Phenix - Revision history

Frodo at 04:05, 14 February 2014

2014-02-14T04:05:43Z

← Older revision		Revision as of 04:05, 14 February 2014
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	==Acknowledgments==		==Acknowledgments==
	Thanks to the Phenix and Pymol developers.		Thanks to the Phenix and Pymol developers.

			[[Category:Software]]
			[[Category:Crystallography]]

Oliv Eidam at 23:34, 6 May 2013

2013-05-06T23:34:17Z

← Older revision		Revision as of 23:34, 6 May 2013
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	set ray_shadow, off		set ray_shadow, off


			==Acknowledgments==
			Thanks to the Phenix and Pymol developers.

Oliv Eidam at 23:55, 30 April 2013

2013-04-30T23:55:07Z

← Older revision		Revision as of 23:55, 30 April 2013
Line 38:		Line 38:
	Pymol wants CCP4 maps as input. To generate those, we use Phenix as described above. <br>		Pymol wants CCP4 maps as input. To generate those, we use Phenix as described above. <br>

	[[File:Sa omit ~~map~~.png\|thumb\|upright=1.35\|right\|alt=SA omit map around kappa ligand in green, 2Fo-Fc map in cyan. The ligand and water molecules show up nicely, although they were omitted during refinement. \|SA omit map around kappa ligand in green, 2Fo-Fc map in cyan. The ligand and water molecules show up nicely, although they were omitted during refinement.]]		[[File:Sa omit map2.png\|thumb\|upright=1.35\|right\|alt=SA omit map around kappa ligand in green, 2Fo-Fc map in cyan. The ligand and water molecules show up nicely, although they were omitted during refinement. \|SA omit map around kappa ligand in green, 2Fo-Fc map in cyan. The ligand and water molecules show up nicely, although they were omitted during refinement.]]
	Here is a Pymol script to show density around the ligand and it's surrounding residues:		Here is a Pymol script to show density around the ligand and it's surrounding residues:

Oliv Eidam at 23:44, 30 April 2013

2013-04-30T23:44:47Z

← Older revision		Revision as of 23:44, 30 April 2013
Line 38:		Line 38:
	Pymol wants CCP4 maps as input. To generate those, we use Phenix as described above. <br>		Pymol wants CCP4 maps as input. To generate those, we use Phenix as described above. <br>

	[[File:Sa omit map.png\|thumb\|right\|alt=SA omit map around kappa ligand in green, 2Fo-Fc map in cyan. The ligand and water molecules show up nicely, although they were omitted during refinement. \|SA omit map around kappa ligand in green, 2Fo-Fc map in cyan. The ligand and water molecules show up nicely, although they were omitted during refinement.]]		[[File:Sa omit map.png\|thumb\|upright=1.35\|right\|alt=SA omit map around kappa ligand in green, 2Fo-Fc map in cyan. The ligand and water molecules show up nicely, although they were omitted during refinement. \|SA omit map around kappa ligand in green, 2Fo-Fc map in cyan. The ligand and water molecules show up nicely, although they were omitted during refinement.]]
	Here is a Pymol script to show density around the ligand and it's surrounding residues:		Here is a Pymol script to show density around the ligand and it's surrounding residues:

Oliv Eidam at 23:38, 30 April 2013

2013-04-30T23:38:39Z

@@ Line 29: / Line 29: @@
   # Run Phenix refinement including simulated annealing
   phenix.refine 4djh-sf.cif 4DJH_no_HETATM.pdb simulated_annealing=true
@@ Line 36: / Line 38: @@
 Pymol wants CCP4 maps as input. To generate those, we use Phenix as described above. <br>
 Here is a Pymol script to show density around the ligand and it's surrounding residues:

Oliv Eidam at 23:18, 30 April 2013

2013-04-30T23:18:34Z

@@ Line 6: / Line 6: @@
 ===1. Download PDB coordinates and structure factors from PDB.ORG===
-[[File:Pdb sf download.jpg|thumb|right]] To calculate a electron density, you need to download PDB coordinates and structure factors (Miller indices and measured intensities) from the PDB. On pdb.org, there is a dropdown menu on the right top corner of each entry site where PDB and structure factors can be downloaded (see image on the right).
+[[File:Pdb sf download.jpg|thumb|right|alt=Where to download files from PDB entry.|Where to download files from PDB entry.]] To calculate a electron density, you need to download PDB coordinates and structure factors (Miller indices and measured intensities) from the PDB. On pdb.org, there is a dropdown menu on the right top corner of each entry site where PDB and structure factors can be downloaded (see image on the right).
 ===2. Calculate electron densities from deposited structure factors===
-You can calculate an electron density (in CCP4 and mtz format) using a PDB and structure factors using Phenix. Simply type:
+You can calculate an electron density (CCP4 format for Pymol and mtz format for Coot) using a PDB and structure factors using Phenix. <br>
   phenix.maps 4DJH.pdb 4djh-sf.cif

Oliv Eidam at 20:40, 30 April 2013

2013-04-30T20:40:10Z

← Older revision		Revision as of 20:40, 30 April 2013
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	Also, you may want to display them in Pymol: here[link] is described how you generate a electron density map in CCP4 format map, which is required for Pymol.		Also, you may want to display them in Pymol: here[link] is described how you generate a electron density map in CCP4 format map, which is required for Pymol.

	===~~Calculate electron densities from deposited~~ structure factors===		===1. Download PDB coordinates and structure factors from PDB.ORG===

	~~You can~~ download structure factors (Miller indices and measured intensities) from the PDB.		[[File:Pdb sf download.jpg\|thumb\|right]] To calculate a electron density, you need to download PDB coordinates and structure factors (Miller indices and measured intensities) from the PDB. On pdb.org, there is a dropdown menu on the right top corner of each entry site where PDB and structure factors can be downloaded (see image on the right).

			===2. Calculate electron densities from deposited structure factors===

			You can calculate an electron density (in CCP4 and mtz format) using a PDB and structure factors using Phenix. Simply type:

			phenix.maps 4DJH.pdb 4djh-sf.cif

Oliv Eidam: Created page with "==Calculate electron densities using Phenix== Here are a couple of useful phenix commands to calculate electron densities. In docking, it is often useful to have a look at el..."

2013-04-30T18:21:57Z

Created page with "==Calculate electron densities using Phenix== Here are a couple of useful phenix commands to calculate electron densities. In docking, it is often useful to have a look at el..."

New page

==Calculate electron densities using Phenix==

Here are a couple of useful phenix commands to calculate electron densities. In docking, it is often useful to have a look at electron densities, especially for proteins and ligands determined at low resolution.
Also, you may want to display them in Pymol: here[link] is described how you generate a electron density map in CCP4 format map, which is required for Pymol.

===Calculate electron densities from deposited structure factors===

You can download structure factors (Miller indices and measured intensities) from the PDB.