reference_xray_structure
Dear all, I want to use “reference model” in a low resolution structure refinement. Do I need to set this parameter “reference_xray_structure”? What does “reference_xray_structure” stand for? Many thanks and best wishes ************************************************ Yamei Yu Associate Professor State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: [email protected] [email protected] [email protected]
Hi,
To add a reference model:
a) GUI: drag and drop the model file into the list control, highlight the
file, click on "Modify file data type" and choose "reference model"
b) Command line (with default values):
phenix.refine data.hkl model.pdb reference_model.enabled=True
reference_model.file=reference.pdb
(more info is on the documentation page
https://www.phenix-online.org/documentation/reference/refinement.html#using-...
)
Best wishes,
Dorothee
On Tue, Dec 5, 2017 at 7:12 PM, yamei yu
Dear all,
I want to use “reference model” in a low resolution structure refinement. Do I need to set this parameter “reference_xray_structure”? What does “reference_xray_structure” stand for?
Many thanks and best wishes
************************************************
Yamei Yu Associate Professor State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 <(588)%20201-3485> Email: [email protected] [email protected] [email protected]
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I’m working on an ensemble refinement but have hit a snag. I have water-coordinated Mg ions, and can restrain them just fine in a regular phenix refinement, but get an error message about supplying a valid restraint file in Ensemble Refinement when I give the same file. Is it because I have water molecules and they need NOT to be mentioned? Any clues appreciated. Maybe I have to make the waters around the Mg special residues so they don’t compete with regular water in an update? George George N. Phillips, Jr. Ralph and Dorothy Looney Professor BioSciences at Rice Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 www.phillipslab.org
George
Can you send me the files directly?
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Wed, Dec 6, 2017 at 10:18 AM, georgep
I’m working on an ensemble refinement but have hit a snag.
I have water-coordinated Mg ions, and can restrain them just fine in a regular phenix refinement, but get an error message about supplying a valid restraint file in Ensemble Refinement when I give the same file. Is it because I have water molecules and they need NOT to be mentioned?
Any clues appreciated. Maybe I have to make the waters around the Mg special residues so they don’t compete with regular water in an update?
George
George N. Phillips, Jr. Ralph and Dorothy Looney Professor BioSciences at Rice Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 <(713)%20348-6951> www.phillipslab.org
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participants (4)
-
Dorothee Liebschner -
georgep -
Nigel Moriarty -
yamei yu