Differences

This shows you the differences between two versions of the page.

--- edp [2022/01/25 22:46] – edit
+++ edp [2024/03/21 18:39] (current) – edit
@@ Line 6: / Line 6: @@
 Updated (2021): Dr. Jeffery Klauda
 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 11: / Line 13: @@
 The scripts that you need are in the following paths:
-DT2 path: **/lustre/jbklauda/scripts/edp_mult_lipids/**
+ZT1 path: **/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/edp_mult_lipids**
 or using the zip file: {{ :edp_mult_lipids.tar.gz |}}
-Also if there is a protein download the {{ :protein_analysis.tar |}} files and run them on as many proteins as there are in the system
+Also if there is a protein download the {{ :protein_analysis.tar |}} files and run them on as many proteins as there are in the system, and combine the data similarly to before
@@ Line 22: / Line 24: @@
 This section is for recentering the lipid bilayer so that it is always at the center of the box. This is essential so that the density profiles have the same reference (minimum bilayer density is a z=0).
-Copy the directory **/lustre/jbklauda/scripts/edp_mult_lipids/** into your namd directory with the DCD files.
+Copy the directory **/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/edp_mult_lipids** into your namd directory with the DCD files.
 .	Edit //cryst.str// file based on your crystal data (A,B,C,Alpha,Beta,Gamma) in dyn.xsc which is the system size of last frame in dyn directory. //box.cry// file is same for all lipids, so no need to edit. \\
@@ Line 87: / Line 89: @@
 </code>
-.2 Update the //psfrtf.str// file to have the correct location of the psf and crd file.\\
+.2 Update the //psfcrd.str// file to have the correct location of the psf and crd file.\\
 .3 Update lipid (file) name in //components.scr// \\
 Note: components2.scr and 1_run2.csh are not needed for systems with only a few kinds of lipids. Also, use lower case for the lipid names not upper case.
@@ Line 106: / Line 108: @@
 Please **make sure include “.” and space** due to the way that bld-sim.f is written). This will create *.sim files of all lipid components that has the combined atomic density which will be used in SIMtoEXP. \\
+**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, 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. 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**
 *Then combine the individual .sim files in excel into one master file that contains all of the individual lipids, peptide, water, ions. To do this copy everything from the first file including the Z column and then from that file onward exclude the Z column.
@@ Line 204: / Line 212: @@
 //
-Additional information for further understanding, performance is not involved in this session//: 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.  e.g. for 100%D, D= 6.67e-5 but this depends on the water density if standard 1 g/cm3 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, D(water)=-5.58e-7 at 1 g/cm3. Therefore, when a different deuterium contrast (??D) files are opened, NSL are 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 210: / Line 218: @@
 #setRHO_wat N 2.915e-006 \\
+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.
-**Part VII. Create own comparison plots**
+**Part VI and 1/2: Create own comparison plots**
 We want to re-plot since the graph in SIMtoEXP is not well formatted for publishing.(e.g. Only one curve is showing at one time; the axe titles are missing etc.). \\
 ) Export the simulated X-ray FFs and Neutron FFs data from SIMtoEXP by go to **Tools->EXPORT-> ALL. Only the D% data shown with the curve will be exported.** To export each D constrast, We need to select each by click on the space in SAM# and scale, and hit **enter** key. The simulated data of that D% will be plotted and exported. Each export one D%. If there are three D%, it would require three export.