Hi Nigel
Thanks for this information. To be more specific. If the ribosome contains
many modified bases then I have to generate restraints for each of these
ligands separately and add them one by one using the Real Space Refinement
Add file menu along with the map and the whole 40S coordinates and run it.
Am I right ? Is there anyway If the protein contains multiple ligands and
you want to generate for all in a single output file as it does in refmac,
in that case a single cif file should work for all. I saw one option here
but it says it is generally not preferred to generate restraints for
multiple ligands from the pdb.
My second question is regarding Elbow which is how to use it in its best
possible way, particularly for determining the final geometry of the
ligand. For example the tool suggests that one can *Use simple optimization*,
or *Optimize using elbow AM1 QM method*, or *Optimize using 3rd party QM
package*, or *Provide final geometry from file.*
What do you think? What to use for a general restraint generation for a
ligand from an already known structure.
I am new to Phenix, would appreciate it if you please share with me a
general workflow for using eLBOW and how to use it during refinement.
Best
Firdous
On Wed, Jun 16, 2021 at 1:19 AM Nigel Moriarty
Firdous
You need to generate restraints for the missing entities. You can use eLBOW.
https://www.youtube.com/watch?v=8qVYTUVKlbQ
and I can help you.
Cheers
Nigel
--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464
On Tue, Jun 15, 2021 at 11:14 AM Firdous Tarique < [email protected]> wrote:
Hi
I am trying to do real space refinement of a 40S rigid body docked model in a cryoEM map of 4.8 Angstrom resolution. The PDB contains some modified nucleic acid bases due to which the program ends with the following error.
Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols; 52 Please edit the model file to resolve the problems and /or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary.
Seems its refinement library is not able to read the modified bases. Can you please advise how to fix this problem. What is the best way to update the library ? Any suggestions are highly appreciated.
Best
Firdous _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]