[phenixbb] Fitting ligand using coot

Nathaniel Echols nechols at lbl.gov
Sun Mar 31 10:17:27 PDT 2013


It's really hard to answer questions like these without seeing the
actual molecules.  Could you please send us the input files off-list?
Usually there is a straightforward explanation (which could be "it's a
bug"), but until we can reproduce the problem we're just guessing
blindly.

thanks,
Nat

On Sun, Mar 31, 2013 at 10:09 AM, Bishwa Subedi <bsubedi at btk.fi> wrote:
> Hi all,
>
> The bigger problem is with the refinement even after fitting the ligand. As
> suggested I have figured out with fitting the ligand. I performed real space
> refinement to the ligand and it fits well. I used the merge function in coot
> to merge ligands with molecules (I have two molecules in asymmetric unit ).
> Now the problem is with the phenix.refine. The CIF file is not accepted.
> Since the restraint file from eLBOW is not accepted during phenix.refine I
> also tried ReadySet. I used the updated pdb file and restraint files
> obtained from ReadySet. But still there is Phenix error:
> Fatal probelms interpreting model file:
> Number of atoms with unknown nonbonded energy type symbols:10
> Please edit the model files to resolve the problems and/or supply a cif file
> with matching restraint defination along with apply_cif_modification and
> apply_cif_link parameter definations.............. (which CIF file does it
> expect?)
>
> I also tried guided ligand replacement in phenix. It works with
> phenix.refine but while rebuilding in coot the real space refinement for
> ligand does not work. It complains that refinement did not start because it
> failed to match the different atom names to the dictionary that could cause
> exploding atoms.
>
> How do i get rid of this. I am graphical user and have no strong command on
> command lines.
>
> Could you please give me specific helps.
>
> Best regards,
>
> Bishwa
>
>
>
>
> On Mar 31, 2013, at 12:13 AM, Nathaniel Echols wrote:
>
> On Sat, Mar 30, 2013 at 3:07 PM, Bishwa Subedi <bsubedi at btk.fi> wrote:
>
> No LigandFit does not crash but when I try phenix.refine directly from the
>
> summary it does not succeed. I added the mtz file to run refinement but it
>
> gives some error message and submits bug report.
>
>
> What is the error message you get?  I don't see any bug reports for
> phenix.refine from you.
>
> -Nat
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