Force enantiomer creation

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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tdgrant1
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Force enantiomer creation

#1 Post by tdgrant1 » 2011.10.06 21:34

Hi all,

Does anyone know of a way to forcibly create the enantiomer of a SAXS envelope? I have a protein complex for which I have saxs envelope of both subunits and the complex. Fortunately the model is quite asymmetric so I am able to predict the placement of each subunit in the complex relatively easily (I think, but I'd like to confirm this). However it appears that the envelope of one of the isolated subunits is the mirror image of what looks to be its location in the complex. I would like to confirm this but I can't seem to create the enantiomer. I know supcomb calculates enatiomers but it doesn't seem to be popping it out for me, but I think it's due to the fact that I'm superimposing the subunit envelope to the complex envelope, and it's throwing it off. Is there a way to force the creation of the enantiomer?

Thanks,
Tom

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AL
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#2 Post by AL » 2011.10.13 15:34

tdgrant1 wrote:Does anyone know of a way to forcibly create the enantiomer of a SAXS envelope? I have a protein complex for which I have saxs envelope of both subunits and the complex.
I guess by "SAXS envelope" you mean "shape restored ab initio from SAXS data" (e.g. a DAMMIN model).
tdgrant1 wrote:I know supcomb calculates enatiomers but it doesn't seem to be popping it out for me, but I think it's due to the fact that I'm superimposing the subunit envelope to the complex envelope, and it's throwing it off.
SUPCOMB20 allows enantiomorphs by default.
In SUPCOMB13 you have to specify it:

Code: Select all

$> supcomb13 crystal-structure.pdb abinitio.pdb /e y
The result will be the rotated 'abinitior.pdb' which might be a mirror image of the original 'abinitio.pdb' if it fits 'crystal-structure.pdb' better.

tdgrant1
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#3 Post by tdgrant1 » 2011.10.13 15:52

I guess by "SAXS envelope" you mean "shape restored ab initio from SAXS data" (e.g. a DAMMIN model).
Yes, indeed.
The result will be the rotated 'abinitior.pdb' which might be a mirror image of the original 'abinitio.pdb' if it fits 'crystal-structure.pdb' better.
I am able to do that (for unrelated samples), but I guess what I'm asking is whether or not there is a way to force supcomb to do it. My problem seems to stem from the fact that 'abinitio-subunit.pdb' is not precisely the mirror image of the entire 'abinitio-complex.pdb' but only a mirror image of a part of the 'abinitio-complex.pdb', since there is another subunit present. In other words, 'abinitio-subunit.pdb' fits 'abinitio-complex.pdb' better than 'abinitio-subunit-enantiomer.pdb' but I would like to force the creation of 'abinitio-subunit-enantiomer.pdb' so I can look at it myself.

It doesn't seem to be something as simple as flip all the signs on the z-axis in the pdb for example, though if someone has a solution of that sort I would be happy to try it too.

Thanks.

andrewmalaby
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Re: Force enantiomer creation

#4 Post by andrewmalaby » 2013.12.10 18:49

I know this is an older post, but has anyone resolved this issue? Is there a way to force supcomb to project both enantiomer structures? I realize you could do this with enough modeling runs, but we are looking for a way to simply visually compare the enantiomers that are produced/searched for.

Thanks!

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Re: Force enantiomer creation

#5 Post by andrewmalaby » 2013.12.10 19:03

We might just try to use other programs to produce the end enantiomer of damfilt results.

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Re: Force enantiomer creation

#6 Post by franke » 2013.12.10 21:38

andrewmalaby wrote:We might just try to use other programs to produce the end enantiomer of damfilt results.
Do not use the damfilt model. It does, in all generality, not fit the data. Run dammin with the damstart.pdb as a search volume and use the its output file instead.

As far as I know, there is no tool to do what you ask for in ATSAS.

sasha
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Re: Force enantiomer creation

#7 Post by sasha » 2017.06.15 15:54

One can create the enantiomorph of an ab-initio model with the ALPRAXIN program from the ATSAS package:
> alpraxin dammifModel.pdb --enantiomorph=Y
As of today the option is also available at the github SASpy PyMOL plugin.

Best,

sasha

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