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PostPosted: 2017.09.07 08:20 
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We would like to use EOM to support some rigid body modelling we did with CORAL. We would like to use EOM to make a pool of PDBs for a molecule with two well-defined structures connected by a flexible linker (see attached cartoon of the model). Internally both of the two structures have P2 symmetry which is very well defined, and which we want to keep fixed. The overall structure does not have perfect P2 symmetry. When using EOM/Ranch we are unable to make the software generate this kind of structure. Either the program will not run, or it pulls apart the P2 symmetry of one of the well-defined structures.

Is it possible to make this kind of model using EOM?


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File comment: system we would like to model
model.png
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PostPosted: 2017.09.12 14:38 
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Okay, lets try the following. Take dimer models of PDB1 and PDB2, put them to origin (e.g. with ALPRAXIN). Split PDB1 dimer into two files each containing a monomer: 'PDB1a.pdb' and 'PDB1b.pdb'.

Let's assume the sequence of PDB1 is:
WAAAAAAAX
The sequence of PDB2 is:
YBBBBBZ
The sequence of the linker is
LLL

Let's assume the monomeric full-length sequence is
WAAAAAAAXLLLYBBBBBZ

Open 'PDB1b.pdb' in a text editor, cut the last residue (X) and paste it to the end of the file.
Open 'PDB2-dimer.pdb' in a text editor, cut the first residue (Y) of the second chain and paste it to the end of the file.

Prepare the following 'sequence.seq' file:
WAAAAAAAX
LLL
YBBBBBZ
BBBBBZY
LLL
XWAAAAAAA

Run EOM online with the following configuration:

Overall symmetry: P1
Sequence: 'sequence.seq'
Number of domains: 3
Domain 1: 'PDB1a.pdb' [monomer] [fixed]
Domain 2: 'PDB2-dimer.pdb' [monomer] [free]
Domain 3: 'PDB1b.pdb' [monomer] [fixed]

If you want to publish one of the resulting models you may want to move the residues X and Y back to where they belong in the original sequence.


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PostPosted: 2017.09.14 09:03 
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Joined: 2015.11.23 14:19
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Thank you for your time and energy! It seems to be running as it is supposed to.


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PostPosted: 2017.09.25 11:44 
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Joined: 2015.11.03 14:38
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Hi,

I thought I would be ok to continue your topic since I'm encountering a sort-of similar issue. I have a protein composed of 3 domains. We know it forms dimers in solution and we suppose it's through domain A (it is the case in proteins of the same family which we have structure from). We have SEC-SAXS data on the dimer peak.
I used this approach: get the model of the dimer domain A (from homologous protein) + model of domain B + model of domain C as separate pdb's. Use them with domain A as fixed multimer + overall P2 symmetry.

The program does run, but the Chi2 is about 43-48 (very high) and the fit (attached) looks super bad and weird. Models don't look bad but well...

A guess on why the fit is so bad and how to fix/process this?
Many thanks!


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profiles_001_1.fit [48.76 KiB]
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