[phenixbb] Phenix elbow taxol

[Ahmad Khalifa]

Thanks a lot Nigel. I can generate the restraint file using chemical
component TA1 and SDF file. However, after doing some testing, the input
ligand should have the same coordinates as in my PDB, otherwise real space
refienemnt complains by saying "unknown nonbonded energy type symbols",
which I'm guessing doesn't match the restraint file to my ligand.

I tried running elbow on the REattached pdb, I couldn't generate the
restraint file (Error: Sorry: Unable to determine the bonding):

[labusr at luxor bin]$ phenix.elbow taxol.pdb
 ------------------------------------------------------------------------------
  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.14-3260 None
    - Nigel W. Moriarty (NWMoriarty at LBL.Gov)
 ------------------------------------------------------------------------------

 Random number seed:  3628800
 Initial processing time : 0.00 seconds
 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing
Parsing P

Input format is PDB

MoleculeClass :  C:43  N: 1  O:14 (PDB format)
58 atoms
63 bonds
0 angles
0 dihedrals
0 rings
0 chirals
 Predicted memory usage by semi-empirical method : 78Mb
 Timing estimates
     Python portion         / ATP : 275%
     c++ optimisation cycle / ATP : 817%
 0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise
Bondise B

    Failed to determine the bonding of a fragment of the molecule.

    PDB file elbow.taxol_pdb.001.pdb written.
    Bonding file elbow.taxol_pdb.001.bonding.py written.

    Edit bonding file to reflect the desired bond.



    ALTERNATIVELY

    Re-run eLBOW with the --reel option and the molecule wil be loaded
    into REEL.  Edit the bonds and save the results as "fixed.cif" to
    allow eLBOW to load the bonding.

    You can also use a pull-down menu to push to eLBOW.

Sorry: Unable to determine the bonding

I tried to superimpose the SDF to my structure but I think there are some
differences in the structure, and number of atoms so the superimposition
didn't work. i would appreciate if soemone can help me generate restraint
of the attached PDB.

On Mon, Apr 1, 2019 at 12:35 PM Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Ahmed
>
> Taxol is quite tricky so using the chemical components option is a choice
> that provides more information than the SMILES.
>
> phenix.elbow --chemical_components=TA1
>
> I have attached the files.
>
> 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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
>
> On Sun, Mar 31, 2019 at 2:12 AM <r.joosten at nki.nl> wrote:
>
>> Before you make restraints yourself, check whether it is already in the
>> dictionary. The name should be TA1 (
>> http://ligand-expo.rcsb.org/reports/T/TA1/index.html).
>>
>> Cheers,
>> Robbie
>>
>> On 31 Mar 2019 10:45, Georg Mlynek <georg.mlynek at univie.ac.at> wrote:
>>
>> Dear Ahmad, one way is to use the smiles string. If taxol if also named
>> Paclitaxel then here it is:
>>
>>
>> https://pubchem.ncbi.nlm.nih.gov/compound/paclitaxel#section=Canonical-SMILES
>>
>> Then just watch this video on phenix.elbow
>>
>> https://www.youtube.com/watch?v=8qVYTUVKlbQ
>>
>> Br, Georg.
>>
>>
>> On 31.03.19 08:08, Ahmad Khalifa wrote:
>> How can I generate restraint files for taxol?
>>
>> I attached my taxol.pdb for reference.
>>
>> Thanks.
>>
>>
>>
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