Re: [ccp4bb] Why nobody comments about the Nobel committee decision?

Dear Axel, Quite so, absolutely. Theoretical physics and theoretical chemistry sweeped the awards at the Nobels this week. As I remarked on that other medium yesterday (twitter):- I confess to preferring a joint theory and experiment approach, but the Nobel Committee didn't ie I think 'that bo

Re: [ccp4bb] how to cut back resolution of a well-refined model

Hi Yafang, perhaps you should calculate the actual resolution first (as described here: *Acta Cryst.* (2013). D*69*, 1921-1934) and then go from that? Pavel On Thu, Oct 10, 2013 at 1:57 PM, Yafang Chen wrote: > Hi All, > > I have a structure at 2.45A which has been well refined. However, sinc

Re: [ccp4bb] how to cut back resolution of a well-refined model

On Thursday, 10 October, 2013 22:44:34 Jim Pflugrath wrote: > Please tell me why Rpim should be looked at. Cannot one have meaningless > data and have lots of multiplicity to drive Rpim lower without any real > benefit? Under what conditions is Rpim useful? > And suppose one looks at (and no

[ccp4bb] Smallest crystal used for a whole dataset (at a synchrotron!)

Dear All, I was wondering if anyone has a more up to date reference on the smallest crystal (fibrils not included!) that has been used to collect a whole dataset? Also, the smallest crystals used for a multi crystal approach? In both cases, not including any X-FEL structures. I'm currently workin

Re: [ccp4bb] how to cut back resolution of a well-refined model

Having run foul of the "R-factor police" on a number of occasions, but having ultimately prevailed, I would like to offer the following opinion: Intensity measurements in the weak outer shells are as valid as any other and, if they are correctly processed and properly assessed for their statisti

Re: [ccp4bb] Why nobody comments about the Nobel committee decision?

Dear John, I surely hope that the recent Nobel Prize will encourage young people to get into into the fields of computational biology and chemistry. Moreover, X-ray sources are undergoing new exciting developments (e.g., XFELs) that require new computational approaches, as does cryo-EM. Chee

Re: [ccp4bb] how to cut back resolution of a well-refined model

Please tell me why Rpim should be looked at. Cannot one have meaningless data and have lots of multiplicity to drive Rpim lower without any real benefit? Under what conditions is Rpim useful? And suppose one looks at (and not /) and CC1/2. What of it? And let me write what Phil wrote in a s

Re: [ccp4bb] how to cut back resolution of a well-refined model

Dear Yafang, Is it the case that you collected these data on a Pilatus detector, using relatively low exposure and high multiplicity? These types of datasets always give what looks like alarmingly high values of R-merge, and many people who are set in their ways (like so many reviewers still

Re: [ccp4bb] how to cut back resolution of a well-refined model

Please explain how you think that cutting back the resolution will improve your model Phil On 10 Oct 2013, at 21:57, Yafang Chen wrote: > Hi All, > > I have a structure at 2.45A which has been well refined. However, since the > R-merge at the last shell is above 1 (although I/sigmaI at the la

[ccp4bb] how to cut back resolution of a well-refined model

Hi All, I have a structure at 2.45A which has been well refined. However, since the R-merge at the last shell is above 1 (although I/sigmaI at the last shell is more than 2), we now decide to cut back the resolution to about 2.6A. Is there a way to do this based on the well-refined model instead o

Re: [ccp4bb] CCP4 Release 6.4.0 out

Dear Felix, It is probably poor formatting in my e-mail, apologies. The download page is http://www.ccp4.ac.uk/download/ and yes it shows 6.4.0 for me. You may be seeing cached page. If so, press down and hold 'Shift' on your keyboard and click 'Reload' control button in your browser (it may b

Re: [ccp4bb] CCP4 Release 6.4.0 out

Dear Felix, No, it does not come through updates. 6.3.0 update line will terminate tomorrow or soon after. This must be a fresh install. It can co-exist with 6.3.0 on Linux platforms and Mac OSX platforms, except for QtMG on Mac OSX, which will be superseded (but it is advisable to supersede i

[ccp4bb] Product Development Scientist and Applications Leader at Microlytic

Microlytic is a leader in the development of tools for protein crystallization. Our team brings tremendous crystallization experience to all aspects of our company, with Ph.D. crystallographers involved in production, development, commercialization, sales and marketing. Our mission is to provide a

[ccp4bb] CCP4 Release 6.4.0 out

Dear CCP4 Users, The CCP4 Core Group is very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 6.4.0 (Long Preston) is now available from the CCP4 download website: http://www.ccp4.ac.uk/download.php The release is avail

Re: [ccp4bb] Why nobody comments about the Nobel committee decision?

Dear Sacha, Dear Colleagues, I also offer my congratulations to the Chemistry Nobellists of yesterday. A very exciting and significant event, which I enjoyed. I recall when my PhD student, Gail Bradbrook, spoke about our harnessing these exciting methods in our crystallographic and structural ch

Re: [ccp4bb] CCP4 Setup manager

This is most probably because of last-minute changes for CCP4 release, you just got us in a *very* wrong moment, we are moving files on the server. Please come back in 2 hours or so. Eugene. On 10 Oct 2013, at 17:55, Swastik Phulera wrote: > Dear All, > I am currently setting up a system runni

Re: [ccp4bb] Why nobody comments about the Nobel committee decision?

Their work has inspired many of us, including my own work on crystallographic refinement. It is so wonderful that Michael, Arieh, and Martin have received this most deserving recognition. Congratulations!!! Axel Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor and Cha

[ccp4bb] CCP4 Setup manager

Dear All, I am currently setting up a system running UBUNTU-12.04.3 (64 bit version), When I try to install CCP4 software suite by using the software suite, it kinda gets hung with the message "Now communicating with CCP4 server, please wait.." for ever Any help would be usefull. Re

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

On Wed, Oct 9, 2013 at 6:56 PM, Marco Lolicato wrote: > Anyway, for those reasons and more, I was wondering if maybe is nowadays > needed to revisit the peer-review process. > Apologies for the lengthy response, but I really do think the current publication system is broken, just not for the sa

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

Another annoying syndrome is people who download your coordinates, don't read the paper, and then assume any insights are their own brand new ideas. A biophysicist once said to me at a meeting "I hope you aren't offended that we've found the DNA bend in your structure is flexible". The TITLE of

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

My editorial suggestion: "My suspicion is that many structural papers are not read beyond the author list and title, if at all" should be corrected as follows: My suspicion is that many papers are not read beyond the author list and title, if at all. Debasish -Original Message- From:

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

I could not resist but comment at the end ... (sorry for cleaning up the thread text) I agree with Roberto that the system is actually not that bad when you think of it. Or, it could be much worse. In my experience, the editors of many journals - professional or academic - try very hard, and m

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

To bolster Adrian's argument about people not reading papers: I periodically identify PDB entries that have not been released becuase they are on hold until publication. But the paper was publshed months earlier. This means that nobody has read the paper, then tried to look at the coordinates,

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

Hi Folmer, > I was hoping to see what kind of science was behind the computer program that > generated the unique papers. Combinatorics in this case. The article was pre-written, he just replaced some names. Typically for hard science texts you would use a formal grammar with random productio

Re: [ccp4bb] Why nobody comments about the Nobel committee decision?

This is amazing - I am so glad the Nobel committee has recognised this ground breaking, rather unglamorous work requiring great intelligence, very hard work, and a lot of disappointments! Congratulations to them all, and to the whole field. Eleanor Dodson On 10 October 2013 09:26, Alexandre OUR

[ccp4bb] Dissolving deoxycholic acid

Dear All, Initially I planned to wash Inclusion bodies using 1% (w/v) sodium salt of deoxycholic acid (Na-Deoxycholate). In our lab, we have Deoxycholic acid (Not Na-salt). Any inputs how to get it solubilized to reach 1% (w/v)? Thanks Kris

Re: [ccp4bb] השב: [ccp4bb] Why nobody comments about the Nobel committee decision?

Also good to remember the contributions of Peter Kollman who also died too young and would certainly have been a contender in this splendidly well directed Nobel prize Laurence H. Pearl PhD FRS FMedSci Professor of

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

…then the issue is to reduce the number of papers people publish: this is the central problem in the system: nobody reads them, nobody cites them, etc etc. There are papers out there - quite a number - that have no cites, meaning that even the authors weren't interested in them. A long time ag

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

Ciao Roberto, I'm sure the current research system works better in some fields than in others. It depends on a number of factors, perhaps the more important of them the amount of publications produced. Or it may be as we say in Spain: everybody talks about the party according to how much fun is ha