export HADDOCK.tbl in XiView

[jimfeng9705]

I could not export HADDOCK.tbl file under XiView. I did use a pdb file with only one chain.

[colin-combe]

Hi, yes, this is a bit tricky, its not that clear how you make the HADDOCK export work.

I think you need to have more than one PDB file loaded for HADDOCK export - so select multiple local PDB files or have the PDB codes separated by spaces in the PDB import panel (https://xiview.org/xidocs/html/import/pdbdata.html).

Then you would need to click SHOW>INTER MODEL DISTANCES in the 3D view, then, hopefully, you can do HADDOCK export.

@grandrea - is that correct? / do you ave anything else to add about how to make this work?

cheers, Colin

[grandrea]

hello, I will expand the documentation for the .tbl export (https://xiview.org/xidocs/html/views/3dngl.html). You upload 2 pdb files, either by using 2 PDB IDs, or by uploading 2 pdbs, each with a single chain, by selecting multiple files in the upload. Because of a quirk in haddock, if you want to dock 2 multi-chain PDBs together, edit each to have a single chain ID and non-overlapping residue numbering.

Once you upload the 2 files, in the 3d view go on "show" and tick inter-model distances to export the .tbl file.

[colin-combe]

thanks andrea

[jimfeng9705]

Hello Colin,

Yes, it works!! I generated two pdb files from my AlphaFold2 file to separate the two proteins, and then imported the files into XiView.

All the best,

Jim

On 7/14/2023 12:42 AM, Colin wrote:

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[EXTERNAL]

Hi, yes, this is a bit tricky, its not that clear how you make the HADDOCK export work.

I think you need to have more than one PDB file loaded for HADDOCK export - so select multiple local PDB files or have the PDB codes separated by spaces in the PDB import panel (https://xiview.org/xidocs/html/import/pdbdata.html).

Then you would need to click SHOW>INTER MODEL DISTANCES in the 3D view, then, hopefully, you can do HADDOCK export.

@grandreahttps://github.com/grandrea - is that correct? / do you ave anything else to add about how to make this work?

cheers, Colin

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[jimfeng9705]

How to define the upper and lower limit for specific crosslinker? For example, DSBU? Is there a way to also modify the numbers within XiView? Or we have to manually edit the pairs in the tbl file.

[colin-combe]

Hi Jim,

How to define the upper and lower limit for specific crosslinker?

It looks like the values of 'restraints' in the exported HADDOCK .tbl are hardcoded into xiVIEW. There isn't a way to change them. You'll need to manually edit the exported file.

Is there a way to also modify the numbers within XiView?

assuming you mean the residue numbers in the exported file then this will be based on the numbering of residues in the PDB files you uploaded. (@grandrea - right?) There isn't really a way to change them (maybe editing the input PDB files), you'll need to edit the exported file.

[grandrea]

the .tbl file is generated with the CNS syntax of

distance, errorMinus, errorPlus.

So- the restraints are currently imposed as a CA-CA restraint between 2 and 30 angstrom (12-10 and 12+18). You can change these values (and the atom selection) to suit your crosslinker of choice in a text editor.

Regarding the residue numbering: the xiview 3d viewer automatically maps the crosslinks to the pdb residue numbering. Meaning the restraints table (and pymol session, chimerax pseudobonds) will already match the pdb you upload and plan to upload to haddock, NOT the original .fasta residue numbering. This means you can export restraints matching the renumbered pdb files you need to have for haddock.

There is no utility to renumber pdb files inside xiview (that is definitely beyond the scope of the software), but this can easily be done for example with PDB-tools https://github.com/haddocking/pdb-tools from the haddock people.

The workflow therefore is: 1) generate pdbs with whatever numbering you need to have for haddock 2) upload to xiview, export restraint table 3) edit restraint table in text editor by bulk replace and find 4) upload to haddock webserver

As an aside, DSBU has a spacer arm of 12.4 angstrom. It crosslinks lysine Nz-Nz. So it is very similar to BS3, which has a spacer of 11.4 angstrom. You can keep these CA-CA restraints, or impose them from Nz to Nz with the appropriate spacer length (I would add some slack for in solution flexibility). To impose 12.4 angstrom, the lines would then look like

assign (segid A and name NZ and resi 509) (segid B and name NZ and resi 58) 10.4 10.4  2.0