Re: [PyMOL] PyMol: incomplete replacement of b- and q-factors

[Thomas H. <tho...@sc...>]

Hi Joe,

There can be atoms without coordinates. In particular, when loading mmCIF files, PyMOL fills in dummy-CA atoms for missing residues, to provide a complete sequence display in the sequence viewer.

"alter" iterates over all atoms, including those without coordinates. "iterate_state" only includes those *with* coordinates.

Your issue can be handled in several ways:

1) Make a selection on the atoms with coordinates in state 1:
   select mysele, state 1, enable=0
   alter mysele, b = next(di)
   spectrum b, selection=mysele

2) Or just remove atoms which don't have coordinates in state 1:
   remove not state 1
   alter all, b = next(di)
   spectrum b

See "Coordinates" section here:
https://pymolwiki.org/index.php/Selection_Algebra

Cheers,
  Thomas

> On Sep 12, 2019, at 6:09 PM, Heffron, Joseph <jos...@ma...> wrote:
> 
> Hello all, 
> 
> I am trying to color several proteins by different factors, e.g., distance from a given point (here the origin). To do this, I replace the q-factor (or b-factor) with my variable of choice. However, most of my files have one or a few residues that are for some reason not affected by the alter_state (e.g., pdb = 1ihm). I can't see any distinction in these residues compared to the others.  
> 
> example code: 
> 
>     fetch 1ihm
>     alldist = []
>     iterate_state 1, all, alldist.append((x**2+y**2+z**2)**0.5)
>     di = iter(alldist)
>     alter all, b = next(di)
>     spectrum b
> 
> Thank you, 
> Joe 
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.