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
-Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Wednesday, December 05, 2012 16:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] thanks god for pdbset The last time I tried the pdbset renumber command because of issues

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ian Tickle
. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Wednesday, December 05, 2012 16:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] thanks god for pdbset The last time I tried the pdbset renumber

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] thanks god for pdbset

2012-12-05 Thread Robbie Joosten
. In practice, as Ed pointed out, it is a big mess. Cheers, Robbie -Original Message- From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Wednesday, December 05, 2012 17:26 To: Robbie Joosten Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] thanks god for pdbset I had always assumed

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] thanks god for pdbset

2012-12-04 Thread Francois Berenger
Especially the renumber command that changes residue insertion codes into an increment of the impacted residue numbers. Regards, F.