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 seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfAmoUxlJ7aRr7hoRArGeAKDgsoIKEADDo6ycaJBpLf6W9tnCFACeOSM6 1gZUOKKWkQ6Ioo+pQkPtw4Y= =DdSc -END PGP SIGNATURE-
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: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UK Subject: 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 seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfAmoUxlJ7aRr7hoRArGeAKDgsoIKEADDo6ycaJBpLf6W9tnCFACeOSM6 1gZUOKKWkQ6Ioo+pQkPtw4Y= =DdSc -END PGP SIGNATURE-
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 04/04/12 10:53, Tom Peat wrote: 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: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? 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 seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfA/AUxlJ7aRr7hoRAmfDAKDleNNb2BVxcNIHg7x81ks3gK5BpACgzQ9J DwQDnMorze1xjTZ+0qqacEg= =wVwe -END PGP SIGNATURE-
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 registers, the faster it runs. Best regards, Takanori Nakane
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 difficult to observe in practice for now. Roger Rowlett On Apr 4, 2012 5:09 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -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 04/04/12 10:53, Tom Peat wrote: 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: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? 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 seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfA/AUxlJ7aRr7hoRAmfDAKDleNNb2BVxcNIHg7x81ks3gK5BpACgzQ9J DwQDnMorze1xjTZ+0qqacEg= =wVwe -END PGP SIGNATURE-
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 bit binaries. Cheers, Roger Rowlett On Apr 4, 2012 6:06 AM, Roger Rowlett rrowl...@colgate.edu wrote: 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 difficult to observe in practice for now. Roger Rowlett On Apr 4, 2012 5:09 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -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 04/04/12 10:53, Tom Peat wrote: 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: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? 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 seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfA/AUxlJ7aRr7hoRAmfDAKDleNNb2BVxcNIHg7x81ks3gK5BpACgzQ9J DwQDnMorze1xjTZ+0qqacEg= =wVwe -END PGP SIGNATURE-
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 software showed any indication) but I am looking forward to do some experiments to confirm this. I was looking for some examples other than known domains (TFIIS, LIM, ring finger ref:encyclopedia of Mol Biol and Mol Med vol 6) which have C2H2 or C3H but doesn't follow the rules zinc finger but still bind to DNA and has been crystallized. I guess I will do more reading. Thanks againRajesh Date: Wed, 4 Apr 2012 00:43:48 +0100 From: hsuu...@u.washington.edu Subject: Re: zinc fingre To: CCP4BB@JISCMAIL.AC.UK; ccp4...@hotmail.com Hi Rajesh, Have you looked at how well conserved these Cys/His residues are? Is the spacing similar to known zinc fingers? Might be good things to consider if you suspect a zinc finger in your protein, of course you probably know this already. Best, Peter
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 http://en.wikipedia.org/wiki/Internet_slang, a *troll* is someone who posts inflammatory,^[2] http://en.wikipedia.org/wiki/Troll_%28Internet%29#cite_note-1 extraneous http://en.wiktionary.org/wiki/extraneous#Adjective, or off-topic http://en.wikipedia.org/wiki/Off-topic messages in an online community, such as an online discussion forum, chat room, or blog, with the primary intent of provoking readers into an emotional http://en.wikipedia.org/wiki/Emotion response^[3] http://en.wikipedia.org/wiki/Troll_%28Internet%29#cite_note-PCMAG_def-2 or of otherwise disrupting normal on-topic discussion. The emotional and disruptive response certainly fit the definition, but that's about all. And while Kevin's tiny blips in my inbox were trivial to delete and ignore, the resulting email hurricane of pompous indignation was not. Yuk. phx On 04/04/2012 00:29, James Stroud wrote: I read the first part of the page you linked to. I'm not sure what the decent into troll etymology says about the CCP4BB community--especially in response to your seemingly innocent post. My understanding is that the goal of the CCP4BB is to educate and not belittle the naivety of other members of the community. I hope I am not alone. James On Apr 3, 2012, at 4:33 PM, Kevin Jin wrote: Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin
[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 saving and restarting CCP4I. I found this setting shortly after posting to the BB. Regards, Wolfram
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 the r.m.s.d. (after superposition) of the aligned C-alphas - yes they have equivalent residues. The residues are tabulated in the output after: Moving Reference Distance Krissinel E, Henrick K Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60, 2256-2268, 2004. http://journals.iucr.org/d/issues/2004/12/01/ba5056/ba5056.pdf (Open Access) HTH, Paul.
[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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris
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 enough). I would try refining it with a different program, e.g. Buster, or even a different version of Refmac (I use 5.6.x routinely, but I see there's a 5.7.x now - Garib will no doubt have an opinion on which is the best one to use). At least that will eliminate the software as the origin of the problem: if it doesn't go away then we'll have to think again. Cheers -- Ian On 4 April 2012 16:16, Chris Meier crystallogra...@christophmeier.com 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, 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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris
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 crystallogra...@christophmeier.com 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, 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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris
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 bound protein ligand was apparently observed in a synchrotron beam. I look forward to hearing from others how best to handle this in refinement. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 4/4/2012 11:16 AM, 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, 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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris
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 from you again and that is good too. But let me explain the Orcus (however, keep in mind, I am only a single contributor and almost always do not represent the majority of CCP4BB users’ opinions. So that alone should be some comfort). ** ** The title of Orcus means that you have earned yourself a nickname. Nicknames are a brutal invention, common in Western civilization, almost always addressing some personal idiosyncrasy, in general politically incorrect, but nevertheless they stick*). ** ** So let me explain: St. Orcus is the patron saint of trolls, hobgoblins and troglodytes, and the defender of off-topic posters and otherwise chastised contributors (just like the Hofkristallrat sitting in his Hofkristallamt is the defender of structures collected from real data. That is for example why I do not get invited to modelers’ conferences. Everything has its price). So you are now in the unique position to evaluate the orcness of a contribution – perhaps first by making sure that your own contributions are not orcish - and exercise your right to identify any contributions you consider orcward. Experiencing a new culture can be a confusing and upsetting experience. If I may offer some comforting example relating to your blogs, and coming from a different planet myself, I once considered it a shocking calamity that protein-ligand structures are published that do not contain a ligand. I have mellowed a lot since and prevented a few cardiac events and assassination attempts by accepting the editorial indifference towards such orcward orcness. Maybe you’ll get there too, and maybe you’ll become a Hofkristallamtsapprentice. ** ** But let me tell you, if you are serious about correcting poor science, you’ve got to be ready to take a lot more flak to get there than being beatified on the BB. Oh, and by the way, no academic career. ** ** Wingardium Leviosa! ** ** Over and out, B ** ** *) Like Kim Jong-il probably means something like Gold Upright Sun. Just to demonstrate how poor those things translate into reality…. ** ** PS: Orcward ligand orcs, the Amt is watching! ** ** PPS: it is still ok to ride a trolley. ** ** *From:* Kevin Jin [mailto:kevin...@gmail.com] *Sent:* Tuesday, April 03, 2012 5:23 PM *To:* b...@hofkristallamt.org *Cc:* CCP4BB@jiscmail.ac.uk *Subject:* Re: [ccp4bb] very informative - Trends in Data Fabrication ** ** Thanks of your education. I got it. By the way, what does Orcus mean here? Regards, Kevin On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: ** ** -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/
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 Training Program email: j-kell...@northwestern.edu ***
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 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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris
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 there is increased mobility (or just as likely, induced static disorder). I'm wondering if this is related to too-tight B-factor restraints. I never use the default settings and always use more relaxed ones: in particular I set the weights of B factor restraints across angles to zero, IMO the across-bond restraints are more than sufficient. There has been a historical obsession with getting B factors as low as possible (too-tight restraints will certainly achieve this if that is your goal!), but isn't the true goal of refinement to obtain the model which best explains the data? Cheers -- Ian On 4 April 2012 16:31, Roger Rowlett rrowl...@colgate.edu wrote: PNAS 2000, 97, 623
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 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 the r.m.s.d. (after superposition) of the aligned C-alphas - yes they have equivalent residues. The residues are tabulated in the output after: Moving Reference Distance Krissinel E, Henrick K Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60, 2256-2268, 2004. http://journals.iucr.org/d/issues/2004/12/01/ba5056/ba5056.pdf (Open Access) HTH, Paul. -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
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_remember.txt do just that? -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
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... Quoting Chris Meier: Message 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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
[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 Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
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 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 Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
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, 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, 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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
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 rrowl...@colgate.edu 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 reviewers with my blessing. Learned a valuable lesson about adopting orphaned data sets though. Cheers, Katherine I look forward to hearing from others how best to handle this in refinement. Cheers, __**_ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 4/4/2012 11:16 AM, 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, 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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-**archive-public/ccp4bb/2004-07/** msg00532.htmlhttp://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris
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 calculated, what was the beam intensity, frame exposure time, number of frames, total rotation of the crystal, crystal size, beam size? If the beam intensity is not known, the beamline and the attenuation factor used might be helpful. What is the space group and how much data were collected? IF you have data with high multiplicity, you may be able to get rid of the latter parts of it maintaining completeness. This would reduce the effects of radiation damage if you are really dealing with it. Alternatively (but again with highly redundant data), you could try zero dose extrapolation. Look up Kay Diederichs' and Dominika Borek's works on this. Regards, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Chris Meier Sent: Wednesday, April 04, 2012 10:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [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 of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks, Chris
[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-scale factor and error model. The space group i used was p312 which i obtained by running a self-rotation function in MOLREP. When i scale my data using p312 spacegroup the chi2 and rejections were huge. But he data was scaling well in p321 spacegroup. can anyone explain whats going on? Thank you very much Deepthi
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 to no utility... -Amazon to some of its cloud customers following their major crash last year http://articles.businessinsider.com/2011-04-28/tech/29958976_1_amazon-customer-customers-data-data-loss -Eric On Apr 3, 2012, at 9:22 PM, Zhijie Li wrote: Hi, Regarding the online image file storage issue, I just googled cloud storage and had a look at the current pricing of such services. To my surprise, some companies are offering unlimited storage for as low as $5 a month. So that's $600 for 10 years. I am afraid that these companies will feel really sorry to learn that there are some monsters called crystallographers living on our planet. In our lab, some pre-21st century data sets were stored on tapes, newer ones on DVD discs and IDE hard drives. All these media have become or will become obsolete pretty soon. Not to mention the positive relationship of getting CRC errors with the medium's age. Admittedly, it may become quite a job to upload all image files that the whole crystallographic community generates per year. But for individual labs, I think clouding data might become something worth thinking of. Zhijie
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 monster allows slicing the data 4-5 times thinner than other detectors do. Some people also like collecting very redundant data sets. Even now, transferring and storage of raw data from a synchrotron is a pain in the neck, but in a few years it may become simply impractical. And all this hassle is for the only real purpose of preventing data fraud? An't there a cheaper and more adequate solutions to the problem? I also wonder why after the first occurrence of data fraud several years ago, PDB did not take any action to prevent its appearance in the future? Or administrative actions are simply impossible nowadays without a mega-dollar grant? On Apr 4, 2012, at 3:45 PM, Eric Bennett wrote: 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 to no utility... -Amazon to some of its cloud customers following their major crash last year http://articles.businessinsider.com/2011-04-28/tech/29958976_1_amazon-customer-customers-data-data-loss -Eric On Apr 3, 2012, at 9:22 PM, Zhijie Li wrote: Hi, Regarding the online image file storage issue, I just googled cloud storage and had a look at the current pricing of such services. To my surprise, some companies are offering unlimited storage for as low as $5 a month. So that's $600 for 10 years. I am afraid that these companies will feel really sorry to learn that there are some monsters called crystallographers living on our planet. In our lab, some pre-21st century data sets were stored on tapes, newer ones on DVD discs and IDE hard drives. All these media have become or will become obsolete pretty soon. Not to mention the positive relationship of getting CRC errors with the medium's age. Admittedly, it may become quite a job to upload all image files that the whole crystallographic community generates per year. But for individual labs, I think clouding data might become something worth thinking of. Zhijie
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 be easily accessed from anywhere. A disaster on the Clouding servers certainly would not be accepted as an valid excuse for not being able to provide the raw images when their very existence is in question. Zhijie From: Eric Bennett Sent: Wednesday, April 04, 2012 6:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: 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 to no utility... -Amazon to some of its cloud customers following their major crash last year http://articles.businessinsider.com/2011-04-28/tech/29958976_1_amazon-customer-customers-data-data-loss -Eric On Apr 3, 2012, at 9:22 PM, Zhijie Li wrote: Hi, Regarding the online image file storage issue, I just googled cloud storage and had a look at the current pricing of such services. To my surprise, some companies are offering unlimited storage for as low as $5 a month. So that's $600 for 10 years. I am afraid that these companies will feel really sorry to learn that there are some monsters called crystallographers living on our planet. In our lab, some pre-21st century data sets were stored on tapes, newer ones on DVD discs and IDE hard drives. All these media have become or will become obsolete pretty soon. Not to mention the positive relationship of getting CRC errors with the medium's age. Admittedly, it may become quite a job to upload all image files that the whole crystallographic community generates per year. But for individual labs, I think clouding data might become something worth thinking of. Zhijie
[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, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
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 deept...@gmail.com Date: Wed, Apr 4, 2012 22:07 Subject: [ccp4bb] problem in scaling the Zn-MAD data To: CCP4BB@JISCMAIL.AC.UK 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-scale factor and error model. The space group i used was p312 which i obtained by running a self-rotation function in MOLREP. When i scale my data using p312 spacegroup the chi2 and rejections were huge. But he data was scaling well in p321 spacegroup. can anyone explain whats going on? Thank you very much Deepthi
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 somehow the temporary files that XDS was creating on the 32bit OS were better handled in memory instead. This off course was done using 32bit compiled XDS vs 64 bit compiled XDS. I did not try to run the 32bit XDS on the 64 bit OS. Maybe I should. This was done on particular machines configuration and would not generalize to all programs and situations. On the topic of 64 bit vs 32 which to choose? Funny enough I can't get iMosflm running reliably on 32 bit CentOS 5 or CentOS 6 and I can on 64 bits versions. We have all running (CCP4, Coot, iMosflm, XDS, phenix, best, etc, etc) running in 64 bit and intent to move all user computers to uniform 64 bit environment on the next shutdown as it is more difficult to support both 32 and 64 bit enviroment. David -- David Aragao, PhD | Research Fellow - MX | Australian Synchrotron p: (03) 8540 4121 | f: (03) 8540 4200 | m: 0467 775 203 david.ara...@synchrotron.org.au | www.synchrotron.org.au 800 Blackburn Road, Clayton, Victoria 3168, Australia From: Roger Rowlett [rrowl...@colgate.edu] Sent: 04 April 2012 20:13 Subject: Re: 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 bit binaries. Cheers, Roger Rowlett On Apr 4, 2012 6:06 AM, Roger Rowlett rrowl...@colgate.edumailto:rrowl...@colgate.edu wrote: 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 difficult to observe in practice for now. Roger Rowlett On Apr 4, 2012 5:09 AM, Tim Gruene t...@shelx.uni-ac.gwdg.demailto:t...@shelx.uni-ac.gwdg.de wrote: -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 04/04/12 10:53, Tom Peat wrote: 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.demailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? 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 seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304tel:%2B613%209662%207304 +614 57 539 419tel:%2B614%2057%20539%20419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edumailto:rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers,
