Re: [PyMOL] Compare two structures with the same connectivity butdifferent stereochemistry?

[Jared S. <jar...@co...>]

Hi Peng - 

You probably want to use `pair_fit` here, to align on a conserved core of atom pairs between the two models.  However, two complicating issues here are 1) equivalent atoms are not listed in the same order in the .mol2 files, and 2) they don't have atom names, which makes selecting them difficult.

To get around this within PyMOL, you can perform atom selection with atom IDs.  You can view the atom IDs for a selection with the command `label <selection>, ID`, and then use `pair_fit` to align atom pairs from the two molecules.

If you save the following code block as a PyMOL script called e.g. "align_mol2.pml" in the same directory as your .mol2 files, launch PyMOL from that directory (or "File > Working Directory > Change" into it), then run the command `@align_mol2.pml` at the PyMOL command line, it should do the trick.  You can choose different atom pairs to align, just be sure to list them in the right order.

```
load MOL002088.mol2, m2088
load MOL002424.mol2, m2424

hide everything, elem H
label visible, ID

python

# Alternate collected atom IDs between models
models = ['MOL002088', 'MOL002424']

# Gather atom IDs from the conserved core
atom_ids = [
    # 5-membered ring
    20, 13,
    19, 12,
    8, 8,
    3, 7,
    9, 14,
    # adjoining 6-membered ring
    29, 42,
    26, 43,
    18, 9,
]

# Combine model names and atom IDs into tuples
from itertools import cycle
zipped_atoms = zip(cycle(models), atom_ids)

# Create a string from each tuple in the zipped atoms list
atoms_str = [f'{x[0]} and id {x[1]}' for x in zipped_atoms]

# Align the atom pai
cmd.pair_fit(*atoms_str)

python end

```

One further note: your molecule 2424 has quite a few chemically unrealistic bond lengths and angles, so I urge you to interpret these models with caution.

Hope that helps.

Cheers,
Jared



From: Peng Yu <pen...@gm...>
Reply: Peng Yu <pen...@gm...>
Date: March 25, 2020 at 10:52:00 AM
To: sujiaqi <su...@im...>
Cc: pymol-users <pym...@li...>
Subject:  Re: [PyMOL] Compare two structures with the same connectivity butdifferent stereochemistry?  

It still very hard to see the differences and similarities. They just
look like a mess. Is there a good way to reveal the differences and
similarities? Are the stereochemistry of all the carbons different? It
seems that the best way is just to show the different ones.

On 3/24/20, sujiaqi <su...@im...> wrote:
> You can just input this command to deal with the problem.
>
> PyMOL>align MOL002088, MOL002424
> Match: read scoring matrix.
> Match: assigning 1 x 1 pairwise scores.
> MatchAlign: aligning residues (1 vs 1)...
> MatchAlign: score 5.000
> ExecutiveAlign: 93 atoms aligned.
> ExecutiveRMS: 2 atoms rejected during cycle 1 (RMSD=5.48).
> Executive: RMSD = 5.238 (91 to 91 atoms)
>
> From: Peng Yu
> Sent: 2020年3月25日 6:28
> To: pym...@li...
> Subject: [PyMOL] Compare two structures with the same connectivity
> butdifferent stereochemistry?
>
> I'd like to compare the difference between the two structures which
> have the same connectivity but different stereochemistry. Could
> anybody show me if there is a way to do so in pymol? Thanks.
>
> http://tcmspw.com/tcmspmol/MOL002088.mol2
> http://tcmspw.com/tcmspmol/MOL002424.mol2
>
> --
> Regards,
> Peng
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>


--  
Regards,
Peng


_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe