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? 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? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
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
Hi Ursula, If I understand you correctly you have two fragments and want to place them one by one with Phaser. If you use Phaser-MR in the automated molecular replacement mode then you shouldn't have to specify the search order of components for Phaser. Nor would you have to specify which placed fragment should be fixed and used in subsequent MR searches for the next fragment. Phaser will take care of this by itself. Simply specify the other search fragments as another ensemble by clicking on the "Add Ensemble" button on the "Ensembles" tabbed sheet. Then click on the "Search Procedure" tabbed sheet and add that ensemble to the MR search. You'll want to let Phaser determine the search order of your fragments as it does this better than humans. So don't alter the defaults. As for the packing test more info can be found on http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#PACK In your case I should probably try and play with the cutoff value for a start. Hope this helps, Robert On Jan 30 2013, Ursula Schulze-Gahmen wrote:
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?
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?
Thanks
Ursula
-- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
participants (3)
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Nathaniel Echols -
R.D. Oeffner -
Ursula Schulze-Gahmen