[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
>
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>
>
--
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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