Note - Positioning of molecules relative to map:
Maps and molecules will be positioned correctly if the coordinate space that was used to calculate the map is left unchanged in the molecule coordinate file.
This option should be used carefully as maps will be positioned correctly only if the 'Origin on grid point' option has been turned on upon calculating the electrostatic map with DelPhi. (The 'Origin on grid point' option can be found in the 'GRID' option in the 'SETUP' menu in DelPhi/InsightII.)
If the 'Origin on grid point' option is left unchecked, then the electrostatic maps will be shifted by a fraction of a grid point in the x and y directions and even more in the z direction.
This results from a bug in Insight II (No. 75400), that simply writes a wrong grid to the ASCII file. This may not have large consequences when inspecting maps derived for large molecules, but nevertheless the error is there and does produce artefacts.
Be aware that reading a formatted map takes a looong time...
After reading the map you can choose to have the extremes removed from the map; i.e. the only values that will be kept are the ones within a specified number of standard deviations from the average value of the potential map.
(See STAELM for information on how the average value is calculated).
It should be noted that the file format differs from the one reported in the Insight II Users Guide page 14-5 with respect to the three 4-byte floating point entries that are described as being the grid dimensions (x, y, z). This is not the case! The error (No. 79062) is, however, correctable as these incorrect grid dimensions have been used to calculate the fractional starting and ending points of the grid.
(Fractional starting pos. X) = (Absolute starting pos. X)/(Grid extent X)The correct starting and ending postions can thus be retrieved by applying the inverse of the above equation. These values can in turn be used to calculate the correct grid extent.
After reading the map you can choose to have the extremes removed from the map; i.e. the only values that will be kept are the ones within a specified number of standard deviations from the average value of the potential map.
(See STAELM for information on how the average value is calculated).
After reading the map you can choose to have the extremes removed from the map; i.e. the only values that will be kept are the ones within a specified number of standard deviations from the average value of the potential map.
(See STAELM for information on how the average value is calculated).
These parameters are calculated twice: first taking all values into account, and secondly taking only ABS(values) greater than 0.0001 into account. (The latter is used for removing extremes after reading a map, GETFDM, GETUDM and GETUUM).
This is done because the large number of grid points bearing a value very close to, or identical to zero for many purposes are better left ignored.
(Still experimental)
DelPhi needs to be installed.
A convex point in this routine is defined as a point having three or more neighbours being more than X% of the map span lower than the value itself, and not having three or more neighbours that have a value X% higher. - X is given by the user Points with a value in the top 5% of the map span is always kept This routine treats all numbers in an 'ABS' way - only 'ABS' statements are used to calculate whether the value falls within the above criteria.
All points deemed convex are next assigned the value of the average of the three or more points that "made" the original point convex.
This option only works well on all maps.
This option works well on all maps, but you may find that it is not possible to trucate the map between the desired limits because of a too low WHAT IF internal resolution of the map. In that case you should try to increase the resolution when reading the map by keeping a lower number of standard deviations.
Compare SMOOTH in the MASMAP menu.
The option CONVEX will loop over all points, and sets all points with a value between 1 and 99 to zero when they border at least 3 other zero points. The option got its name because it removes the points that are at a convex surface. See also the OUTER option.
This option only works well on WHAT IF generated maps, or maps scaled such that the values fall in the 0 till 100 range. Other maps will cause this option to produce strange error messages.
This will be corrected ......
This option only works well on WHAT IF generated maps, or maps scaled such that the values fall in the 0 till 100 range. Other maps will cause this option to produce strange error messages.
This will be corrected......
This option only works well on WHAT IF generated maps, or maps scaled such that the values fall in the -115 till 115 (but preferably between 0 and 100!) range. Other maps will cause this option to produce strange error messsages.
This will be corrected.
All residues within the distance wifpar(1080)/100 A are included.