CRYSOL prediction error

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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jadeshi
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CRYSOL prediction error

#1 Post by jadeshi » 2016.07.19 02:25

Hey all,
This is my first post on the forum, so nice to meet all of you! I have a quick question. I'm currently using CRYSOL to predict the scattering profile for an ensemble of conformations for the beta/alpha repeat protein CheY, which I obtained using molecular dynamics simulation. I'm wondering if there's a straightforward way to estimate the CRYSOL prediction error for the scattering intensity for each structure, since all of these structures, with the exception of the native state, do not have experimental SAXS profiles. My current thought is to compute the error between the experimental native state profile vs. the CRYSOL-simulated native state profile and apply it to all other structures, but intuitively I'm thinking CRYSOL's performance may depend significantly on what structure I'm considering, for example, folded vs. unfolded. Any tips would be greatly appreciated.

Thanks a lot!

ckerr
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Re: CRYSOL prediction error

#2 Post by ckerr » 2016.07.19 08:37

If the structure has voids, deep pockets, or extended unfolded chains, the prediction from crysol 2 will have systematic errors because of the way it calculates excluded volume (everything between the origin and the furthest atom in any given direction is considered to be excluded). Crysol 3 (the program is called crysol_30) fixes this at the cost of using more CPU time.

jadeshi
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Re: CRYSOL prediction error

#3 Post by jadeshi » 2016.07.21 02:33

Thanks, that's great to know. I think I'll definitely run into this issue because my ensemble of structures is very diverse and contains several extended random-coil-like structures. Is there a paper in literature that quantifies this error by benchmarking CRYSOL 2 against experimental data on, say, intrinsically disordered proteins?

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