See also the accompanying document giving background information.
In the following instructions, when you need to type something, or click on something, it will be shown in red. Output from the programs or text from the interface is given in green.
Files in directory DATA:
| rnase25.mtz | An MTZ file containing experimental data (including anomalous), extending to 2.5Å, for the native protein and three derivatives (mercury, platinum and iodine), as used for experimental phasing by MIR and experimental phasing by MAD |
| rnase25_scaleit1.mtz | Reflection file as output by SCALEIT |
Files in directory RESULTS:
| scaleit-rnase.log | .log of scaling RNase native and derivative data |
| shelx-rnase.log | .log of heavy atom search with SHELX (through CCP4i) |
There is a file $CEXAM/tutorial/data/rnase25.mtz which contains native data, plus three derivatives; Hg, Pt and I with their anomalous signals. First, we scale each derivative to the native dataset, so that all data is on the same scale. At the same time, we analyse the heavy atom data to estimate the strength of the signals.
Select the Experimental Phasing module, and open the Scale and Analyse Datasets task window.
On the first line, enter a suitable job title such as:
On the second line, select
On the next line, select
On the next line, select
and de-select
using the radiobuttons.
Select the input MTZ file
Now select the columns from the MTZ file. The first line has the native FNAT and SIGFNAT. Then select columns for the 3 derivatives, using the button Add Derivative Data to add more columns. You should end up with:
| FP | FNAT | SigmaFP | SIGFNAT |
|---|---|---|---|
| FPH1 | FHG2 | SigFPH1 | SIGFHG2 |
| DPH1 | DANOHG2 | SigDPH1 | SIGDANOHG2 |
| FPH2 | FPTNCD25 | SigFPH2 | SIGFPTNCD25 |
| DPH2 | DANOPTNCD25 | SigDPH2 | SIGDANOPTNCD25 |
| FPH3 | FIOD25 | SigFPH3 | SIGFIOD25 |
| DPH3 | DANOIOD25 | SigDPH3 | SIGDANOIOD25 |
Check that the output MTZ file is given as
You should not need to change anything else. Select Run -> Run Now.
When the job has finished, return to the main window, highlight the job in the Job List, and select View Files from Job -> View Log Graphs. This task outputs a large number of graphs for analysing the data, and we will just look at some of them.
We can gauge the strength of the isomorphous differences by looking at the graphs:
Centric Normal probability v resolution and
Acentric Normal probability v resolution ...
for each pair of wavelengths, e.g. ... FP = FNAT FPH = FHG2 SIGFHG2 , FPTNCD25 etc DANOHG2 SIGDANOHG2. For each graph, look at the line Gradient_on_reflection_prob.lt.0.9. Use the crosswires to estimate a rough value, e.g. for the native against the Hg derivative, the value is about 2.5 for centric data and 2.05 for acentric data.
The values can be summarised as (these values are contained in the file View Files from Job -> ...scaleit.summary):
Table: Normal Probability for acentric data Normal Prob. |FNAT FHG2 FPTNCD25 FIOD25 ---------------------------------------------------------------- FNAT | 2.051 9.458 10.873 FHG2 |2.051 3.124 3.804 FPTNCD25 |9.458 3.124 11.484 FIOD25 |10.873 3.804 11.484 Table: Normal Probability for Centric data Normal Prob. |FNAT FHG2 FPTNCD25 FIOD25 ---------------------------------------------------------------- FNAT | 2.521 9.517 8.939 FHG2 |2.521 3.482 4.042 FPTNCD25 |9.517 3.482 9.946 FIOD25 |8.939 4.042 9.946
This shows that the isomorphous difference (i.e. difference between native and derivative) is smallest for the Hg derivative, and largest for the Iodine derivative.
Before carrying out any experimental phasing it is necessary to know the atomic coordinates of the heavy atoms. We do this using isomorphous or anomalous differences. The isomorphous difference is a component of FH, and the anomalous difference is a component of 2F"H.
For the Hg derivative there is 1 Hg atom to be positioned.
For the Pt derivative there are 4 Pt atoms to be positioned.
For the I derivative there are 2 I atoms to be positioned.
One site can be found quite easily by a Patterson search. For four sites, a Patterson search is quite complicated. However it is always good practice to calculate Pattersons using both the isomorphous and anomalous for each derivative. Each pair should show a similar pattern of peaks.
Select the Experimental Phasing module, and open the Generate Patterson Map task window.
On the first line, enter a suitable job title such as
On the next line, select
then select with the radio button
Select the input MTZ file
(If you do not have this file from the previous session, take the file from the DATA directory.)
Now select the columns from the MTZ file:
| F1 | FHG2 | SIG1 | SIGFHG2 |
|---|---|---|---|
| F2 | FNAT | SIG2 | SIGFNAT |
Check that the output MAP file is given a sensible name
It is VERY important to exclude outliers which are often due to measurement errors.
In the folder Exclude Reflections:
You should not need to change anything else, so select Run -> Run Now.
The Harker sections will be plotted - click on View Files from Job -> jobid...plt. It is a good idea to compare these plots for the dispersive and anomalous Pattersons. They should have a similar pattern of peaks.
Now also generate an anomalous Patterson Map using DANOHG2, using the same MTZ file. Enter a meaningful job title.
On the next line, select
Now select the columns from the MTZ file:
| AnomDif | DANOHG2 | SigmaD | SIGDANOHG2 |
|---|
Check that the output MAP file is given as
You should not need to change anything else, so select Run -> Run Now.
The Harker sections will be plotted - click on View Files from Job -> jobid...plt. It is a good idea to compare these plots for the isomorphous and anomalous Pattersons. They should have a similar pattern of peaks. Have a look at RNase Harkers for pictures, comparison and discussion. The outcome of this is a heavy atom at x~±0.1±1/2, y~±0.1±1/2, z~±0.2±1/2.
You are now going to use a direct methods approach for locating the Hg sites. This is more useful (and more successful) when there are many sites. In this section, you will prepare the Isomorphous data for use in the direct methods program SHELX.
Select the Experimental Phasing module, and open the Prepare Data for HA Search task window.
On the first line, enter a suitable job title such as
On the next line, select
Select the input MTZ file
Now select the columns from the MTZ file:
| FP | FNAT | SigFP | SIGFNAT |
|---|---|---|---|
| FPH | FHG2 | SigFPH | SIGFHG2 |
Check that the output SHELX hkl file is given as
Again it is VERY important to exclude outliers due to measurement errors. Use the same criteria as you chose for the Patterson. In the folder Exclude data when converting to Shelx format, use the radio buttons and fill in the following:
The value of 272.07 can be found in the log file of the difference Patterson (see above); search log file for "reflections excluded" and adapt as you see fit.
Select Run -> Run Now.
When the data preparation has finished, open the ShelxS - Heavy Atom Search task window.
On the first line, enter a suitable job title such as
On the next line, select
And the next line should read
Select the input HKL and MTZ files
Most of the Cell Parameters folder should be filled in automatically. It now only needs the desired number of heavy atoms to find, and its/their type:
No other parameters need to change, so select Run -> Run Now.
When the job has finished, return to the main window, highlight the job in the Job List, and select View Files from Job -> View Log File. Near the end of the log file, find:
Heavy-atom assignments:
x y z s.o.f. Height
HG1 0.8945 0.0947 0.8000 1.0000 418.3Comparing this with the outcome of the Patterson map calculations above:
xHG1 = -xPatt (+ whole cell shift)
yHG1 = yPatt
zHG1 = -zPatt (+ whole cell shift)
Experience has shown that, for situations where only one or a few heavy atoms are sought, Shelx 'PATT' (CCP4i Protocol option 'Patterson search' rather than 'direct methods') may perform more reliably. For the mercury search in RNase, however, this does not seem to be the case. Try it, if you like. No other options need to change, although Try 4 superposition vectors (Shelx Patterson Search Parameters folder) sometimes helps.
We now have an initial solution for 1 Hg site. Heavy atom refinement and phasing is done using the program MLPHARE. We will calculate cross-peak and difference map(s) to start looking for more heavy atoms.
Stage 1. Refine Hg solution and search difference maps for more peaks.
Select the Experimental Phasing module, and open the Run Mlphare task window.
On the first line, enter a suitable job title such as
In the Protocol folder, select:
There are enough centric observations to refine the Hg parameters.
Select
Select the input MTZ file:
Now select the columns from the MTZ file.
| FP | FNAT | SigmaFP | SIGFNAT |
|---|---|---|---|
| FPH1 | FHG2 | SigFPH1 | SIGFHG2 |
| Choose other derivatives for cross-peaks maps (Use 'Add Another Cross-Peak Derivative' for this) | |||
| FPH1 | FPTNCD25 | SigFPH1 | SIGFPTNCD25 |
| FPH2 | FIOD25 | SigFPH2 | SIGFIOD25 |
Check that the output MTZ file has a sensible name, especially if you intend to save intermediate versions of it.
Enter a memorable MTZ output column label identifier, such as:
In the folder Key Parameters, select and enter:
In the folder Describe Derivatives & Refinement, select and enter:
Select Run -> Run Now.
When the job has finished, return to the main window, highlight the job in the Job List, and select View Files from Job. In the list of output files, note the following:
| TEST_jobnumber_1.ha | refined Hg parameters |
| TEST_jobnumber_FHG2.map | difference map calculated with coefficients FHG2-FNAT and phases from the mlphare run refining Hg parameters |
| TEST_jobnumber_FHG2_peaks.pdb | peaks found in difference map, can be viewed with graphics program |
| TEST_jobnumber_FHG2.ha | peaks from the difference map, in fractional coordinates, to be re-used by CCP4i |
| TEST_jobnumber_FPTNCD25.map | difference map ('cross-peaks map') calculated with coefficients FPTNCD25-FNAT and phases from Hg |
| TEST_jobnumber_FPTNCD25_peaks.pdb | as for HG derivative |
| TEST_jobnumber_FPTNCD25.ha | as for HG derivative |
| TEST_jobnmuber_FIOD25... | as for PT derivative |
Select View Files from Job -> TEST_jobnumber_1.ha. The occupancy of the Hg site has refined to around 0.4. This is respectable.
Select View Files from Job -> View Log Graphs. Graphs are given for the last refinement cycle and the final phasing cycle. Look in particular at:
Stage 2. Refine all plausible-looking Hg sites (coordinates and occupancy) and search for more peaks in all derivatives.
In the Run Mlphare task window, adapt the job title:
In the Files folder, adapt the MTZ output filename if you wish. Re-using the same is not a problem in most cases. Adapt the column label for the output:
In the folder Describe Derivatives & Refinement, select and enter:
Then click the View button to check and edit the ...FHG2.ha file.
In the .ha File Viewer, click Change all. This results in hashes (#) at the beginning of each line. CCP4i ignores any ATOM lines in .ha files which start with a hash, so remove the hash at the beginning of lines we want to keep through a click on the first four atom lines. Then click the Edit Columns button and enter:
Back in the .ha File Viewer, click Save&Exit.
Select Run -> Run Now. If you have left the name of the output MTZ file as it was, you will have to delete the old version of it.
When the job has finished, View Log Graphs. The phasing power for the centrics is now above 1 for some of the resolution ranges, and the Cullis Rfactor is coming down a little.
Including heavy atoms for other derivatives in the refinement can be a process of trial-and-error. It may be necessary to take a step back and remove sites to try others. Proposed stages are:
Some tips:
To do this, you need to run MLPHARE several times. Steps using centric data (or a subset of the full data set) will be very fast. The heavy atom parameters are held in a .ha file, which is updated after each pass. The output MTZ file will be used as input for the difference Fouriers.
Stage 1a. Phase with and refine potential Pt sites. The first peak found for Pt is actually in exactly the same position as the original Hg solution. At this stage it cannot be determined whether this is an artefact of the Mlphare refinement, or a real solution for Pt. It is therefore best to exclude it from phasing and refinement.
In the Run Mlphare task window, adapt the job title:
In the Files folder, select the input MTZ file column labels according to the following:
| FP | FNAT | SigmaFP | SIGFNAT |
|---|---|---|---|
| FPH1 | FPTNCD25 | SigFPH1 | SIGFPTNCD25 |
| Choose other derivatives for cross-peaks maps | |||
| FPH1 | FHG2 | SigFPH1 | SIGFHG2 |
| FPH2 | FIOD25 | SigFPH2 | SIGFIOD25 |
Adapt the MTZ output filename if you wish. Re-using the same is not a problem in most cases. Adapt the column label for the output:
In the folder Describe Derivatives & Refinement, select and enter:
Then click the View button to be able to edit the ...FPTNCD25.ha file. If all is well, ATOM1 will have coordinates of x~0.4, y~0.4, z~0.2. This is also the position of the first Hg solution, so to be safe, this should not be used as a Pt site in the first instance.
In the .ha File Viewer, click Change all. Then click on the lines beginning ATOM2 and ATOM3 (i.e. the two highest scoring ones but not the one in the Hg position). These can now be used to phase and refine. Click the Edit Columns button and enter:
Back in the .ha File Viewer, click Save&Exit.
Select Run -> Run Now. If you have left the name of the output MTZ file as it was, you will have to delete the old version of it.
When the job has finished, View Log Graphs. The phasing power and Cullis Rfactor for the two Pt sites are better than those for the four Hg sites. This is very promising. Also view the file TEST_jobnumber_FPTNCD25.ha. The peak for the 'Hg site', which was not included in phasing and refinement, comes up high in the list and is therefore almost certainly a genuine Pt site, too. It can be included in the next stage.
Stage 1b. Phase with and refine all plausible-looking Pt sites.
In the Run Mlphare task window, adapt the job title:
In the Files folder, adapt the MTZ output filename if you wish. Re-using the same is not a problem in most cases. Adapt the column label for the output:
In the folder Describe Derivatives & Refinement, select and enter:
Then click the View button to be able to edit the ...FPTNCD25.ha file.
In the .ha File Viewer, click Change all and then the first four ATOM lines (which should include the 'Hg site'). Click the Edit Columns button and enter:
Back in the .ha File Viewer, click Save&Exit.
Select Run -> Run Now. If you have left the name of the output MTZ file as it was, you will have to delete the old version of it.
When the job has finished, View Log Graphs. The phasing power and Cullis Rfactor for the Pt derivative have improved considerably. From the ...FPTNCD25.ha file it can be seen that there is a fifth probable Pt site. It is worth considering whether to include that in the next stage.
Stage 2. Phase with and refine Pt and Hg sites.
In the Run Mlphare task window, adapt the job title:
In the Files folder, select the input MTZ file column labels according to the following:
| FP | FNAT | SigmaFP | SIGFNAT | |
|---|---|---|---|---|
| FPH1 | FPTNCD25 | SigFPH1 | SIGFPTNCD25 | |
| FPH2 | FHG2 | SigFPH2 | SIGFHG2 | (Use 'Add another derivative') |
| Choose other derivatives for cross-peaks maps (Use 'Edit list -> Delete selected item', and RIGHT mouse button on any widget in the HG2 line) | ||||
| FPH1 | FIOD25 | SigFPH1 | SIGFIOD25 | |
Adapt the MTZ output filename if you wish. Re-using the same is not a problem in most cases. Adapt the column label for the output:
In the folder Describe Derivatives & Refinement, subfolder Derivative number 1, select and enter:
In subfolder Derivative number 2, select and enter:
For the HG .ha file, click the View button. Click on the lines concerned with ATOM4 (ATOM4 and ATREF below it), because the occupancy refined to an unbelievably low value (0.049). Then click Save&Exit.
Select Run -> Run Now. If you have left the name of the output MTZ file as it was, you will have to delete the old version of it.
When the job has finished, View Log Graphs. The phasing powers and Cullis Rfactors have not improved (if anything, they have deteriorated) compared to the phasing and refinement runs for the derivatives separately. Checking the refined Hg parameters against those calculated from the difference map, something seems to have gone awry. The first three peaks of the difference map do not match the three Hg sites from the refinement. Time to re-run with the three highest peaks from the difference map.
Stage 2b. Phase with and refine 4 previously refined Pt sites and 3 different Hg sites from the difference map.
In the Run Mlphare task window, adapt the job title:
Adapt the MTZ output filename if you wish. Re-using the same is not a problem in most cases. Adapt the column label for the output:
In the folder Describe Derivatives & Refinement, subfolder Derivative number 1, select and enter:
In subfolder Derivative number 2, select and enter:
For the HG .ha file, click the View button. In the .ha File Viewer, click Change all and then the first three ATOM lines. Click the Edit Columns button and enter:
Back in the .ha File Viewer, click Save&Exit.
Select Run -> Run Now. If you have left the name of the output MTZ file as it was, you will have to delete the old version of it.
When the job has finished, View Log Graphs. The phasing power and Cullis Rfactor for the Pt derivative have improved marginally. However, the statistics for the Hg derivative have improved markedly. Time to include the iodine derivative.
Stage 3a. Include the iodine derivative. Take peaks from the difference map calculated with phases from the best derivative (Pt, i.e. from the end of stage 1) only, or from both derivatives together (i.e. from the end of stage 2).
In the Run Mlphare task window, adapt the job title:
Un-select the option to output cross-peaks map(s).
In the Files folder, select the input MTZ file column labels according to the following:
| FP | FNAT | SigmaFP | SIGFNAT | |
|---|---|---|---|---|
| FPH1 | FPTNCD25 | SigFPH1 | SIGFPTNCD25 | |
| FPH2 | FHG2 | SigFPH2 | SIGFHG2 | |
| FPH3 | FIOD25 | SigFPH3 | SIGFIOD25 | (Use 'Add another derivative') |
Adapt the MTZ output filename if you wish. Re-using the same is not a problem in most cases. Adapt the column label for the output:
In the folder Describe Derivatives & Refinement, subfolder Derivative number 1, select and enter:
In subfolder Derivative number 2, select and enter:
In subfolder Derivative number 3, select and enter:
For the I .ha file, click the View button. In the .ha File Viewer, click Change all and then the first three ATOM lines. Click the Edit Columns button and enter:
Back in the .ha File Viewer, click Save&Exit.
Select Run -> Run Now. If you have left the name of the output MTZ file as it was, you will have to delete the old version of it.
When the job has finished, View Log Graphs. The statistics for Pt and Hg are still improving slightly, and the iodine derivative looks promising. Investigate possible improvements from inclusion of more sites for any of the derivatives.
Stage 3b. [Optional] The heavy atom structure is now probably complete enough for final refinement and phasing. The statistics may, however, improve with the inclusion of more sites for any or all of the derivatives. Investigate. Be aware of symmetry-related sites and 'shoulders'.
Try including 5 Pt, 4 Hg, 4 I from their respective difference maps. Edit the occupancies to a slightly lower value of what they refined to in the previous run. If the occupancy refines back to the previous (higher) value, this gives an additional check on the validity of the site. Suggested values: 0.4 for PT, 0.3 for HG and I.
When the job has finished, View Log Graphs and compare with the graphs from the previous run (4 Pt, 3 Hg, 3 I). Also, check the refined values for the occupancies of new and previously included heavy atom sites, and whether the refined sites are at the top of the peak list from the difference map calculations. The fourth Hg site does not refine to a satisfactory value, and the statistics for the Hg derivative do not improve. The fifth Pt and fourth I, however, improve statistics and refine to a satisfactory occupancy, and the first four Pt and first three I sites behave as hoped.
Try taking out the worst Hg site again. Use the refined sites from step 450 as input, without re-setting occupancies.
When the job has finished, View Log Graphs, refined sites and difference map peak lists as before. The refinement is now stable, and no new sites suggest themselves for inclusion.
Phasing and refining (coordinates, real occupancy and anomalous occupancy parameters), against all data, including anomalous.
In the Run Mlphare task window, enter a suitable job title such as:
In the first folder:
In the Files folder, select the input MTZ file:
Now select the columns from the MTZ file.
| FP | FNAT | SigmaFP | SIGFNAT |
|---|---|---|---|
| FPH1 | FPTNCD25 | SigFPH1 | SIGFPTNCD25 |
| DPH1 | DANOPTNCD25 | SigDPH1 | SIGDANOPTNCD25 |
| FPH2 | FHG2 | SigFPH2 | SIGFHG2 |
| DPH2 | DANOHG2 | SigDPH2 | SIGDANOHG2 |
| FPH3 | FIOD25 | SigFPH3 | SIGFIOD25 |
| DPH3 | DANOIOD25 | SigDPH3 | SIGDANOIOD25 |
Check that the output MTZ file is given as
Enter a memorable MTZ output column label identifier, such as:
In the folder Key parameters, enter resolution limits to include all the data between 50 and 2.5Å:
In the folder Describe Derivatives & Refinement, subfolder Derivative Number 1, select and enter:
In subfolder Derivative number 2, select and enter:
In subfolder Derivative number 3, select and enter:
For all three .ha files, click the View button, then the Edit Columns button and enter:
Back in the .ha File Viewer, click Save&Exit.
Select Run -> Run Now.
When the job has finished, return to the main window, highlight the job in the Job List, and select View Files from Job -> View Log Graphs. The statistics look good for all three derivatives. Then look at Anomalous lack of closure analysis .... / Ano Cullis Rfactor ..... For good data the anomalous Cullis Rfactor should be significantly less than one. However, none of the three derivatives has particularly good data (and the Hg derivative is the worst of the three). This explains why the anomalous Patterson maps are (almost) uninterpretable.
Also, look at the refined sites (in the ..._1.ha, ..._2.ha and ..._3.ha files). All (or nearly all) anomalous occupancies have refined to a negative value. This means that the refinement has been performed on the wrong hand.
The procedure for locating the Hg sites cannot distinguish between a particular set of sites and the same set of sites transformed through a point of inversion, i.e. it cannot distinguish the hand of the solution. Therefore, the previous phasing run should be repeated using the opposite hand.
In the Run Mlphare task window, adapt the job title:
Make sure to generate difference maps, which will be used later to shift the heavy atom coordinates to a 'friendly' asymmetric unit.
Use the MTZ file and column selection from the previous run (step 500).
Choose a suitable name for the output MTZ file, reflecting the different hand, such as:
It should be no problem to re-use the output column label identifier.
For the derivative descriptions, start from the same set as for step 500.
For the Pt .ha file, click the View button. In the .ha File Viewer, click the Reverse hand button. A small 'Change Hand' window will appear. Our spacegroup is P212121, so there is no need to type the spacegroup name. Just click OK. Back in the File Viewer window, all coordinates have changed to negative values. Click Save As.. and change the output filename to reflect the change of hand (e.g. TEST_jobnumber_1h.ha). Back in the File Viewer, click Quit. Back with the description for Derivative number 1 (Five Pt anom), click the Browse button and select the .ha file just saved (TEST_jobnumber_1h.ha).
Repeat this for the Hg and I .ha files (i.e. create ..._2h.ha and ..._3h.ha respectively, and select those for Derivative number 2 and 3).
Select Run -> Run Now.
When the job has finished, View Log Graphs. The Anomalous Cullis Rfactor has improved, at least for the Pt and I derivatives. All but one (one of the iodine sites) of the anomalous occupancies have refined to a value higher than the starting value of 0.1.
Comparing TEST_jobnumber_1.ha with TEST_jobnumber_FPTNCD25.ha, it should be easy to see how to transfer the heavy atom sites to a 'friendly' asymmetric unit.
[Optional] It is easy to transfer the heavy atom sites to an asymmetric unit with all positive coordinates (which fits with the refined coordinates as they can be found in the Protein Data Bank).
In the Run Mlphare task window, adapt the job title:
Leave all MTZ input and output data as before.
In the folder Describe Derivatives & Refinement, subfolder Derivative number 1, select and enter:
In subfolder Derivative number 2, select and enter:
In subfolder Derivative number 3, select and enter:
Edit all three .ha files such that only the desired sites are included for refinement, and give appropriate names and occupancies. Suggested values:
| atom | sites | occupancy | anomalous occupancy |
| PT | first 5 | 0.4 | 0.3 |
| HG | first 3 | 0.3 | 0.2 |
| I | first 4 | 0.4 | 0.3 |
This still includes the low-occupancy iodine site.
Select Run -> Run Now.
When the job has finished, check everything is in order. The low-occupancy iodine site seems to be just that.
Before going on to model building and refinement, the phases can be improved through density modification/improvement. For this, the program 'dm' is used.
Select the Density Improvement module, and open the Run DM
On the first line, enter a suitable job title such as
Select Input Hendrickson-Lattman coefficients
Select the input MTZ file:
Now select the columns from the MTZ file.
| FP | FNAT | SIGFP | SIGFNAT |
|---|---|---|---|
| PHIO | PHIB_mlp-all-anom | Weight | FOM_mlp-all-anom |
| HLA | HLA_mlp-all-anom | HLB | HLB_mlp-all-anom |
| HLC | HLC_mlp-all-anom | HLD | HLD_mlp-all-anom |
In the Required Parameters folder, enter the solvent content as
Everything else can be left as default, so Run -> Run Now.
When the job has finished, look at the log file and loggraph to check statistics and solvent boundaries. To really appreciate the results, it would be best to calculate maps (one with the phases from just MLPHARE, one with phases from DM) and compare.
On to the next tutorial - Experimental Phasing (by MAD).
Back to the previous tutorial - Data Processing and Reduction.
Back to the index.
Prepared by Liz Potterton and Martyn Winn, 2000
Adapted by Eleanor Dodson and Maria Turkenburg, 2002-2003