Hello
Sure, here is the header info from mapdump:
-----------------------------------------------------
Logical Name: MAPIN Filename:
Entry-A12A-event_1_1-BDC_0.24_map.native.ccp4
File name for input map file on unit 3 :
Entry-A12A-event_1_1-BDC_0.24_map.native.ccp4
file size 32401024 ; logical name MAPIN
Number of columns, rows, sections ............... 250 180 180
Map mode ........................................ 2
Start and stop points on columns, rows, sections 0 249 0
179 0 179
Grid sampling on x, y, z ........................ 180 180 250
Cell dimensions ................................. 89.7790
89.7790 122.8390 90.0000 90.0000 120.0000
Fast, medium, slow axes ......................... Z Y X
Minimum density ................................. -1.41814
Maximum density ................................. 2.22625
Mean density .................................... -0.02193
Rms deviation from mean density ................. 0.27754
Space-group ..................................... 154
Number of titles ................................ 1
Labels:
Map from pandda
Title from map: Map from pandda
Number of sections 180
Fast, medium, slow axes 3 2 1
Sampling intervals on xyz 180 180 250
-----------------------------------------------------
Best regards,
Aline
On Tue, Jul 23, 2024 at 12:17 PM Jon Cooper <jon.b.coo...@protonmail.com>
wrote:
> It would be interesting (to me anyway) if you could run mapdump and post
> *just* the header info.
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>
> -------- Original Message --------
> On 22/07/2024 19:28, Aline Dias da Purificação <
> 0000d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> 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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