Unexpected behavior of CRYSOL

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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mattia.b
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Joined: 2019.05.08 11:27

Unexpected behavior of CRYSOL

#1 Post by mattia.b » 2019.05.08 14:26

Hi all,
I have been using CRYSOL for a while now, and I have a couple doubts that I would like to discuss.

1. First of all, I recently noticed an unexpected behavior of CRYSOL. As far as I understood, the program is strongly dependent on the input pdb formatting and uses the atom names therein to understand which type of atoms (= chemical elements) are in the system, and thus compute the scattering profile from them: for instance, C4’ and C5 of a cytosine will both be interpreted as Carbons.
By chance, I had some atom names changed to the corresponding chemical element in the input pdb file (i.e. both C4’ and C5 to simply C, while the residue names were maintained), and noticed that, unsurprisingly, the atoms were still correctly recognized, as demonstrated by the “Number of ” line in the log file that was correct for each chemical element present in the input pdb. However, the spectrum obtained was different. I played around a bit with this thing of the atom names, changed just some of them and checked the output spectrum. Curiously, changing some of them changes the resulting spectrum, while changing some others it does not; for instance, replacing “O5’” with “O “ (and maintaining the correct formatting) does not change the result, while it does if I replace “O2 “ with “O “. Is this an expected behavior or am I missing something?

2. In order to compute SAXS spectra, waters are stripped away by CRYSOL, as the solvent is treated implicitly. Contrarily, all the ions in the system, that is both those close/complexed with the solute, which is an RNA in my case, and those far away in the bulk, will be instead kept in place and used in the scattering profile computation. Is that going to be correctly interpreted by the program? Or should I only keep those ions that are in close vicinity to the RNA?


Thanks a lot in advance to anyone that might clarify these points,

All the best,

Mattia

SaxsMax
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Joined: 2007.08.03 19:16

Re: Unexpected behavior of CRYSOL

#2 Post by SaxsMax » 2019.05.13 09:59

1. Crysol not only evaluates the element, but rather an atomic group,
e.g. C, CH, CH2, CH3. For this the complete atomic name is needed.

2. Only the ions that are in close vicinity to the RNA should be kept

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