilan MacCHESS

Re: [ccp4bb] alternatives to IZIT

Several people have asked about the concentrations we use for various dyes. In the case of fluorescein, we started with 45mg/ml as a stock solution. This is quite arbitrary and we often found that our initial stock solutions needed to be diluted 1:10 or 1:100 before use. It is more art

[ccp4bb] MacCHESS on F2 station available

users should contact Kathy Dedrick [EMAIL PROTECTED] Best Richard Gillilan MacCHESS, Cornell Ithaca NY

[ccp4bb] Fit2D?

with Fit2D? Is it still being supported? Richard Gillilan MacCHESS Cornell

[ccp4bb] ACA Microcrystals Session: deadline approaching

in the schedule for new contributions. Submit your abstract online at this link: www.amercrystalassn.org/ AbsSubmit/ Microcrystallography Session ACA 2008, Knoxville TN (Session 13.14, Thursday June 5) Organizers: Richard Gillilan, Ruslan Sanishvili Frontiers of structural biology are continuously

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

Oops, sorry. The x axis of the previous plot is actually not resolution, but Q. My bad. Richard On Nov 27, 2007, at 11:26 AM, Richard Gillilan wrote: Just a couple small images that may be of interest. The x scale is resolution in Angstroms, the y scale is intensity (arbitrary units). I

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

users have any control over. I don't have any hard data on this. Richard Gillilan MacCHESS

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

idea. Unfortunately the datasets were kept incomplete on purpose to reduce possible radiation damage effects. Richard On Nov 26, 2007, at 11:38 AM, Juergen Bosch wrote: Richard Gillilan wrote: I am currently working on guidelines for when helium and microbeam are necessary (based

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

the smallest beamstop. Next time, I'll have to whip out a ruler and see what distance makes them happy. It would be interesting to know typical distances for other facilities. Anyone else made these measurements? Richard Gillilan MacCHESS Note the density of air is approximately 1000 times

[ccp4bb] Microcrystallography: Call for Papers

and will be considered for the Etter Student Lecturer Award if invited to speak. A limited amount of funds will be available for speakers from outside the U.S. Please contact Richard Gillilan for details: [EMAIL PROTECTED] The deadline for online abstract submission is December 15, 2007

[ccp4bb] What not to publish?

resolved enough to warrant deposition. How much would you, as a reader, want to see? Crystallization conditions, unit cell, space group? Omit maps with very partially- built ligand? Nothing at all? Richard Gillilan MacCHESS Cornell