Experimental Phasing - Revision history

Randy: /* Combined MR and SAD Phasing */ Explain how to get an initial log-likelihood-gradient map before any sites have been added.

2019-11-06T15:30:01Z

‎Combined MR and SAD Phasing: Explain how to get an initial log-likelihood-gradient map before any sites have been added.

Randy: /* Cluster Compounds */ Further clarification.

2019-06-24T08:00:42Z

‎Cluster Compounds: Further clarification.

Randy: /* Cluster Compounds */ Clarify difference between sites file and cluster file.

2019-06-24T07:58:36Z

‎Cluster Compounds: Clarify difference between sites file and cluster file.

Airlie: /* Cluster Compounds */

2011-05-23T11:24:01Z

‎Cluster Compounds

Airlie: /* How to Define Data */

2011-05-23T10:48:55Z

‎How to Define Data

Airlie: /* Cluster Compounds */

2011-05-23T10:48:36Z

‎Cluster Compounds

Airlie: /* How to Define Atoms */

2011-05-23T10:27:29Z

‎How to Define Atoms

Randy: /* Combined MR and SAD Phasing */ Clarify that MR model contributes to phases.

2011-04-12T19:51:52Z

‎Combined MR and SAD Phasing: Clarify that MR model contributes to phases.

Randy: /* Combined MR and SAD Phasing */ Update script

2010-12-09T10:00:00Z

‎Combined MR and SAD Phasing: Update script

Randy: /* SAD Phasing */ Add (now required) wavelength keyword

2010-12-09T08:58:36Z

‎SAD Phasing: Add (now required) wavelength keyword

@@ Line 68: / Line 68: @@
    eof
 </pre>
 ==Density Modification after Phaser==

@@ Line 20: / Line 20: @@
 ===Cluster Compounds===
-Cluster compounds can be used as the scattering type. The coordinates for Ta₆Br₁₂ are stored internally and have the cluster name TX. Coordinates of other cluster compounds must be supplied (coordinates are translated to the origin internally before spherical averaging of the structure factors) and are given the cluster name XX. Note that the cluster PDB file should contain the full atomic coordinates of one copy of the cluster. In contrast, if you provide a sites file this will contain the coordinates of the centres of individual clusters.
+Cluster compounds can be used as the scattering type, if the individual atoms within a bound cluster compound cannot be resolved. The coordinates for Ta₆Br₁₂ are stored internally and have the cluster name TX. Coordinates of other cluster compounds must be supplied (coordinates are translated to the origin internally before spherical averaging of the structure factors) and are given the cluster name XX. Note that the cluster PDB file should contain the full atomic coordinates of one copy of the cluster. In contrast, if you provide a sites file this should contain the coordinates of the centres of individual clusters.
 <pre>
     CLUSTER PDB <PDBFILE>

@@ Line 20: / Line 20: @@
 ===Cluster Compounds===
-Cluster compounds can be used as the scattering type. The coordinates for Ta₆Br₁₂ are stored internally and have the cluster name TX. Coordinates of other cluster compounds must be supplied (coordinates are translated to the origin internally before spherical averaging of the structure factors) and are given the cluster name XX.
+Cluster compounds can be used as the scattering type. The coordinates for Ta₆Br₁₂ are stored internally and have the cluster name TX. Coordinates of other cluster compounds must be supplied (coordinates are translated to the origin internally before spherical averaging of the structure factors) and are given the cluster name XX. Note that the cluster PDB file should contain the full atomic coordinates of one copy of the cluster. In contrast, if you provide a sites file this will contain the coordinates of the centres of individual clusters.
 <pre>
     CLUSTER PDB <PDBFILE>

@@ Line 20: / Line 20: @@
 ===Cluster Compounds===
-Cluster compounds can be used as the scattering type. The coordinates for Ta₆Br₁₂ are stored internally and have the cluster name TX. Coordinates of other cluster compounds must be supplied (coordinates are translated to the origin internally before spherical averaging the structure factors) and are given the cluster name XX.
+Cluster compounds can be used as the scattering type. The coordinates for Ta₆Br₁₂ are stored internally and have the cluster name TX. Coordinates of other cluster compounds must be supplied (coordinates are translated to the origin internally before spherical averaging of the structure factors) and are given the cluster name XX.
 <pre>
     CLUSTER PDB <PDBFILE>

@@ Line 8: / Line 8: @@
 You need to tell Phaser the name of the mtz file containing your data and the columns in the mtz file to be used. For SAD phasing, a single CRYSTAL and DATASET with anomalous data (F(+), SIGF(+), F(-) and SIGF(-)) must be given. The columns must have the correct CCP4 column type: 'G' for F(+) and F(-) and 'L' for SIGF(+) and SIGF(-). If the columns on your mtz file have somehow acquired the incorrect column type, you should change the column type with an mtz editing programme (e.g. sftools).
 <pre>
-    CRYStal insulin DATAset sad LABIn F+ = F(+) SIG+ = SIGF(+) F- = F(-) SIG- = SIGF(-)
+    CRYSTAL insulin DATASET sad LABIN F+ = F(+) SIG+ = SIGF(+) F- = F(-) SIG- = SIGF(-)
 </pre>

← Older revision		Revision as of 10:48, 23 May 2011
Line 21:		Line 21:

	Cluster compounds can be used as the scattering type. The coordinates for Ta₆Br₁₂ are stored internally and have the cluster name TX. Coordinates of other cluster compounds must be supplied (coordinates are translated to the origin internally before spherical averaging the structure factors) and are given the cluster name XX.		Cluster compounds can be used as the scattering type. The coordinates for Ta₆Br₁₂ are stored internally and have the cluster name TX. Coordinates of other cluster compounds must be supplied (coordinates are translated to the origin internally before spherical averaging the structure factors) and are given the cluster name XX.
		+	<pre>
		+	CLUSTER PDB <PDBFILE>
		+	</pre>

	==How to Control Output==		==How to Control Output==

@@ Line 17: / Line 17: @@
 A partial structure, for example a partial and poor MR solution (which may or may not contain anomalous scatterers) can be used to start the phasing, either alone or in addition to some anomalous scattering sites entered with the ATOM keyword. The partial structure is entered with the PART keyword.
 If you do not have a partial MR structure, anomalous scatterers must be found using Patterson methods, Direct methods or Dual Space methods (e.g. phenix.hyss, SHELXD, SnB, Rantan) prior to running Phaser. Note that SHELXD outputs a pdb file with the scatterers labelled sulphur (S) regardless of the correct scattering type: you need to change the pdb so that it contains the correct scattering type prior to using it in Phaser.
 ==How to Control Output==

@@ Line 44: / Line 44: @@
 ===Combined MR and SAD Phasing===
-MODE EP_SAD when used with the PART keyword phases SAD data and completes the structure from log-likelihood gradient maps using a partial structure as (at least part of) the initial atomic substructure. Only the real (i.e. non-anomalous) signal from the partial structure is used. The final solution is output to the files FILEROOT.sol, FILEROOT.mtz and FILEROOT.pdb .
+MODE EP_SAD when used with the PART keyword phases SAD data and completes the structure from log-likelihood gradient maps using a partial structure as (at least part of) the initial atomic substructure. Only the real (i.e. non-anomalous) signal from the partial structure is used. The final solution is output to the files FILEROOT.sol, FILEROOT.mtz and FILEROOT.pdb. Note that, because the substructure after log-likelihood-gradient completion includes the partial model, the phases automatically combine information from the partial model and the anomalous scatterers.
 Do SAD phasing of insulin starting from partial model of one helix only. This is the minimum input, using all defaults (except the ROOT filename)

@@ Line 49: / Line 49: @@
 <pre>
-   #insulin_sad.com
+   #insulin_mr_sad.com
    phaser << eof
    MODE EP_SAD
-   TITLe sad phasing insulin with intrinsic sulphurs
+   TITLe sad phasing insulin with intrinsic sulphurs, starting from a helix
    HKLIn S-insulin.mtz
    CRYStal insulin DATAset sad LABIn F+=F(+) SIG+=SIGF(+) F-=F(-) SIG-=SIGF(-)
-   LLGComplete CRYStal insulin COMPLETE ON SCATtering ELEMent S
+  WAVElength 1.5418
    PART PDB helix.pdb ID 100
    ROOT insulin_mr_sad

@@ Line 36: / Line 36: @@
    HKLIn S-insulin.mtz
    CRYStal insulin DATAset sad LABIn F+=F(+) SIG+=SIGF(+) F-=F(-) SIG-=SIGF(-)
    LLGComplete COMPLETE ON SCATterer S
    ATOM CRYStal insulin PDB S-insulin_hyss.pdb