[ccp4bb] BDB rsync

Has anyone successfully accessed the BDB lately? I downloaded the whole thing by rsync about a year ago, but I am no longer able to do so. I don't seem to be getting any response from the rsync server at all. If others are able to access it, I should be looking for a problem on my end. Thanks. :)

Re: [ccp4bb] Validation reports for all X-ray structures in the PDB

Any chance validation reports will ever be made for obsoleted entries? Eric On Wed, Apr 16, 2014 at 1:01 PM, Gerard DVD Kleywegt wrote: > Hi all, > > You may not have noticed, but 19 March 2014 was VR Day - the day that new > style wwPDB validation reports for all X-ray structures were made publ

Re: [ccp4bb] sf_convert

On Wed, Mar 26, 2014 at 10:36 AM, Pavel Afonine wrote: > I would say that troubles you face are a good reason to talk to developers > of respective problems (off list). Thanks to everyone who has provided helpful responses to my query. I've learned of resources I was unaware of, and had misconc

Re: [ccp4bb] sf_convert

any other of these variants, > all of are sh-compatible. The best solution to your problem is to use > cif2mtz, and the best answer to your question would be the author of > sf_convert to modernise the program. > > Best, > Tim > > On 03/26/2014 05:00 AM, Eric Williams wrote: > &

[ccp4bb] sf_convert

Does anyone here have experience running sf_convert? I know it's not part of CCP4, but it does rely on CCP4 for converting structure factors to MTZ format. When I try to run it, I get errors that suggest that my shell isn't bash, but it really is. The program output is as follows. sf_convert -o M

Re: [ccp4bb] Of topic, trying to identify a reference for multiple crystal data collection

The table also appears in chapter 16 of this book: Sanderson, Mark R., and Jane Skelly, eds. *Macromolecular Crystallography: conventional and high-throughput methods*. Oxford University Press, 2007. Eric On Thu, Jul 18, 2013 at 11:29 PM, Edward Snell wrote: > Dear All, > > On a beamline visit

Re: [ccp4bb] Of topic, trying to identify a reference for multiple crystal data collection

This may be the publication you seek: Fry, Elizabeth E., Jonathan Grimes, and David I. Stuart. "Virus crystallography." *Molecular biotechnology* 12.1 (1999): 13-23. http://link.springer.com/article/10.1385/MB:12:1:13 Eric On Thu, Jul 18, 2013 at 11:29 PM, Edward Snell wrote: > Dear All, > > O

Re: [ccp4bb] Why the name "aimless"

I've always thought "gormless" is a woefully underused word. Eric On Thu, May 2, 2013 at 11:53 AM, Mark van Raaij wrote: > i.e. the next program will be Graceless or Feckless? > > On 2 May 2013, at 12:10, Phil Evans wrote: > > > Reference: > > Gibbons, S. (1932) Cold Comfort Farm, Longmans, Lond

Re: [ccp4bb] Boveral in SFCheck

BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Boveral in SFCheck > > > > Hi, > > > > 2HR0 I would stay far away from that one! It is a made up model, not > based on any real data. Unfortunately, for reasons unclear to me, this > structure has still not been retrac

Re: [ccp4bb] Boveral in SFCheck

.. > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912&L=CCP4BB&D=0&P=88327 > > Regards, > > Michael > > > On Fri, Dec 14, 2012 at 3:34 AM, Eric Williams wrote: > >> Please pardon me if this is a dumb question with an obvious answer... >> &

[ccp4bb] Boveral in SFCheck

Please pardon me if this is a dumb question with an obvious answer... I'm parsing SFCheck's plain text output as part of my dissertation, and I'm having trouble identifying one of the values. There are three overall B-factor values reported, one based on the Patterson origin peak, one based on the

Re: [ccp4bb] vitrification vs freezing

How about Latin? It already has a long and distinguished history of use in science. :) Eric On Fri, Nov 16, 2012 at 4:54 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi James, > > I once heard that in (European) law French is the language of choice > because it we

Re: [ccp4bb] Off-topic: Best Scripting Language

Another option that could be cheap or free (if your university offers license deals, as mine does) is SPSS. It has a lot of the quick and dirty spreadsheet functionality of Excel, is much faster than Excel with large tables, has lots of good analysis tools, has its own scripting language, and is co

Re: [ccp4bb] Off-topic: Best Scripting Language

Try R. :) http://www.r-project.org/ Eric On Wed, Sep 12, 2012 at 10:32 AM, Jacob Keller < j-kell...@fsm.northwestern.edu> wrote: > Dear List, > > since this probably comes up a lot in manipulation of pdb/reflection files > and so on, I was curious what people thought would be the best language

Re: [ccp4bb] information received through the AFC: iycr2014

I'm guessing disorder is a major limiting factor on effective resolutions. ;) Eric On Thu, Jul 5, 2012 at 2:36 PM, Bernhard Rupp (Hofkristallrat a.D.) < hofkristall...@gmail.com> wrote: > **Ø **enjoy that the U.N.'s declaration of the International Year of > Crystallography comes in the form of

Re: [ccp4bb] off-topic: Verify3D

ay be needed, but once everything compiles and runs properly, I'll let the list know (assuming anyone's interested). Thanks again. :) Eric On Fri, Jun 8, 2012 at 10:47 AM, Eric Williams wrote: > I recently acquired the source for Verify3D and have tried unsuccessfully > to compile it.

[ccp4bb] off-topic: Verify3D

u 11.04 in particular? Thanks. :) Eric Williams PhD candidate, Intelligent Systems Program University of Pittsburgh

Re: [ccp4bb] parameters defining crystallographic model quality

I'd head to Gerard Kleywegt's "Practical Model Validation" web course post-haste: http://xray.bmc.uu.se/embo2001/modval/ Eric On Mon, Jan 18, 2010 at 11:00 AM, james09 pruza wrote: > Dear all, > > What are the standard methods for the crystallographic mo