SVDPLOT, POLYSAS, PRIMUS_SVD

Interactive and automated data processing and analysis tools: PRIMUS, CHROMIXS, GNOM, AUTORG, DATCMP, DATOP etc.
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Heidos95
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Posts: 2
Joined: 2021.06.29 06:44

SVDPLOT, POLYSAS, PRIMUS_SVD

#1 Post by Heidos95 » 2021.11.22 08:56

Dear All,

I'm trying to run mixture analysis on my protein concentration series - I'm fairly certain I'm seeing a dimer-tetramer transition. I've tried OLIGOMER but it hasn't been that fruitful.

I'd like to try and use POLYSAS or SVDPLOT to attempt some mixture analysis.

Does SVD calculate a ratio of components? Or just estimate how many components are in your solution?

Is POLYSAS still a running app or has it been retired?

Best regards,

Heidar

konarev
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Posts: 56
Joined: 2007.09.14 15:38

Re: SVDPLOT, POLYSAS, PRIMUS_SVD

#2 Post by konarev » 2021.11.22 10:34

Hi Heidar,

SVDPLOT estimates the number of components.
The volume fractions of the components can be estimated by OLIGOMER (if you have PDB models of dimers/tetramers) or
MIXTURE (if their shape can be approximated by simple geometrical bodies, like spheres or cylinders).
One can run the programs in a command-line mode or via POLYSAS (Windows) / PRIMUS(Qt) (cross-platform) menus.
POLYSAS will be available in ATSAS (Windows) if one checks the box 'Legacy applications' during ATSAS installation.

Best regards,
Petr

Heidos95
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Posts: 2
Joined: 2021.06.29 06:44

Re: SVDPLOT, POLYSAS, PRIMUS_SVD

#3 Post by Heidos95 » 2021.11.23 05:55

Hi Konarev,

Thanks for the response - I've managed to load the data into POLYSAS.

The eigenvector/values calculations seem to go ahead. However, the program then reports some " _U_.dat " file is missing from my directory.

SASPLOT automatically opens up and asks me to open a file. If I open say my highest concentration experiment file I end up with 2 curves? one of which is just horizontal at Y = 0 and the other looks like my experimental data on an absolute scale.

Running SVD in PRIMUS 3 seems to not work either I'm not sure why.

Does this mean my data isn't suitable for SVD? Do you know if there are any tools that can explain how it works in PRIMUS?

Best regards,

konarev
Administrator
Posts: 56
Joined: 2007.09.14 15:38

Re: SVDPLOT, POLYSAS, PRIMUS_SVD

#4 Post by konarev » 2021.11.23 09:34

For SVD one needs to load into POLYSAS not a single curve but multiple concentration data set (at least 3 curves or more).
For a single curve, SVD is not applicable.

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