Re: [ccp4bb] Who is using 64-bit Linux?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Tom, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. Cheers, Tim On 04/03/12 22:07, Tom Peat wrote: > We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc

Re: [ccp4bb] Who is using 64-bit Linux?

Hello Tim, I believe the notion comes about as one can thread 64 instead of 32 addresses concurrently, thereby boosting performance. If it has no performance boost, why would they bother? Cheers, tom -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednes

Re: [ccp4bb] Who is using 64-bit Linux?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Tom, because there are PCs out there with more than 200GB RAM, as well as programs and systems that make use of them. As far as I understand a 32-bit compiled kernel would have not possibility to address anything beyong 4GB. Regards, Tim On 04/04

Re: [ccp4bb] Who is using 64-bit Linux?

Dear Tim, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. The x86_64 architecture has more registers than 32bit (x86) architecture. Register access is faster than memory access so the more data programs can put on

Re: [ccp4bb] Who is using 64-bit Linux?

A 32 bit Linux OS with PAE enabled (which is all of the current Linux distros) can actually address 64 Gb of memory, but no more than 3 Gb per process. 3 Gb may not be that much of a limitation for many processes, so large performance increases on a 64-bit system compared to a 32-bit may be difficu

Re: [ccp4bb] Who is using 64-bit Linux?

Thanks everyone for the info. To summarize, it looks like 64-bit Linux is not the issue it was a few years ago for crystallography software. Many typically used crystallography packages are compiled for 64 bit now and the ia32 libs typically provide compatibility for those not yet compiled as 64 bi

Re: [ccp4bb] zinc fingre

Dear All, Thanks everyone for the suggestions. I did go to library to look up some chapters in books which gave me lot of information about conserved zinc finger domain. My protein has Cx4C and Cx3C and with very large spacing, so I suspect it could be zinc finger like protein (though no softw

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

No James, you're not alone - astonishing petty pile-on (bullying?) on this board the last few days. Wikipedia says: "In Internet slang , a *troll* is someone who posts inflammatory,^[2]

[ccp4bb] ccp4i project display

Thank you, Zhijie and Hans. I may resort to your fixes once this temporary fix is no longer effective: "System Administration"|"Configure Interface"|->"Maximum length of drop-down menu columns" I still had some space to spare vertically to increase it from 25. The change becomes effective after sav

Re: [ccp4bb] core rmsd in coot

On 03/04/12 21:51, Ursula Schulze-Gahmen wrote: When superimposing 2 structures in coot, I get a core rmsd in the output. What does this mean? Which residues are included in the core rmsd? Are these all the residues that have equivalent residues in the moving and reference molecule? It is t

[ccp4bb] negative difference density around sulphur and oxygen atoms

Dear all, I am refining the X-ray structure of a protein: Data to ~2A were collected at a latest-generation synchrotron. The 2fo-Fc maps are crisp, the model of the protein is complete and I am reasonably happy with the stats (R below 20%, Rfree below 25% in Refmac 5.5). However, I am seeing a lot

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

Hi Chris I would say there's something very wrong if you're seeing -6 sigma difference peaks at O atoms. I don't see how this can be explained by radiation damage. I for one have never seen that before in a structure where there weren't other obvious issues (or maybe I just haven't looked hard e

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

PS you say the model is complete, but just as important how complete is (are?) the data. -- Ian On 4 April 2012 16:16, Chris Meier wrote: > Dear all, > I am refining the X-ray structure of a protein: > Data to ~2A were collected at a latest-generation synchrotron. > The 2fo-Fc maps are crisp, th

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

Radiation damage induced loss of definition of disulfide bridges, side chain carboxylates, and certain histidine residues has been observed in synchrotron-irradiated protein crystals. For example, see Weik et al., PNAS 2000, 97, 623. I have also seen a recent paper where radiation damage of a b

Re: [ccp4bb] very uninformative

Cool! You are a good tutor for Greek culture. Orcus blesses you. ^_^ On Tue, Apr 3, 2012 at 10:07 PM, Bernhard Rupp (Hofkristallrat a.D.) < hofkristall...@gmail.com> wrote: > Ok Kevin, > > ** ** > > thank you for your response. You got it, and that is good, and I am sure > we’ll hear fro

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

> > 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 Tr

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

Hello Chris, Are you refining individual atomic B factors or grouped? Perhaps the B factors of the terminal atoms of the side chain are being restrained to too low of a B factor resulting in excessive negative density? Scott On Apr 4, 2012, at 8:16 AM, Chris Meier wrote: > Dear all, > I am r

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

The PNAS paper you refer to talks about a "loss of definition" of exposed carboxyl O atoms, i.e. an increase in B factor, but presumably if this is modelled properly then it shouldn't leave a big hole in the difference map. After all, the paper is not claiming that C-O bonds are broken, only that

Re: [ccp4bb] core rmsd in coot

I wish Paul, that at least SOME of the great info that coot prints to the screen then scrolls out of sight could be directed to a "very-useful-things-to-remember" box.. Eleanor On Apr 4 2012, Paul Emsley wrote: On 03/04/12 21:51, Ursula Schulze-Gahmen wrote: When superimposing 2 structures i

Re: [ccp4bb] core rmsd in coot

On Wed, 2012-04-04 at 17:31 +0100, Eleanor Dodson wrote: > I wish Paul, that at least SOME of the great info that coot prints to > the > screen then scrolls out of sight could be directed to a > "very-useful-things-to-remember" box.. > > Eleanor > Won't "coot | tee very_useful_things_to_rememb

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

apart from radation damage it could be a combination of: - too tight restraints on the B-factors - 9 sigma not being that much on a the e/A3 scale, i.e. your difference map is very flat (which is good) and the few peaks that remain stand out a lot, even if their absolute height is low... Quot

[ccp4bb] PEG MME 2000 in powder form?

Dear All, is PEG MME 2000 still available in powder form? I think Fluka used to sell it, but Fluka is no more and Sigma-Aldrich don't sell it. Hampton Research and Molecular Dimensions (and perhaps others) do sell 50% (w/v) solutions. Mark Mark J van Raaij Laboratorio M-4 Dpto de Estruc

Re: [ccp4bb] PEG MME 2000 in powder form?

ok, I stand corrected, Sigma DOES sell it, but under a slightly different name: 81321 FLUKA Poly(ethylene glycol) methyl ether average Mw 2,000 81321-250G, 23.60 euros 81321-1KG, 71.80 euros (prices given for Spain) thanks! Quoting "VAN RAAIJ , MARK JOHAN": > > > Dear All, > > is P

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

Dear Chris Could you please try later version of refmac then if the problem persists please let me know. Before making any suggestions it would be good to make sure that the problem is not related with particular software version (as Ian suggested) regards Garib On 4 Apr 2012, at 16:16, Ch

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

could it be that the scattering table would be slightly different for the sulfur atoms at the collected wavelength? Are they Cys or Met residues? if Cys is there a possibility of oxidation to the disulfides?

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

On Wed, Apr 4, 2012 at 10:31 AM, Roger Rowlett wrote: > I have also seen a recent paper where radiation damage of a bound protein > ligand was apparently observed in a synchrotron beam. > That was a manuscript were I would have happily given the coordinates and structure factors to the reviewer

[ccp4bb] Cell dimensions

Hello, One of my crystal diffracted to 20A. I collected 4 snaps and would like to get the information on space group and cell dimensions. I opened the images in iMosflm. The files are .cbf Is there way I can find such information in iMosflm? Thank you for advice. Ros

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

Hi Chris, As has been suggested already, and seems quite plausible to me, it sounds like tell-tale signs of radiation damage. To have little more substance behind this suspicion, some more experimental details could help: What was the dose accumulated during data collection? If the dose cannot be

[ccp4bb] problem in scaling the Zn-MAD data

Hello everyone I have a problem scaling the MAD data which was collected a week ago.The data was collected at 1.5A resolution using three wavelengths for Zn-MAD experiments. Scaling the data for MAD experiments, the number of rejections and chi2 values were very high even after adjusting the error-

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

Then everyone's data can be lost at once in the next cloud failure. Progress! "The hardware failed in such a way that we could not forensically restore the data. What we were able to recover has been made available via a snapshot, although the data is in such a state that it may have little

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

People who raise their voices for a prolonged storage of raw images miss a simple fact that the volume of collected data increases proportionally if not faster than the cost of storage space drops. I just had an opportunity to collect data with the PILATUS detector at SSRL and say you that monst

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

Hi Eric, My previous email may have been a little misleading, but I do not recommend deleting the originals from the hard drives/discs/tapes. Clouded data should be better viewed as an extra copy (considering that our lab/office are quite prone to catch fire, and theft too), or a copy that can

[ccp4bb] arp_waters still available?

Dear Developers, in some older scripts I still call the ccp4 version of arp_waters, which worked well for dummy atom picking. It does not seem to be included in recent 64 bit CCP4 packages. Does anyone perhaps have a precompiled 64 bit version of arp_waters that might run on RHEL62? Best regards,

Re: [ccp4bb] problem in scaling the Zn-MAD data

Sounds then like your spacegroup is p321... It's your data (scaling) that determines that, not your preconceptions (which wasn't clear how arrived at either?) cheers Phx Sent from tiny silly touch screen - Reply message - From: "Deepthi" Date: Wed, Apr 4, 2012 22:07 Subject: [ccp4bb]

Re: [ccp4bb] Who is using 64-bit Linux?

Hi All, I did quite a bit of performance comparison with XDS between two centOS 5 (64 vs 32) and did notice performance boost when writing results to a remote NFS directory. Interestingly, using same OSs writing locally the performance boost was not noticeable. At the time I thought that someho