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Reduce image sizes in README
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lafita authored Apr 16, 2018
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Expand Up @@ -103,22 +103,22 @@ The results are split into the following table files:
In order to visualize the mapping of the alchemical free energy onto the native domain structure, a new `PDB` file [sh3-dG_cut.pdb](example/sh3-dG_cut.pdb) is generated with the `ΔGc` values in the B-factor column.
To take a look at it in `PyMOL`, open the structure and select `Action` > `preset` > `b factor putty` to obtain a representation like the one below:

![pymol](example/sh3-dG_cut.png)
<img src="example/sh3-dG_cut.png" width="400">

In addition, two R scripts are provided to plot the free energy profile of the domain as a barplot and the Go contacts as a matrix.
Use the following commands:

```
Rscript ~/tadoss/go_contacts.R -i go_sh3/go_sh3_gomodel_golist.dat -o sh3_go-contacts.pdf
Rscript ~/tadoss/dGc_profile.R -i sh3-dG_cut.tsv -o sh3-dG_cut.pdf
```

![contacts](example/sh3_go-contacts.jpg)
<img src="example/sh3-dG_cut.jpg" width="400">

```
Rscript ~/tadoss/dGc_profile.R -i sh3-dG_cut.tsv -o sh3-dG_cut.pdf
Rscript ~/tadoss/go_contacts.R -i go_sh3/go_sh3_gomodel_golist.dat -o sh3_go-contacts.pdf
```

![profile](example/sh3-dG_cut.jpg)
<img src="example/sh3_go-contacts.jpg" width="400">


## Publications
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