Re: [ccp4bb] Tcl error - Snow Leopard OSX

2009-09-17 Thread William G. Scott
On Sep 15, 2009, at 4:43 PM, José Trincão wrote: foundversion conflict for package "Tcl": have 8.5.7, need exactly 8.5 while executing "load $library BLT" I've committed to fink cvs a patched version of blt that builds with tcl/tk 8.5 and at least loggraph works now. I really can't cope

[ccp4bb] Staff Scientist and 2 Research Technician positions in Vienna

2009-09-17 Thread Kristina Djinovic Carugo
*Staff Scientist and 2 Research Technician positions in the Laura Bassi “Center for Optimised Structural Studies*“ *The Center for Optimised Structural Studies (COSS)* is a joint, FFG (www.ffg.at ) funded venture between Max F. Perutz Laboratories at the University of Vienna

[ccp4bb] high z-scores, negative LLG in Phaser

2009-09-17 Thread Sean Gay
I have a 2.0A data set that I solved using an ensemble of 5 related structures in Phaser. My Z-scores for the solution are fantastic (RFZ= 28.7, TFZ=24.6), but my LLG is very negative (-698.2). The LLG increases by almost 800 (started at -1488.6) during the course of the run. The density for th

[ccp4bb] Solvent mask in refinement programs

2009-09-17 Thread Karthik S
How is the solvent mask handled for zero occupancy atoms? In general is it justified that i fear some of the electron density belonging to the protein in the periphery of the molecule can be solvent flattened and i never see them thereafter in my electron density maps or is this just not going to

Re: [ccp4bb] Solvent mask in refinement programs

2009-09-17 Thread Karthik S
How is the solvent mask handled for zero occupancy atoms? In general is it justified that i fear some of the electron density belonging to the protein in the periphery of the molecule  can be solvent flattened and i never see them thereafter in my electron density maps or is this just not going to

Re: [ccp4bb] Solvent mask in refinement programs

2009-09-17 Thread Pavel Afonine
Hi Karthik, in phenix.refine there is a parameter for this: ignore_zero_occupancy_atoms=True It tells phenix.refine: "Yes, please, do not include atoms with zero occupancy factors into mask calculation (that is: ignore such atoms while computing the mask)". This is what I had in mind when int

Re: [ccp4bb] high z-scores, negative LLG in Phaser

2009-09-17 Thread Mark J. van Raaij
try building (an autobuilding program like Arp-Warp comes to mind) and refining the structure, then you'll know that you've solved the structure for sure (or not). or, if you'll permit a tongue-in-cheek reply: stop bragging now, build and refine the structure, write the paper, publish it and

Re: [ccp4bb] high z-scores, negative LLG in Phaser

2009-09-17 Thread Mark J. van Raaij
maybe my message was a bit abrupt, what I meant was: - if it (auto)builds using the real sequence and refines, you are sure to have found the right solution. At 2.0 Angstrom this should only take a few hours. - if it doesn't, you may still have the right solution, but perhaps you made a mis

[ccp4bb] Project Scientist Opportunity--DOE Joint Genome Institute

2009-09-17 Thread Cheryl Kerfeld
*Project Research Scientist- Synthetic Biology / Structural Genomics* The Synthetic Biology / Structural Genomics Program at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA has an exciting scientific research opportunity available. Will serve as a Project Scientist and design and imp

[ccp4bb] I compressed my images by ~ a factor of two, and they load and process in mosflm faster

2009-09-17 Thread William G. Scott
If you have OS X 10.6, this will impress your friends and save you some disk space: % du -h -d 1 mydata 3.5Gmydata mv mydata mydata.1 sudo ditto --hfsCompression mydata.1 mydata rm -rf mydata.1 % du -h -d 1 mydata 1.8Gmydata This does hfs filesystem compression, so the images are s