SASREF set up

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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kpeter30
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Joined: 2015.08.13 17:20

SASREF set up

#1 Post by kpeter30 » 2015.08.13 18:05

I have SAXS data for my apo protein, as well as my protein bound to two different RNAs (X and Y). I have crystal structures of the individual components (protein, X and Y) but not the complexes. I would like to model the complexes using SASREF and then generate a theoretical SAXS curve to compare to my experimental data. I have a few questions:

1. CRYSOL
I know that I need to run CRYSOL to generate .alm files to input into SASREF, but I do not know if I should be running CRYSOL on the individual component's pdbs or if I should merge the pdbs to make a hypothetical complex and then run CRYSOL on the merged pdb.


2. SASREF
Once the .alm files are generated, where do I upload them in the SASREF 6 online program?

Here is what I have tried:

Step 1 of 3:
experimental data: SAXS, x-ray only (standard)
number of curves: 1
number of subunits: 2
overall symmetry: P1 ( I left this as P1 because I do not know the symmetry of the complex since the complex has not been crystallized)

Step 2 of 3:

Curve: (I uploaded the experimental .dat file for the complex that I used in CRYSOL)

Subunit 1: pdb for protein (from the crysol output files)
Subunit 2: pdb for X (or Y) (from the crysol output files)

(everything else I left as default)

Step 3 of 3

I left these values as zero.


I ran the program, and it seems to have worked, but I don't know if I ran the program correctly, since I never input any .alm files.

Thanks in advance for any help or suggestions!

ckerr
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Posts: 86
Joined: 2015.03.25 09:03
Location: EMBL Hamburg

Re: SASREF set up

#2 Post by ckerr » 2015.08.19 08:36

1. To get the .alm files you run crysol on the individual PDBs

2. SASREF online is actually sasrefcv / sasrefmx, which do not require the user to supply .alm files.

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