Re: [ccp4bb] Does Scala merge anomalous/non-anomalous?

2012-12-05 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 If you don't want scala to keep your Bijvoet-pairs separate, you should uncheck the appropriate button in the ccp4i-GUI. However, since you have SIGF_New, your mtz-file already contains the merged Bijvoet-pairs. Scala is not a refinement programm and

Re: [ccp4bb] Does Scala merge anomalous/non-anomalous?

2012-12-05 Thread Phil Evans
Note that Scala Aimless always put I+, I- and Imean into the output file, which then get propagated through [c]truncate. This is irrespective of whether the Anomalous data flag is switched on: that only affects outlier rejection and some statistics. Note also that Aimless (recent versions

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ed Pozharski
Francois, I did not realize Phil Evans is god (perhaps a minor one as he did not yet earn a capital G). I do concur that insertion code is evil. I had to re-refine an old antibody structure recently and it messes up coot sequence window and breaks refmac bond restraints. Evil, evil,.evil.

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Phil Evans
not god I don't think I wrote that bit! Phil On 5 Dec 2012, at 15:06, Ed Pozharski wrote: Francois, I did not realize Phil Evans is god (perhaps a minor one as he did not yet earn a capital G). I do concur that insertion code is evil. I had to re-refine an old antibody structure

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ian Tickle
The last time I tried the pdbset renumber command because of issues with insertion codes in certain programs, it failed to also renumber the LINK, SSBOND CISPEP records. Needless to say, thanking god (or even God) was not my first thought! (more along the lines of why can't software developers

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Robbie Joosten
Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the PDB standard. Does 128A come before or after 128? There is no strict rule

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ian Tickle
I had always assumed that ASCII sort order was the standard so ' 128A' comes after ' 128 ' in the collating sequence, and indeed the PDB documentation seems to make it clear that it comes after, e.g. in the section describing the ATOM record: REFERENCE PROTEIN NUMBERINGHOMOLOGOUS

[ccp4bb] Postdoctoral Position in Structural Biology of Immune Receptors

2012-12-05 Thread ronan . keegan
Dear All, I repost this message on behalf of Dr. Jia-huai Wang, as this position needs to be filled as soon as possible. For inquiries please contact Dr. Wang directly at jw...@red.dfci.harvard.edu Postdoctoral Position in Structural Biology of Immune Receptors: There is an immediate opening

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Peter Keller
Hi Robbie, On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote: Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ed Pozharski
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote: Does 128A come before or after 128? Robbie, shouldn't it simply depend on which residue record comes first in the pdb file? Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy?

Re: [ccp4bb] Bug of GUI of ACORN?

2012-12-05 Thread ronan . keegan
Dear Jiawei, Thanks for spotting this and bringing it to our attention. It is a serious bug in the interface when using the default protocol for Acorn. When running Acorn to determine heavy atoms the default is to truncate the resolution to 3.5 Angstroms. However this default is there for all

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Robbie Joosten
Hi Ian, The 'standard' you describe below is more of a suggestion than a rule. The PDB does not enforce a numbering scheme which is particularly annoying when dealing with engineered proteins with linkers or domains of different proteins (they come with all sorts of numbering schemes). Of course,

[ccp4bb] Postdoctoral position in the lab of Dr. Michael Marletta

2012-12-05 Thread MARK HERZIK
The Marletta Lab at The Scripps Research Institute is looking for a postdoctoral fellow to study the structure and function of Heme- Nitric Oxide/Oxygen binding (H-NOX) domains, a family of gas sensing proteins that are prevalent in prokaryotes and higher eukaryotes. The ideal candidate will

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Robbie Joosten
Hi Peter, Thanks for the info. I'd better go check whether my code assumes insertion codes are not digits. Cheers, Robbie Date: Wed, 5 Dec 2012 17:57:58 + From: pkel...@globalphasing.com Subject: Re: [ccp4bb] thanks god for pdbset To: CCP4BB@JISCMAIL.AC.UK Hi Robbie, On Wed,

[ccp4bb] 4 year PhD studentship Imperial College London

2012-12-05 Thread Bubeck, Doryen A
I would like to call your attention to a BBSRC-funded PhD studentship in the lab of Doryen Bubeck at Imperial College London starting October 2013. Title: Complement-mediated pore formation The immune complement system in blood kills microbes by making ‘membrane-attack complex’ (MAC) pores in