a question about the 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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frankhaha
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Posts: 3
Joined: 2017.05.17 17:16

a question about the sreflex

#1 Post by frankhaha » 2017.10.30 07:45

Dear administrator,

Hello,this is a user of the sreflex and I research the complex about protein and DNA by sreflex.I have two questions about this soft.
1.Now I write the structure information above (DNA protein)in one and the same pdb,then usethe sreflex.(the command -sreflex -experiment.dat -complex.pdb). I'm wondering whether I can just respectively input two pdb,then use the sreflex.(the command -sreflex -experiment.dat -DNA.pdb -Protein.pdb).I find it can't work now.

2.When I use the sreflex.For the output pdb about the complex, I find the DNA will be two parts. I wonder whether can remain the DNA structure as the initial condition.

Best wishes,
Frank

sasha
Active member
Posts: 46
Joined: 2014.03.05 17:56

Re: a question about the sreflex

#2 Post by sasha » 2017.11.01 15:25

Dear Frank,

Thanks for your question.
To input different parts of the structure in different PDBs, just type as stated in the manual:
sreflex experimental.dat Dna.pdb,Protein.pdb
This syntax overrides the partitioning of the structure, so DNA and Protein will be kept intact and only moved relatively to each other.
Note: both PDB filenames are separated by a comma (no whitespace).

Alternatively, you can use the following to deactivate the RESTRAINED refinement stage (which is where the structure partition occurs).
sreflex experimental.dat complex.pdb -s RESTRAINED

This is explained in the manual as well, available at:
https://www.embl-hamburg.de/biosaxs/man ... eflex.html

Best,

sasha

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