On 07/04/2021 07:46, Hari shankar wrote:
I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit
maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D
space around it. I have tried phenix for this purpose but get this error message consistently.
"Fatal problems interpreting model file: no of atoms with unknown nonbonded energy type symbols: 15 Please
edit the model file to resolve the problems and/of supply a CIF file with matching restraint definitions,
along with apply_cif_modification and apply_cif_link parameter definitions if necessary."
This error occurs despite supplying the CIF file for the ligand. I have tried to remake the CIF/PDB files
from SMILES strings, by drawing the molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset
go). Nothing seems to work.
1. Is there something I have missed out that can solve this issue?
2. Is there a program in CCP4i that can be used to generate the required omit
maps?
3. In general, how do I omit 3.5 ang of the space around the ligand during this
map calculations?
Let's imagine that you'd like to use refmac.
1: By drawing the ligand [1] or by other means, create a mmCIF restraints file
2: Using Coot or other means, fit the ligand (it doesn't need to be exact) and
add the ligand to the protein
3: Refine a couple of cycles with refmac (to test that it comprehends the
ligand)
4: If fine, calculate SFs with refmac (0 cycles) excluding the ligand and other
residues that you desire
using keywords: refinement exclude all from A 1001 to A 1 10001 # for example
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html
Paul
[1] Lidia is part of Coot for the record
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