[phenixbb] Fitting ligand using coot

Nathaniel Echols nechols at lbl.gov
Sun Mar 31 10:18:04 PDT 2013


PS. For this particular problem, we can generate fake data for
testing, so only the PDB/CIF/parameter files are really essential.

On Sun, Mar 31, 2013 at 10:17 AM, Nathaniel Echols <nechols at lbl.gov> wrote:
> 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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