On 23/07/2024 15:12, Aline Dias da Purificacao wrote
--
Hello
Thank you for your response.
You’re right, I shouldn’t need to use |phenix.map_box|. I tried it as
an attempt to make the map cover the selected region since the map’s
origin does not cover the protein properly. The issue is that in
PyMOL, the map appears misaligned, meaning that the density box has
another origin than the model, and it doesn't align with the
asymmetric unit of the protein. In Coot, however, the map loads and
aligns perfectly with the PDB.
Here is an image showing how the event map looks in Coot (properly
aligned):
And here is an image showing how the map looks in PyMOL, following the
instructions on 'displaying CCP4 maps':
And this is how it looks like when I try to 'force' to cover the
protein, selecting all the protein as 'sele' and setting:
PyMOL>isomesh map2, Entry-A12A-event_1_1-BDC_0.24_map.native, 1, sele.
I haven’t yet used ChimeraX, but I am open to trying it if it helps
with map representation
It seems to me that your putting in a lot of effort to not use Coot. Why
not just use Coot?
As noted recently, Coot 1.1 is quite good at graphics now, see for
example Catapano et al. (2023)
https://journals.iucr.org/d/issues/2023/12/00/qe5005/index.html
or Moorhen (moorhen.org) - that's good at graphics too.
Paul.
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