On Wed, Jan 30, 2013 at 9:21 AM, Ursula Schulze-Gahmen
I am trying to solve a structure by molecular replacement in phaser using 2 model fragments. I think I may have placed the 1st fragment correctly. I don't quite understand how to best proceed with a fixed ensemble searching for the second fragment in phaser-MR. If I select "use partial solution from previous job", do I still need to read in the coordinates of that previous solution for one ensemble? And If I do, should I read in the starting coordinates or the placed output from this 1st molecular replacement?
I think there are two ways to do it: 1. Use the previous solution, but input the original ensemble (with the same ID). This works because that solution has the matrices to place the ensemble correctly - if you input the model from MR, these will no longer be valid. 2. Instead of re-using the previous solution, input the placed model, and check the box "Ensemble is fixed partial solution", which tells Phaser to simply accept it as-is. I believe in either case you do not need to specify a separate search for the already placed component, but I'm not positive about (2).
The second question is about how to relax the restraints fr the packing. In the "other settings" sub window is a section for packing. Could someone explain to me what the different options in this packing section mean? Which of them should I change to allow for more close contacts?
Partial explanation here: http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#PACK (hopefully it will be reasonably clear which options in Phenix correspond to the listed keywords...) -Nat