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Mod:Hunt Research Group/Jan profit points

From ChemWiki

you can plot the MK/CHELPG fitting points in profit

example profit plot of MK mesh for ch3oh
  • 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				
  • 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.