Re: [ccp4bb] quote source

Re: [ccp4bb] quote source

Hi Bernhard, Google books is your friend... It returns 2 hits for "Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy" Both are essays / chapters by Max Perutz I Wish I'd Made You Angry Earlier: Essa

[ccp4bb] quote source

Dear All, does someone know the proper reference of this L. Pauling statement? "Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy and the small activation energy involved in its formation and rupture, t

[ccp4bb] openmp version of CNS 1.21

An openmp multi-processor version of CNS 1.21 is now available at the CNS download site (see http://cns-online.org/cns_request/ to obtain downloading instructions). This parallelized version of CNS 1.21 contains openmp directives (courtesy Kay Diederichs, Universität Konstanz) that enable p

Re: [ccp4bb] os x wiki

Hi Patrick: I'm afraid all the insidious stupidness originates from moi. Anyway, the machine hosting this thing has a roached power supply, thanks to the fact that the University electrical supply resembles that produced by, in terms of its stability and reliability, an underfed gerbil- w

[ccp4bb] os x wiki

Does anyone know if the Crystallography on OS X Wiki is down? I haven't been able to access the site for a few days, but I don't know if the site is down, or if some new and insidious stupidness has been perpetrated by the rocket scientists who control IT in our institution...thanks. Pat

Re: [ccp4bb] Acorn question

shelxe can do a pretty good imitation of Acorn (amongst other things) and is kinder to your computer. 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. +49-551-39-22582 On Wed,

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

Dear Bram, Thankyou for the plug, but your email could be misunderstood. In fact we integrated and scaled the domains (2 for insulin, 3 for glucose isomerase) SIMULTANEOUSLY, taking the overlap into acount. This produced two data files (SHELX HKLF 4 and 5 formats). The HKLF 4 file that we used

Re: [ccp4bb] Acorn question

On Wed, 23 Jul 2008, [EMAIL PROTECTED] wrote: All, In the past couple of days I have been trying to use Acorn (in the CCP4 suite of programs). Consistently it starts up fine and after some small amount of time (5-10 minutes) it has taken up all the physical memory and then it starts to slowly

Re: [ccp4bb] Na Acetate Buffer

Yes, Diana brings up really important point. Not only is acetic acid volatile, certain salt mixtures (like NH4 salts) can make the matter worse. Drifting pH, particularly in poorly designed vapor diffusion experiments, can yield irreproducible results if the volatility of the buffer compo

[ccp4bb] Acorn question

All, In the past couple of days I have been trying to use Acorn (in the CCP4 suite of programs). Consistently it starts up fine and after some small amount of time (5-10 minutes) it has taken up all the physical memory and then it starts to slowly gobble up all the swap space until the only opt

Re: [ccp4bb] Na Acetate Buffer volatility

One important consideration with acetate buffer is volatility. All the care in the world to painstakingly reproduce the pH of the buffer will not help you if store your acetate buffer for long periods of time in a container that doesn't minimize evaporation (so all of you out there trying t

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

Hi Hari, I have seen a poster last year's DGK by Ina Dix and Madhumati Sevanna from George Sheldricks' group. Not sure it was published yet. They collected data on non-merohedrally twinned crystals and processed and scaled the domains separately and merged them afterwards, thus increasing the

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

Scala has an option (ANOMALOUS MATCH INRUN) to select "matching" Bijvoet pairs, which will have a similar effect to average DelAnom, but when I've tried it, it has given worse results than just chucking everything in together Phil On 23 Jul 2008, at 16:53, Bart Hazes wrote: Jacob Kelle

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

Jacob Keller wrote: Shouldn't all of the "crystal-to-crystal" differences be taken out automatically by scaling, Scaling only takes out differences in overall scale, B-factor and, if you have enough data, it can correct to some extend for absorption or other more local effects. Systematic dif

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

Shouldn't all of the "crystal-to-crystal" differences be taken out automatically by scaling, and is there not the same proportional anomalous signal in every isomorphous crystal, regardless of the background? I would think that using multiple crystals would give a better idea of "the truth," as

Re: [ccp4bb] Na Acetate Buffer

Michael's comments are correct and follow indeed appropriate chemistry theory. In practice however, as said earlier, it is less likely to read a correct pH value with a pH-meter (unless extensive care and adjustments are taken beforehand) than to predict amounts of acid and base to use reliably

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

Increasing redundancy only helps if all data draw from the same distribution so you get a more accurate estimate of the mean of the distribution. When dealing with different crystals, crystal-to-crystal variation is likely larger than the anomalous signal you are looking for and I'm therefore n

[ccp4bb] Post-doctoral position in Montreal

Several post-doctoral positions in the area of structural biology are available in the laboratory of Dr. Mirek Cygler and funded by CIHR. The research activities of the group focus on structural and functional characterization of proteins to gain detailed understanding of their mode of acti

Re: [ccp4bb] Na Acetate Buffer

Methods in Enzymolgy has published several articles on buffers over the years. One handy and comparatively recent reference is:

[ccp4bb] Omit interactions of alternate conformations manually?

> Hi all, > I am trying to model an alternate conformation in my structure, but the > alternate conformation is a completely different residue. I saw an old > posting about this same issue and they recommended giving different segids > to different ligands and omitting their interactions, and

Re: [ccp4bb] Na Acetate Buffer

Buffer making is very much an empirical process, but there is a comment that needs to be made about the use of the H-H equation and pKa values. I have to teach our department's biochemistry laboratory, and I sadly would have to take off points from all the discussions as the H-H equation

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

hari jayaram schrieb: ... I was wondering if anyone could comment on combining datasets from multiple P1 crystals to increase the redundancy even further for such heavy atom ( SAS / SAD ) or MAD experiments. Hari, well, my comment would be that it should be possible in principle from what

Re: [ccp4bb] SUMMARY: synchrotron remote data collection

Hi Juergen, if the list at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Synchrotrons were converted to a table, one column could be the type of puck, another the information about whether not only mail-in, but also remote control are possible. An example of a Wiki table is at