Question regarding sreflex

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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nature
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Joined: 2017.07.01 06:38

Question regarding sreflex

#1 Post by nature » 2017.07.18 19:19

Hi everyone,
I want to use the sreflex to estimate the flexibility of high-resolution crystal models using scattering curve of SAXS. My protein is a dimer. And my question is how do breakdown my pdb file to provide the constraint for the sreflex? I have tried to break one of monomer into individual alpha and beta chain files. However, the program is aborted due to clash. Here is the message that I received.

--INPUT SAXS data filename: 13_26_Apo_Merge01.dat
--INPUT PDB filename: BB.pdb,alpha1.pdb,alpha2.pdb,alpha3.pdb,alpha4.pdb,alpha5.pdb,alpha6.pdb,beta1.pdb,beta2.pdb
--INPUT PDB contains 3088 ATOM entries, of which 396 are centroids.
WARNING - Input structure contains 104 clashes.
Found 104 clashes, covering 52.5253 % of input coordinates file: BB.pdb,alpha1.pdb,alpha2.pdb,alpha3.pdb,alpha4.pdb,alpha5.pdb,alpha6.pdb,beta1.pdb,beta2.pdb
SREFLEX ERROR 288 Aborting execution, please check input coordinates.

BB: is the complete pdb model.

Can anyone what should I do to get the sreflex running?
Thank you very much,

Rosie

nature
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Joined: 2017.07.01 06:38

Re: Question regarding sreflex

#2 Post by nature » 2017.07.19 17:59

Does anyone have an example of how to divide your pdb file in separated small files to share? Thank you.

sasha
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Joined: 2014.03.05 17:56

Re: Question regarding sreflex

#3 Post by sasha » 2017.07.22 08:51

Dear Rosie,

I guess the clashes are between BB.pdb (the complete model) and the rest of the pdb files (parts of it). Do not provide the complete model (BB.pdb) to SREFLEX, just the fractions of the model.

If the protein is a dimer, I would recommend trying first with the two separated monomers (1.pdb,2.pdb) to see if a slight rearrangement can improve the fit.

There is an example of divided file provided with the ATSAS package for SREFLEX in the documentation (open1.pdb & open2.pdb, to compare to open4akeA.pdb), but the idea is just to put the different residues/atoms in different files.

I hope that helps and please let me know how things go.

Best,

sasha

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