[PyMOL] Pymol-Alignment Module

[Ecem Güngör]

Dear Pymol community,

I have a question about alignment module of Pymol. I have two different pdb
ids and each have about 100 amino acid long. I would like to align the
specific parts of these proteins and see both how the rest of the proteins
and also these specific parts superimpose with each other. In other words,
if I align the proteins based on their 20-30 amino acids, I would like to
first see what the RMSD is for these specific regions (20-30 aa) and then
the RMSD of the rest (1-20 and 30-100) is. I truly appreciate your
suggestions and guidance on this. Thank you!

Have a great week/weekend,
Ecem
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[PyMOL] saving info regarding protein-ligand interactions in the log

[Enrico Martinez]

Dear Pymol users!
I am using a multi-model pdb containing the 80 predicted docking
solutions as well as the receptor (the both presented in each frame).
I need to calculate all hydrogen bonds (and possible other
interactions) observed in each frame (=docking solution)? I've already
used pymol for the visualizations of the interactions, and find it
very useful for the visual inspection. May I use some pymol script in
order that I could save the information regarding the observed
interactions in the log file?
Many thanks in advance
Cheers,
Enrico


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Re: [PyMOL] Pymol-Alignment Module

[Jared Sampson]

Hi Ecem -

If I understand correctly, you first want to align on one set of residues
and calculate their RMSD, then to calculate the RMSD for the remaining
residues without moving the structures.  This is straightforward using
PyMOL's internal command line.

```
# Create two selections called "sel1" and "sel2"
select sel1, resi 1-20
select sel2, resi 30-100

# Note: if the numbering is different between the structures, you may need
something like this instead:
# select sel1, (struc1 and resi 1-20) or (struc2 and resi 2-21)

# Superimpose the structures (this prints the RMSD to the console)
super struc1 and sel1, struc2 and sel1

# Calculate the "in-place" RMSD for the remaining residues (also printed to
the console)
rms_cur struc1 and sel2, struc2 and sel2
```

Note that if there are any residues with alternate conformations, or if the
numbering is different between the two structures, the `rms_cur` step may
need to be modified as indicated in the examples on its wiki page
.

Hope that helps.

Cheers,
Jared


On Fri, Mar 4, 2022 at 5:37 AM Ecem Güngör  wrote:

> Dear Pymol community,
>
> I have a question about alignment module of Pymol. I have two different
> pdb ids and each have about 100 amino acid long. I would like to align the
> specific parts of these proteins and see both how the rest of the proteins
> and also these specific parts superimpose with each other. In other words,
> if I align the proteins based on their 20-30 amino acids, I would like to
> first see what the RMSD is for these specific regions (20-30 aa) and then
> the RMSD of the rest (1-20 and 30-100) is. I truly appreciate your
> suggestions and guidance on this. Thank you!
>
> Have a great week/weekend,
> Ecem
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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[PyMOL] Query about inserting ligand at preferred base pairs of DNA

[Sneha Kandapal]

Hello Team,

I need help in inserting ligand to base pair in DNA. I have a drug molecule and 
want to insert in between the base pairs I am interested in ( it is 12-mer 
dsDNA). I tried to follow the tutorials but cannot find something where I can 
insert ligand into the custom DNA sequence I have generated.

I will appreciate if you can please help me or guide me where I can study and 
understand how to do it.

Thank you,
Sneha
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