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I am often asked how to do this. Many years ago I wrote a mixture editor for the Windows and Mac programs, but I was bombarded with comments about how someone had entered the details of their favorite protein and it had not behaved in the simulation exactly as it did in their laboratory. I tried to explain that this program is not intended as an exact research tool, but only as a teaching aid. No joy, so I withdrew the mixture editor. But I still keep getting requests...
OK - this only applies to the Java and Javascript versions.
If you want to design new mixtures, you will need to understand the mixture file format. The program uses text files with comma-delimited data. Here is the data file for the default mixture - I hope it is self-explanatory.
//The first non-comment line must contain the number of proteins in this
mixture
//and nothing else.
//
20
//
//The subsequent lines contain the data for each protein in the mixture.
//Each line must contain only comma-separated numbers with no white space or
breaks.
//On each line the fields are as follows:
// Fields 1-7 contain the total numbers of ASP,GLU,HIS,LYS,ARG,TYR
and CYS-SH
// residues respectively in the whole protein
molecule (i.e aggregated over
// all polypeptide chains). These data are
used to calculate the protein's charge
// at any pH value, and hence also to calculate
the isoelectric point.
// Field 8 contains the overall native molecular weight of the protein.
// Each protein can have up to three different types of polypeptide
chains.
// Field 9 contains the number of polypeptides of type 1. This must
always be greater than zero.
// Field 10 contains the number of polypeptides of type 2 if any
or zero if not.
// Field 11 contains the number of polypeptides of type 3 if any
or zero if not.
// Field 12 contains the molecular weight of polypeptide type 1.
This cannot be zero.
// Field 13 contains the molecular weight of polypeptide type 2
// or zero if there is only one type of polypeptide.
// Field 14 contains the molecular weight of polypeptide type 3
// or zero if there is no such type of polypeptide.
// Field 15 contains the amount (in mg) of this protein in the initial
mixture
// Field 16 contains the amount (in mg) of this protein in the mixture
in its
// current state. This is to allow partially purified
mixtures to be saved and
// reloaded. When designing a mixture, set this
field to the same value as field 15.
// Field 17 contains the temperature below which the enzyme activity
is stable.
// Fields 18 and 19 contain the pH values between which the enzyme
activity is stable
// Field 20 contains a number which sets the 'surface hydrophobicity'.
This is
// used to set the behaviour of the protein during
ammonium sulfate fractionation
// and hydrophobic interaction chromatography.
// Field 21 contains an integer which represents the initial specific
enzymic activity
// of the protein.
// Field 22 contains an integer which represents the current specific
activity.
// This will normally be the same as the value
of field 21.
//
// Comment lines must begin with //.
// Blank lines are not allowed except at the end of the file.
// Be careful - there is almost no value/error checking done on these values.
// The usual disclaimers apply.
//
//
Andrew Booth 10th February 2012
//
// These are the data for the default mixture:
//
16,23,6,31,10,18,3,53500,1,0,0,53500,0,0,10,10,40,2.5,9.5,126,4,4
22,25,8,19,26,12,5,320000,4,4,0,50000,30000,0,42,42,60,5,10.5,167,2,2
23,28,8,18,17,16,4,42000,1,0,0,42000,0,0,14,14,50,3.5,10,61,4,4
14,15,3,12,14,7,0,37000,1,0,0,37000,0,0,35,35,40,4.5,10,139,2,2
12,15,8,15,11,19,1,200000,4,0,0,50000,0,0,20,20,50,3,11,82,3,3
13,15,4,13,11,6,3,32000,1,0,0,32000,0,0,34,34,40,5,11,81,1,1
24,28,10,20,22,10,0,58000,2,0,0,29000,0,0,15,15,40,4.5,11.5,105,2,2
9,11,3,15,3,2,0,27000,1,0,0,27000,0,0,49,49,40,5.5,10,199,4,4
7,18,2,16,8,2,0,23000,1,0,0,23000,0,0,24,24,50,4,9.5,141,3,3
16,14,4,13,11,3,1,45000,2,0,0,22500,0,0,34,34,50,3.5,11.5,182,3,3
17,13,2,9,9,4,0,22000,1,0,0,22000,0,0,11,11,50,3,11,167,3,3
20,7,6,12,6,7,0,21000,1,0,0,21000,0,0,21,21,50,4,11,83,7,7
6,7,2,9,12,19,0,20000,1,0,0,20000,0,0,21,21,40,3.5,10.5,91,2,2
7,14,9,18,2,2,1,140000,2,2,0,50000,20000,0,35,35,50,3.5,10,141,2,2
28,32,36,44,12,12,4,68000,4,0,0,17000,0,0,31,31,40,4.5,9.5,172,1,1
4,4,3,2,5,2,5,14500,1,0,0,14500,0,0,46,46,40,5.5,9.5,246,2,2
3,8,3,18,2,3,1,14000,1,0,0,14000,0,0,12,12,50,4,10.5,151,2,2
6,24,4,18,8,6,0,22000,2,0,0,11000,0,0,36,36,40,4.5,9.5,209,1,1
7,12,5,9,3,3,0,11000,1,0,0,11000,0,0,3,3,50,4,10.5,238,2,2
1,5,0,2,3,2,0,67000,1,0,0,67000,0,0,18,18,60,4,11.5,206,3,3
In addition, the filename of each mixture that you want to allow your users
to access must be listed in the file mixtures.txt.
The first line of mixtures.txt should contain the number of mixtures
and subsequent lines should give their filenames.
Here is the content of a typical mixtures.txt:
3
Default_Mixture
Easy3_Mixture
Example_Mixture
Put your mixture files and mixtures.txt in the same folder/directory
on the web server as the program files.