Thanks Warren,
However, in my case, I don't want to cycle through distances between the same
two atoms but each distance object contains references to different atom pairs.
To be more specific, I have a set of ten different protein-ligand interaction
types, represented by distance measurements
Dear All,
Thanks to everyone who replied to my query about extracting an amino
acid sequence from a PDB file!
Here is a summary of responses of my query;
1. Use SwissPDBViewer
2. Use Pymol 1.2
load $TUT/1hpv.pdb
save 1hpv.fasta
# or by selection
save 1hpv_A.fasta, chain A
3. With Phenix
Buz Barstow wrote:
> Thanks to everyone who replied to my query about extracting an amino
> acid sequence from a PDB file!
>
> Here is a summary of responses of my query;
>
> 1. Use SwissPDBViewer
...
> 6. Use PDBSET (part of CCP4)
t_coffee comes with s perl script "unpack_extract_from_pdb".
Hello,
I am trying to modify dihedral angles of a polymer chain. Once I
perform all the required steps, I am able to orient the chain and
align the chain along the same axis as the original chain. But
unfortunately, pymol moves the chain to a different position.
Basically, it changes the coordinat
Vivek,
Create a copy of the original chain, modify the chain, and fit the copy to the
original. For example
# PyMOL 1.2 .pml input
fab AAA, orig
create copy, orig
set_dihedral orig///3/C, orig///4/N, orig///4/CA, orig///4/C, 180
unpick
fit origCA, copyCA
Cheers,
Warren
