Hello,
I'm trying to recolour the B factors in a pymol file with chemical shift
differences (from NMR data). There's a nice script here for this
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ (data2bfactor.py) and
also a simpler one here
Hi Mark,
In that data2bfactor.py script (which I wrote) you need to provide the
molecular object name, not a file name. In other words in your example you
should load the 1d3z.pdb file as an object (defaults to 1d3z as object name).
Then after using the run command to load the script into
Thank you, that certainly brought the chains together, but sill no completed cartoon even after a rebuild.Attached is chain F, can you see anything wrong with this file that won’t let it display a complete chain? It must be with how I joined the missing atoms?I also notice that every time I open
Hi Adam -
The characters between the object names and the chain IDs are the segment IDs.
You can remove them by setting them to the empty string using `alter`:
alter all, segi=""
Hope that helps.
Cheers,
Jared
On March 22, 2019 at 12:14:46 PM, h. adam steinberg
Hi Adam,
The atom naming is nonstandard. If you fix that, the cartoon will be complete.
alter name P01, name="P"
alter name O01, name="O5'"
alter name O02, name="OP1"
alter name O03, name="OP2"
unbond name OP1, name O3'+O5'
unbond name OP2, name O3'+O5'
PyMOL doesn't yet write bonds to mmCIF
Thank you.
Interestingly…
These alter commands do work on the DNA in my original working .pse file, the
file that contains all of the structures.
They do work on the “save molecule” as a cif file that I shared with you, if I
open it into PyMOL by itself.
They also work if I open the chain F.cif
