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--- crystallography:collection:frx:usage [2016/07/12 08:55] – bonnefon
+++ crystallography:collection:frx:usage [2023/11/01 20:19] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-==== Rigaku FR-X Usage ====
+====== Rigaku FR-X Usage ======
 Training on 2015.03.30
-FR-X generator: 45 kV, 66 mA, 70 μ cross-section, 180 μ beam, 1.7 miliradians divergence
+**FR-X generator**:
+  * 45 kV,
+  * 66 mA,
+  * 70 μ cross-section,
+  * 180 μ beam,
+  * 1.7 miliradians divergence
 **XG Control** tells you the settings values (45 kV and 66 mA vs 20 kV and 10 mA when not used) .
 You can screen as soon as the parameters have reached the target values, but wait one more hour to collect, so that the beam is stable.
-Pilatus 300K detector: 3 chips, shorter exposure time, no readout (no shutter closing), almost never overloaded (>1.5 millions), water circulation at room temperature, dry air
+**Pilatus 300K detector**:
+  * 3 chips,
+  * shorter exposure time,
+  * no readout (no shutter closing),
+  * almost never overloaded (>1.5 millions),
+  * water circulation at room temperature,
+  * dry air
 <code>>thread</code> command on camserver gives the temperature and humidity level
@@ Line 30: / Line 41: @@
 Set the directory /data/user/project1_crystal1
-=== dtdisplay ===
+==== dtdisplay ====
   * middle click > zoom area
@@ Line 41: / Line 52: @@
 ----
-=== Index ===
+==== Index ====
   * Refine in triclinic (P1)
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 ----
-=== Strategy ===
+==== Strategy ====
   * HKL_3000 strategy only works for single axis
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 ----
-=== Zoom window ===
+==== Zoom window ====
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 ----
-=== Integrate ===
+==== Integrate ====
 All scans are processed
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 ----
-=== Scale ===
+==== Scale ====
 **Check the boxes**:
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 ----
-=== Report ===
+==== Report ====
 The log file contains merged I+/I- an the end of the file and tables with unmerged I+/I- in the middle of the file.
+----
+==== SAD-Phasing ====
+The sequence is necessary. Give the source or the signal or define if you have a heavy atom.
+Software used: Arp/Warp, CCP4-6.3.0, CCP4-6.4.0(Coot), ShelX
+**Data analysis**:
+Grey area 1.3 for anomalous signal (can be used up to 1.0)
+**Find sites**:
+Choose the resolution limit (>1.8 Å to distinguish disulfide bonds, test 0.1 Å increments)
+Check the absolute value and the spread of solutions (a few in the up-right corner)
+**Site view**:
+Sphere size correlates with the occupancy
+**Phase**:
+High resolution limit; try different resolution cutoffs
+**Check hand** (//ShelXE//):
+You should see the difference, dark red/dark blue, difference of one graduation in scale.
+If necessary, increase the cycle number so that a plateau is reached.
+**Phase**:
+//Mlphase//, //DM-phase extension//
+**NCS**:
+//DM// or //Parrot// (a bit better)
+At least try it if you have more than 1 molecule in the Asymmetric Unit
+**Build**:
+//ARP/WARP// for high resolution
+//Buccaner// for lower resolution (∼ 3 Å)
+Let ARP/WARP build/refine several times if has difficulties building. Start several times witha few cycles rather that once with many cycles.
+----
+==== Molecular Replacement ====
+**Analyze data**
+**Prepare Model**: Edit the PDB file (delete ligands, waters, side-chains if you want)
+**Run MR** (//MolRep//): 3 Å by default; rigid body at 3.0 Å, then refine at max resolution