Re: [ccp4bb] Tricky MR problem

2012-10-01 Thread Jan Abendroth
Hi Rhys, there is nothing wrong with experimental phases. If a few MR attempts fail, there aren't any real red flags with your crystal form, and you have a few decently diffracting crystals at hand, soak them for a little bit in your favourite heavy atom. We found that soaks in 500-1000mM Na or

Re: [ccp4bb] Tricky MR problem

2012-10-01 Thread Francis E Reyes
[1] In addition to using lower resolution data, you should check a variety of RMSDs as well. In fact constructing an RMSD / high resolution contour plot would be beneficial to determine the optimum set of parameters. (That is if you're using PHASER). [2] You say you suspect two molecules per

Re: [ccp4bb] Tricky MR problem

2012-10-01 Thread Pete Meyer
I agree with Carlos's suggestions (search for your two domains separately, and as poly-Ala models). There's a few other things that may help MR, which you may or may not have tried: 1. Reset the B-factor of your search models to the wilson B-factor of your dataset. 2. Search using only lower

[ccp4bb] Phenix version 1.8.1 released

2012-10-01 Thread Paul Adams
The Phenix developers are pleased to announce that version 1.8.1 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interf

Re: [ccp4bb] Tricky MR problem

2012-10-01 Thread Carlos Kikuti
Not sure I understood your problem but it looks like it's related to flexibility. You can try cutting the domains apart (and chopping off the loops) in two different pdbs. They can be used as separate ensembles. Try to find the bigger one first. 35% homology is not that low, just search with pol

[ccp4bb] Tricky MR problem

2012-10-01 Thread RHYS GRINTER
Hi All, I'm currently working on solving the structure of a protein by molecular replacement. The protein is around 30kDa and likely has a two beta-prism domains, linked by a long curved two stranded sheet based on the structure of an analogue. There are also a number of other structures which

[ccp4bb] Post-Doc position at Diamond Light source

2012-10-01 Thread Martin Walsh
Dear all - this is a reminder for the Postdoc post detailed below - closing date is THIS FRIDAY - don't hesitate to contact me directly for more information. Application details can be found on the Diamond web pages (http://www.diamond.ac.uk/Home/Jobs/Current/DIA0766_TH.html) Martin

Re: [ccp4bb] Coot Release 0.7 in CCP4 Software Update?

2012-10-01 Thread eugene . krissinel
We are thinking of including MG into core in one of future releases, probably by next summer. As to Coot, it will probably stay autonomous. Eugene On 1 Oct 2012, at 13:14, Dirk Kostrewa wrote: > Dear Eugene, > > thank you for your kind reply and your explanation! > > Since the CCP4 download s

Re: [ccp4bb] Coot Release 0.7 in CCP4 Software Update?

2012-10-01 Thread Dirk Kostrewa
Dear Eugene, thank you for your kind reply and your explanation! Since the CCP4 download site offers Coot either as a stand-alone-package or via the new package manager, I was hoping that new Coot releases could also be handled by the wonderful CCP4 software update. A software update mechani

Re: [ccp4bb] Coot Release 0.7 in CCP4 Software Update?

2012-10-01 Thread eugene . krissinel
Thanks for nice question. Currently, CCP4 update is applicable only to what is distributed as "CCP4 core", which guarantees a definite location in $CCP4 directory. Also, updates are not supposed to deliver releases ("upgrades"), but rather smallish changes between them. Coot is not part of CCP

[ccp4bb] Coot Release 0.7 in CCP4 Software Update?

2012-10-01 Thread Dirk Kostrewa
Dear CCP4 developers, this question might be interesting for many CCP4/Coot users: will the Coot release 0.7 and future releases be made available to CCP4 users via the CCP4 software update? Best regards, Dirk. Original-Nachricht Betreff:[COOT] Release 0.7 Datum: