[phenixbb] Ligandfit bug report

Nigel Moriarty nwmoriarty at lbl.gov
Mon Jan 24 16:03:43 PST 2011


Kendall

Please send all the files directly (not the list). I believe your
first problem has been fixed recently but the second is strange.

Cheers

Nigel

On Mon, Jan 24, 2011 at 1:46 PM, Kendall Nettles <knettles at scripps.edu> wrote:
> We are generating pdb files with chemdraw3D, which turn out to not be “real”
> pdb files. PHENIX.ELBOW fixes them, but leaves some of the atom ID numbers
> blank, such as Oxygen #2, and Carbon #18:
> HETATM   17  C16 LIG     1     -83.510  -0.856   0.582  1.00 20.00
>           C
> HETATM   18  O01 LIG     1     -86.640  -2.401  -0.357  1.00 20.00
>           O
> HETATM   19  O   LIG     1     -75.199   2.925   2.145  1.00 20.00
>           O
> HETATM   20  C17 LIG     1     -83.058  -0.188   1.872  1.00 20.00
>           C
> HETATM   21  C   LIG     1     -76.676   0.780  -1.835  1.00 20.00
>           C
>
> After editing it to add in the missing numbers, I re-ran elbow, and found
> that the resulting optimized ligand had imploded, producing altered atom
> connectivity. If I ran it with --final_geometry it came out OK. If you would
> like files to reproduce the error, I am happy to send them.
>
> Best,
> Kendall Nettles
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>



-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
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



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