Pcs / tensor residues

HADDOCK
1

Hi,
Still fiddling with pcs data in Haddock…
I have 2 questions:

#1 Is there a way to have haddock/cns write out it’s predicted PCS values from the structure, or make a list of pcs-restraints and violations?

#2. I noticed that sometimes the chirality of the tensor residues (XAN) is inverted in the docked structures. This is not a problem with the PCS calculations, which should not be affected, but when distance restraints to the X,Y, Z atoms are used to keep the tensor in a specific orientation this can screw up the location/orientation of the tensor.
I tried to add an improper but I’m not sure which files are used in the setup of the tensor residues There’s tensor_par.psf par_axis.pro top_axis.pro? Do all need change? Would all need change?

Any tips?

Thanks,
Eiso

2

Hi Eiso,

#1 Is there a way to have haddock/cns write out it’s predicted PCS values from the structure, or make a list of pcs-restraints and violations?

If you set runana=“cluster”`` in run.cns, a pcs.dispfile should be created in the analysis dir. And the violated ones should be present inprint_xpcs.out`
You can probably write a nice awk script to extract the information as you did actually for the distance violations… (we still use your good old script!)

#2. I noticed that sometimes the chirality of the tensor residues (XAN) is inverted in the docked structures. This is not a problem with the PCS calculations, which should not be affected, but when distance restraints to the X,Y, Z atoms are used to keep the tensor in a specific orientation this can screw up the location/orientation of the tensor.

For PCS, the tensor used is XAN.
It is defined in [top_axis.top](http://top_axis.top) and the parameters in [par_axis.top](http://par_axis.top) (thinking of it this one should rather be named par_axis.param …)

If you get it to work, let me know, worth adding it to the main distribution.

Cheers
Alexandre

3

Hi Alex,

runana was already set to “cluster”, but I see none of the files that you mention ? maybe the analysis is not starting?

Adding the improper to keep the XAN chirality seems to have worked - but I used the .psf and par_axis.pro file. Will send you the files later.

Eiso

4

Should be set to “full”

Adding the improper to keep the XAN chirality seems to have worked - but I used the .psf and par_axis.pro file. Will send you the files later.

Great

5

Hi Alex,

I’ve added impropers for the chirality of tensor to
par_axis.pro top_axis.pro and tensor_para.psf

IMPROPER XX YY OO ZZ 500.0 0 90.0

With only the changes in par_axis.pro and top_axis.pro I still get inverted/distorted tensors in it/water.
With the changes in par_axis.pro and tensor_para.psf I still get distorted tensors in 1/200 it1/water structures in my test, with all 3 files changed none (granted that could be coincidence)

It’s not clear to me how these files are actually used so I’m not sure if the change in .top file is needed, but I guess it can’t hurt.

Shall I email the files to you or is there a place to drop them ?

Eiso

6

On 2nd check, it turns out that using there’s also 1 distorted tensor if all 3 files are changed. in fact, leaving out the improper in the top_axis.pro yields exactly the same results. (pdb files etc)

E

7

Please email them