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[FEATURE] - Add option for electrostatics color scale value #16

Closed nchenche closed 1 week ago

nchenche commented 6 months ago

Description

Currently, the electrostatics min/max values are automatically inferred from computed values. This prevents the visual comparison of different maps since their color scale will be different.

Solution

Add an option to set the min/max values from the command line

SuneFjermedal commented 4 months ago

Hi, with a pdb2pqr calculated .pqr file input I have values much higher than eg. 5, can I force the program to not remove everything that is above the set color max values?

nchenche commented 4 months ago

Hi Sune,

I am not sure to understand your issue.

When mapping on a proteins surface its electrostatics properties, the color scale value used in the map is automatically set from the min and max computed electrostatics values. At least that is what happens when using a pdb file, but may be something is going wrong when using the additional "--pqr" argument.

Have you tried to use the "--color-max-val" optional argument to manually set/enforce the value to be used for the electrostatics color scale?

Also, if you think something is wrong and does not work as expected, create a specific BUG report for it (this topic is actually not meant for it), describing precisely what you are doing (the command line) and what you will expect.

Regards

SuneFjermedal commented 4 months ago

Hi, The issue is because I want to display the surface potential at a specific ph (is this an option that is included in SURFMAP because I have not been able to find it) I use a --pqr with corresponding file and use the argument --color-max-val 5 so I can do this on several ph and compare, however all the values that was calculated above 5 is removed, i.e. no color at all when doing as such.

see the attachment

best regards

EEY684_electrostatics_map.pdf

nchenche commented 4 months ago

Dear Sune,

In this case, all you have to do is modifiy the value specified as "--color-max-val" so that it corresponds to the maximum OR the minimum value found among ALL the pqr files you want to compare.

Please let me know if it answered your question,

Best