Differences

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--- edp [2023/07/20 16:18] – edit
+++ edp [2024/03/21 18:39] (current) – edit
@@ Line 7: / Line 7: @@
 Updated (2021): Robert Allsopp (Combining the .sim and renaming atoms)
 Updated (2023): Abhi Senthilkumar (Python scripts to automatically rename atoms and combine .sim files into xlsx)
+Updated (2023): Joshua Lucker (Clarification on Step 6)
 Example of analysis: {{ ::e.g._thickness.xlsx |}}
@@ Line 109: / Line 110: @@
 **New method of renaming the atoms and compiling in an excel file**
-  - First edit the script **format.py**. Edit the LIPID_NAMES and LIPID_ABBRS lists. The script automatically changes the .cmp and.sim files, but this can be changed by editing the FILE_ENDINGS list. One side effect is that the comments at the start of the file will also be targeted by the regex, but this effect is minimal. The script will substitute all 'z's in atom names with a 26. If there is a different substitution you would prefer you can change that. You can also choose to either modify the original .sim files or create new formatted files. It is recommended to leave MODIFY_FILES to False to avoid having to regenerate the .sim and .cmp files if something goes wrong. Once you have edited the script, run it with **python format.py**
+  - First edit the script **format.py**. Edit the LIPID_NAMES and LIPID_ABBRS lists. The script automatically changes the .cmp and.sim files, but this can be changed by editing the FILE_ENDINGS list. One side effect is that the comments at the start of the file will also be targeted by the regex, but this effect is minimal. The script will substitute all 'z's in atom names with a 26. If there is a different substitution you would prefer you can change that. You can also choose to either modify the original .sim files or create new formatted files. It is recommended to leave MODIFY_FILES to False to avoid having to regenerate the .sim and .cmp files if something goes wrong. Once you have edited the script, make sure you have loaded python with **module load python**. Then run the script with **python format.py**
-  - Next, edit the script **generate_excel_file.py**. Edit the LIPIDS list to add the lipid.sim files you want to compile. If in the previous step you generated new files, make sure to set USE_NEW_FILES to True. Run the script with **python generate_excel_file.py**
+  - Next, edit the script **generate_excel_file.py**. Edit the LIPIDS list to add the lipid.sim files you want to compile. If in the previous step you generated new files, make sure to set USE_NEW_FILES to True. If this is the first time you have run this, you will need to install xlsxwriter for python. Do this with the following command: **pip install %%--%%user XlsxWriter**. Then, run the script with **python generate_excel_file.py**
   - This will generate an excel file titled **sim_data.xlsx** along with .csv files for each lipid.
 **Old method of renaming atoms and compiling in an excel file**
@@ Line 211: / Line 212: @@
 //
-Note: when the each neutron scattering file is opened, the **scattering length** window will pop out with automatically updated NSL (neutron scattering length) of D which are defined in the experimental data file. If the window doesn't pop out, go to Tools -> Scattering Length. For example, for 100%D, D=6.67e-5 (this depends on the water density). If standard 1 g/cm3 is used, then D=6.38e-6 Angs^2; 50D means 50%D2O and 50%H2O, (D=frac_water*D(water) + frac_d2o*D(D2O)). For water, note that D(water)=-5.58e-7 at 1 g/cm3. Therefore, when a different deuterium contrast (??D) file is opened, NSL are usually automatically updated based on the definition of D. To verify this, open a 50D NFF experimental data, it shows something like: \\
+Note (please read): when the each neutron scattering file is opened, the **scattering length** window will pop out with automatically updated NSL (neutron scattering length) of D which are defined in the experimental data file. If the window doesn't pop out, go to Tools -> Scattering Length. For example, for 100%D, D=6.67e-5 (this depends on the water density). If standard 1 g/cm3 is used, then D=6.38e-6 Angs^2; 50D means 50%D2O and 50%H2O, (D=frac_water*D(water) + frac_d2o*D(D2O)). For water, note that D(water)=-5.58e-7 at 1 g/cm3. Therefore, when a different deuterium contrast (??D) file is opened, NSL are usually automatically updated based on the definition of D. To verify this, open a 50D NFF experimental data, it shows something like: \\
 ## redefinition of scattering power for D such that water corresponds to 50% D2O \\
 #SLwin \\
@@ Line 219: / Line 220: @@
 As a note if this does not occur, go to the scattering length window and change the deuterium number in the NSL column manually based on the equation: D=frac_water*D(water) + frac_d2o*D(D2O), where D(D2O)=6.67e-5, and D(pure water)=-3.74e-5. Then, change the NSLD_wat number in the main window based on the maximum value in the Neutron SL Densities window (Note: you can also use the above equation where D(D2O)=6.38e-6 and D(water)=-5.58e-7 as well if you wish).
+//
 )	Update/Enter the ED_wat and NSLD_wat based on the values of water level off in Electron Densities and Neutron SL Densities windows, respectively, click the fix’s, and then click Click **Fourier Transform**, and **Calculate Volume**. **(Make sure to click these two icons each time a new file is opened/loaded.)** Go to X-ray FFs and Neutron FFs to compare the data. I recommend you make sure your plot is reasonable before you export the data and plot. POPG may behave like POPC, so the curves will be probably similar.