Hello,
Do you really need to use phenix.map_box ?
If your goal is to make e-density figure, in principle *.ccp4 map format
contain all the informations needs by pymol. So you should be able to
open it and represent it directly.
I found a wiki for pymol which should help you here :
https://pymolwiki.org/index.php/Display_CCP4_Maps
To be honest I am not an heavy user of pymol, I do rather prefer
chimeraX especially regarding the map representation.
Just to clarify, when you said "misaligned" it's a small error, like the
molecules is slightly of, or it's more like you have a density box which
has another origin than the model you want to see in ? If it's this, you
may have miss an option in the phenix.map_box, I know that for
phenix.maps, it's there is a syntax which "ask" to have the maps
calculated using the pdb as reference.
Hope this help,
Nicolas
On 22/07/2024 20:28, Aline Dias da Purifica ção wrote:
Hi everyone,
I’m having trouble aligning a map generated by PanDDA (event map) with its
corresponding PDB file in PyMOL. The map is in `native.ccp4` format and it
loads correctly in Coot, aligning perfectly with the PDB. However, when I load
the same files in PyMOL, the map appears misaligned with the structure.
### What I've Tried:
1. **Loading in Coot:** The map and PDB align correctly in Coot.
2. **Using `phenix.map_box`:**
```bash
phenix.map_box map_file=Entry-A12A-event_1_1-BDC_0.24_map.native.ccp4
pdb_file=Entry-A12A.pdb
```
This generates a new map, but it still appears misaligned in PyMOL.
Has anyone faced similar issues with PanDDA maps in PyMOL? Any suggestions for
ensuring the map aligns correctly in PyMOL?
Any help or suggestions would be greatly appreciated, as I need charming
figures for publication.
Thank you a lot!
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--
Nicolas Foos PhD - ARISE fellow
https://orcid.org/0000-0003-2331-8399
EMBL Grenoble, McCarthy Team
71 av. des Martyrs,
38000 Grenoble FRANCE
+33 4 57 42 84 67
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