Mod:Hunt Research Group/Jan profit points
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you can plot the MK/CHELPG fitting points in profit

- this will produce a file with the balls at mesh points coloured according to charge
- run gaussian with pop and IOP commands
- save a copy of the *.esp file to edit: copy the *.esp file to *.data
- vi the file and delete all the lines upto the ESP
- then convert all the “D”s to “E”s with the command
:%s/old-text/new-text/g :%s/D/E/g
- then add column headers esp, x, y, z
- open the file in excel save as *.xlsx
- add 3 extra columns R B G for the colour data
- here is the top of a file
ESP X Y Z radius ESP R G B 0.0350 -1.6189 -4.4086 -0.9810 4.7978 0.70 1.00 0.30 0.30 0.0350 -1.6189 -4.4086 0.9811 4.7978 0.70 1.00 0.30 0.30 0.0336 -3.6529 -4.0499 -0.9810 5.5415 0.67 1.00 0.33 0.33 0.0336 -3.6529 -4.0499 0.9811 5.5415 0.67 1.00 0.33 0.33
- now we deal with the geometry
- copy the *.esp file to mol.data
- delete everything except the structural information
- then convert all the “D”s to “E”s
- remove the atomic charges from the last column replace these with the VdW radius values
- https://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page)
- open this file with excel and copy across the data into two sets of columns based on H or heavy atoms
- as shown below, ie H,x1,x2,x3 and atoms x1,x2,x3
atom H X1 H Y1 H Z1 atom atom X1 atom Y1 atom Z1 H -2.1432 -1.4351 0.0000 C 1.2541 -0.0370 0.0000 H 2.0465 1.8661 -0.0013 O -1.4175 0.2300 0.0000 H 1.9561 -1.0256 -1.6852 H 1.9563 -1.0234 1.6864
- here is an example of the excell file: File:Excell ch3oh mk grid 1.xlsx
- you will want to show a scale on your graph relating the colour to the ESP values
- now add columns scale x, scale y, scale z and scale R, scale B, scale G for the colour scale on the graph
- put your scale on the z-axis below the max negative z-coordinate value
- set all the y coords to zero, then give a range of x values
- I typically use 3 to -3 in steps of 0.5
- you can put the scale in other places, I have it along the x axis as well and then toggle to the scale I want showing
- then we need to define the colours
- to find a colour ramp go here "http://www.zonums.com/online/color_ramp/"
- I like red as positive, blue as negative, fading to white for values close to zero
- I found it easier to create the 255,255,255 values data first and then convert this to a scale 1 to 0, see the colomns below
- note that the colors in profit are RBG not RGB
color R color G color B 255.00 0.00 0.00 255.00 42.50 42.50 255.00 85.00 85.00 255.00 127.50 127.50 255.00 170.00 170.00 255.00 212.50 212.50 255.00 255.00 255.00 212.50 212.50 255.00 170.00 170.00 255.00 127.50 127.50 255.00 85.00 85.00 255.00 42.50 42.50 255.00 0.00 0.00 255.00
- now you need to convert the esp data to RGB values
- it helps if you assign the column format as decimal with 4 values after the decimal
- I also converted the esp range to values between 1 to -1
- find the max positive and max minimium ESP, MAX(A2:AXX) and MIN(A2:AXX) determine which is the larger absolute value ESP=MaxEsp
- this will give us the step size =(1/MaxEsp)
- F2=EspRel=Esp*(1/MaxEsp)
- then the RGB values can be defined relative to EspRel
- For example the formula for the above colour-range are
- R=IF(F2>0,1,(1+F2))
- G=IF(F2>0,(1-F2),((1+F2)))
- B=IF(F2>0,(1-F2),1)
- useful excel commands are:
- enter range in far left box above “A” column
- use colon to specify range eg A2:A420
- propagate this down the column (control+shift+down arrow)
- select a column then expand the selection by (shift+arrow)
scaleX1 scaleY1 scaleZ1 scaleX2 scaleY2 scaleZ2 scale scaleR scaleG scaleB 3.0000 0.0000 -6.5000 -6.5000 0.0000 3.0000 0.0000 1.0000 0.0000 0.0000 2.5000 0.0000 -6.5000 -6.5000 0.0000 2.5000 1.0000 1.0000 0.1667 0.1667 2.0000 0.0000 -6.5000 -6.5000 0.0000 2.0000 2.0000 1.0000 0.3333 0.3333 1.5000 0.0000 -6.5000 -6.5000 0.0000 1.5000 3.0000 1.0000 0.5000 0.5000 1.0000 0.0000 -6.5000 -6.5000 0.0000 1.0000 4.0000 1.0000 0.6667 0.6667 0.5000 0.0000 -6.5000 -6.5000 0.0000 0.5000 5.0000 1.0000 0.8333 0.8333 0.0000 0.0000 -6.5000 -6.5000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 -0.5000 0.0000 -6.5000 -6.5000 0.0000 -0.5000 5.0000 0.8333 0.8333 1.0000 -1.0000 0.0000 -6.5000 -6.5000 0.0000 -1.0000 4.0000 0.6667 0.6667 1.0000 -1.5000 0.0000 -6.5000 -6.5000 0.0000 -1.5000 3.0000 0.5000 0.5000 1.0000 -2.0000 0.0000 -6.5000 -6.5000 0.0000 -2.0000 2.0000 0.3333 0.3333 1.0000 -2.5000 0.0000 -6.5000 -6.5000 0.0000 -2.5000 1.0000 0.1667 0.1667 1.0000 -3.0000 0.0000 -6.5000 -6.5000 0.0000 -3.0000 0.0000 0.0000 0.0000 1.0000
- save-as the excell file as tab deliminated *.txt
- in profit import this file (select “with title”) and save as *_profit.data
- in the prog menu select Plot3D and select data xy
- choose your xyz data as xyz
- choose single data points and balls, smooth
- and then print colour is variable and match the RGB columns (make sure R->R, G->B, B->G)
- for the MK data points you want small balls about 0.03
- for the ChelpG data points you want small balls about 0.02/0.015
- click OK
- to add another plot on-top goto the edit menu and select Plot3D
- to add the scale select the scale x, y, z and their RGB scale, make the balls slightly larger 0.04
- for the atoms you want a fixed colour
- add the H atoms as larger balls 0.15 and add the heavy atoms as larger balls 0.3
- change the colour to very light grey by selecting “other”
- you can play with lighting using camera&illumination in the edit menu
- you can change the axis options in the edit menu
- use the Plot pull down to toggle between the representations.