[ccp4bb] Error in CAD during ARP/wWARP run in sharp/autoSHARP - also posted in sharp discuss

2009-12-13 Thread Narayanan Ramasubbu
Hi: Sorry for the same posting in here as well but I thought may be some of you might have encountered the same problem but may not be subscribing to sharp list. I am trying run sharp/autoSHARP on a mac (os x 10.4) using the guven example file: krel1-SAD.0 I am getting an error at the CAD as

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

2009-12-13 Thread Nicholas M Glykos
Dear Robbie, List, This thread is steadily diverging. Apologies for my contribution to its diversification. > Who knows what they did to the maps in terms of (unwarrented) density > modefication to make them look cleaner? > > The advantage of the EDS is that it is impartial and > uniform. The

[ccp4bb] Validation and maps (was: Retraction of 12 Structures...)

2009-12-13 Thread Robbie Joosten
Dear Nicholas, Yes we are diverging, but you make a few important and valid points. So let's diverge some more... I fully agree that validation tools should not tell people how to do science. That would kill free thought and lead to circularity in the results. A typical example is the question wh

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

2009-12-13 Thread Anastassis Perrakis
I just scrapped most of my answer, Robbie was quicker, and I guess Gerard is on holiday ;-) As 'honorary Dutch' though here are my two cents. It is only fair that a well-informed and well-educated human being can do a better job than a fixed-frozen automated procedure. This is exactly the w

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

2009-12-13 Thread Nicholas M Glykos
Those Greeks again ... > Finally, validation tools are not there to pass judgement. They are > tools to be used by depositors, referees, and users alike, to help them > make a better informed interpretation of crystallographic *models*. > Servers like EDS and PDB_REDO must be seen in that light

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

2009-12-13 Thread Jürgen Bosch
Not sure if in any of the 112 posts regarding either the retraction theme or 'was 12 retraction' theme did mention, that after all despite good or as good as possible refinement of the structure, the goal is still to describe as accurately as possible the biological system using crystallogr

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

2009-12-13 Thread James Stroud
On Dec 13, 2009, at 11:00 AM, Jürgen Bosch wrote: If you can't confirm your structure by solid biochemical or biophysical methods what conclusions should you draw ? Don't you wish it worked the other way in that every time someone had a biochemical, physiological, or genetic result, they wo

[ccp4bb] Post Doctoral Position at UCLA. Membrane Protein Complexes.

2009-12-13 Thread Pascal Egea
*Post-Doctoral Researcher. Structure and Function of Membrane Protein Complexes*. We seek a motivated individual to join our laboratory in the Department of Biological Chemistry at the University of California in Los Angeles. We are interested in studying the mechanisms of protein folding/transloc

[ccp4bb] MR question

2009-12-13 Thread Sylvia Fanucchi
Morning all Apologies for the simple question. I have a structure I would like to solve using molecular replacement. I am a bit confused by the patterson peaks. There appears to be a large non-origin peak (although it is apparently symmetry-related to the origin?). Does this mean that there is