search

3dem / model-angelo

Automatic atomic model building program for cryo-EM maps
MIT License
110 stars 18 forks source link

ModelAngelo output is the wrong or incomplet sequence #35

Open gilcantero opened 1 year ago

gilcantero commented 1 year ago

Hello, when I run the ModelAngelo command as in the guide, providing the fasta sequence, the output is only half of the sequence for the non-raw .cif or a wrong sequence but complete map occupation for the raw.cif. Why is that?

Thank you in advance, David.

jamaliki commented 1 year ago

Hi David,

Hard to say without seeing the data. Is the sequence file correct? Is the handedness of the map correct? Do you notice that the ModelAngelo output is very disjoint and doesn't seem to get the secondary structures correctly?

Best, Kiarash.

gilcantero commented 1 year ago

Hi Kiarash, the sequence is the fasta file downloaded directly from the NCBI so it should be correct. The handedness of the map is correct, checked by the helix turn direction. The secondary structure and alpha carbon is fine in the raw.cif but the sequence is not the one provided by us. We do not understand why it has mutated the aa sequence provided in the fasta. We tried the same command with another different map and protein (smaller, mine is 982 aa) and it worked well in that case.

Thank you, David.

jamaliki commented 1 year ago

Interesting, would you be willing to share your data so that I can take a look? I am not sure what is wrong other than the sequence having an issue.

Best, Kiarash.

gilcantero commented 1 year ago

We can share the data with you. However, the map is unpublished data so it should be handle appropriately. How do you want me to send the map and the sequence? The sequence is available in the NCBI database so there is no problem with it being shared here or whatever.

jamaliki commented 1 year ago

You can email me at kjamali@mrc-lmb.cam.ac.uk. Is that alright?

gilcantero commented 1 year ago

ok, I send you the map and the sequence to that email. Thank you.

gilcantero commented 1 year ago

I have sent them by wetransfer due to the file size. Thank you!