Re: [ccp4bb] Fo simulators - summary

2013-09-10 Thread Jrh
I prepared this on Sunday, here it is now:- Well, I was 'shaken but not stirred' to see a program 'fake_Fobs'. However James' posting on the Rfactor gap in MX is a more respectable, Sunday morning, topic. I tried to find the previous threads on this via google and couldn't. So apologies to all

[ccp4bb] About twin refinement in Refmac

2013-09-10 Thread miyatake
Dear all, I run a twin refinement using Refmac, but it was in failure saying the message below; Why did it happen? H. Miyatake - free R flag 0 Number of free reflections 12993 Number

Re: [ccp4bb] About twin refinement in Refmac

2013-09-10 Thread Eleanor Dodson
It seems you cannot read either your data or a scratch mtz file - the log file should tell you its name. There is obviously something funny - see the discussion of free r reflections.. You dont say your pointgroup - presumably P/mmm or P3m or P6/mmm - they have that twin law. But with perfect

Re: [ccp4bb] Calculated vs Measured pI

2013-09-10 Thread Roger Rowlett
I don't know of such a program, but I would think that an algorithm that considered solvent-exposed ionizable residues only (and everything ionizable in any disordered/missing loops) of a PDB structure, and applied the typical pKa values of side chains from Thurlkill et al. (2006) Protein Sci.

[ccp4bb] Calculated vs Measured pI

2013-09-10 Thread Hargreaves, David
Dear CCP4bbers, I was wondering whether anyone knew of a program that would calculate the pI of a protein based on its structure rather than its sequence and whether such a calculation might correlate better with the measured pI Dave David Hargreaves Associate Principal Scientist

[ccp4bb] CCP4 Study Weekend 2014

2013-09-10 Thread Cooper, Jon
CCP4 STUDY WEEKEND 2014 The next CCP4 study weekend will be held on 4th and 5th January 2014 at the University of Nottingham. The meeting is entitled Two Way Street - Complementary Methods and the aim is to explore methods that can be used to complement X-ray structure analysis and to learn

[ccp4bb] IAEA- UPAT-GAEC Meeting: Program available online

2013-09-10 Thread Irene Margiolaki
    ANNOUNCEMENT SECOND RESEARCH COORDINATION MEETING (RCM) ON UTILIZATION OF ACCELERATOR - BASED, REAL - TIME METHODS IN INVESTIGATION OF MATERIALS WITH HIGH TECHNOLOGICAL IMPORTANCE   _24-27 SEPTEMBER

[ccp4bb] shape complimentarity for small molecule

2013-09-10 Thread Brett, Thomas
Hi all: If have used SC previously to calculate shape complimentarity for macromolecular complexes. Can this also be used to calculate shape complimentarity for a (say) protein/small molecule inhibitor complex? Or is there some other metric/software that can/should be used to quantitate how

Re: [ccp4bb] shape complimentarity for small molecule

2013-09-10 Thread Zhijie Li
Hi Tom, Yes, SC can be used for calculating protein-small molecule ligand SC. Simply put the ligand and protein on two separate chains. You probably need to edit the $CLIBD/sc_radii.lib file to add some atom radii for your ligand. For example: ABC N* 1.65 ABC C* 1.90 Zhijie

[ccp4bb] MRBUMP - PHASER ?

2013-09-10 Thread Bailey, Douglas (NIH/NCI) [E]
Hello Everyone, PHASER is returning the following error Input Error: No Mode Set when called from MRBUMP. CCP4-6.3.0 running on Centos5-x64. Any help , ideas, comment would be greatly appreciated. Thanks, Doug

Re: [ccp4bb] shape complimentarity for small molecule

2013-09-10 Thread Mike Lawrence
Hi Brett, SC was not developed for this purpose and hence may not be very useful with its default parametrization. Nevertheless, it could be useful for cross-comparing the complementarity of different inhibitors to the same site, but I have not experimented this. The TRIM parameter may need to