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Obtaining Profiles With Explicit Waters

Posted: 2017.06.01 07:24
by pmanninghall
For example:
I submitted two files to crysol, one file with a DNA molecule that is run as is. Another molecule which is the same DNA molecule but includes water in that PDB file. It appears that CRYSOL delets sed water before calculating the curves as all four output curves in the PDB with water and the PDB without water are identical. My goal is to obtain the scattering profile of added ions and added waters. The ions which i added to the PDB files do change the scattering curves but the waters do not. I am wondering how to make crysol consider those as regular atoms such that they show up in the in vacuo plots.
here is an example of a formatted water molecule the last two columns are charge and radius respectively since this is derived from a pqr file.
HETATM 6145 O WAT 1521 -10.505 -10.129 -32.251 -0.8340 1.6612
HETATM 6146 H1 WAT 1521 -10.330 -10.815 -32.895 0.4170 0.0000
HETATM 6147 H2 WAT 1521 -11.203 -9.604 -32.643 0.4170 0.0000
Porter Hall

Crysol Discards waters

Posted: 2017.06.10 20:22
by pmanninghall

I have PDB files where I have added waters myself. Unfortunately, CRYSOL discards the waters that I add before calculating the SAXS profiles and says so in the output. Looking through the options, there doesn't appear to be one that does not discard the waters I've added. How do I keep them?

Thank you,

Re: Obtaining Profiles With Explicit Waters

Posted: 2017.06.19 12:47
by SaxsMax
One can change "WAT" to "H2O" for example and then use "-eh" and "-dro=0" keywords in the command line