Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 1 October 2016 at 20:14, Mahdi, Sam  wrote:
> Hi Edward,
>
> Oh ok. Thank you for your help, I was able to resolve the problems I had
> with both proteins, and now they are both running. Since there is symmetry
> within the dimer, both chain A and chain B will give me the same S^2 results
> correct?

Hi Sam,

That depends.  If you superimpose A and B and have an RMSD of
0.0, then the S2 values will be identical.  But if
the docking software changed the monomer structures slightly so the
RMSD is not exactly zero, then the S2 values will be slightly
different for some residues.  You can use relax to superimpose
structures and determine the RMSD to very high precision, if you like,
but I'll leave that to you as a learning exercise ;)

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

Oh ok. Thank you for your help, I was able to resolve the problems I had
with both proteins, and now they are both running. Since there is symmetry
within the dimer, both chain A and chain B will give me the same S^2
results correct?

Sincerely,
Sam

On Sat, Oct 1, 2016 at 2:21 AM, Edward d'Auvergne 
wrote:

> On 30 September 2016 at 23:42, Mahdi, Sam 
> wrote:
> > Hi Edward,
> >
> > So when I ran it as read_mol=0, it gave me the same error. But it worked
> > once I changed it to read_mol=1. I thought mol=0 was for set A and mol=1
> was
> > for set B?
>
> Sorry, I just remembered that the molecule numbering starts from 1.
> So read_mol=1 gives chain ID A and read_mol=2 gives chain ID B.  I
> should add a check for this argument.
>
> Regards,
>
> Edward
>
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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 30 September 2016 at 23:42, Mahdi, Sam  wrote:
> Hi Edward,
>
> So when I ran it as read_mol=0, it gave me the same error. But it worked
> once I changed it to read_mol=1. I thought mol=0 was for set A and mol=1 was
> for set B?

Sorry, I just remembered that the molecule numbering starts from 1.
So read_mol=1 gives chain ID A and read_mol=2 gives chain ID B.  I
should add a check for this argument.

Regards,

Edward

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