[phenixbb] Creating cif file of ligands by Elbow/ReadySet
Nigel Moriarty
nwmoriarty at lbl.gov
Thu Apr 21 14:40:02 PDT 2011
Ngan
You can very easily access the files in the chemical components that
are installed with PHENIX using
phenix.elbow --chemical_components=CR2
or to view the ligand
phenix.reel --chemical-components cr2
(case is unimportant)
You can also get the Mogul values (if you have Mogul installed and in
you $PATH and a recent PHENIX version)
phenix.elbow --chem=cr2 --mogul
Using the chemical components input in the latest eLBOW release, I
tabulated the bond lengths for C3-CA3 in CR2
eLBOW : 1.492
AM1 : 1.567
Mogul GUI: 1.528 with a range up to 1.56
Mogul command-line : 1.511
I'm sure you will agree that not every C-C bond should be 1.51A. There
is a range so any attempt to construct a ligand with exactly 1.51A for
all C-C bonds is wrong. The range in Mogul is about 0.02 Angstrom.
There are of course limits to the accuracy of any method used to
determine a bond length but I believe that eLBOW and AM1 gets within
the acceptable range for most ligands.
Some of the other problems you are seeing may be due to using a PDB
file as input. Its always better to use the --chemical-components or
some other chemically rich format.
Nigel
On Wed, Apr 20, 2011 at 3:23 AM, Ngan Nguyen Bich
<ngan.nguyenbich at student.kuleuven.be> wrote:
> Dear Phenix developers,
> I'm quite new in crystallography and use PhenixGUI for refinement my
> protein.
> I got a problem when I had to create cif file of the new ligand to feed
> in phenix_refine by Elbow/ReadySet
> I saw that program creates some bonds shorter or longer compared to the
> statistic value from the CSD for example.
> Here are some examples when I play with Elbow (same problem with ReadySet)
> 1. when I feed program the chemical string, (template PDB file is the
> mylidand_idea.pdb)
> CR2 C3 CA3 single 1.569 0.038
>
> and if I choose AM1 optimization
> CR2 C3 CA3 single 1.602 0.040
> 2. when I feed program the .pdb file, choose Use geometry for Initial
> geometry.
> GYC N CA1 single 1.409 0.020 *
> GYC N HN1 single 0.902 0.020
> GYC N HN2 single 0.901 0.020
> GYC SG1 CB1 single 1.797 0.020
> GYC SG1 HG1 single 1.204 0.020
> GYC CB1 CA1 single 1.500 0.020
> GYC CB1 HB11 single 1.006 0.020
> GYC CB1 HB12 single 0.972 0.020
> GYC CA1 C1 single 1.528 0.020
> GYC CA1 HA1 single 1.010 0.020
> GYC C1 N2 aromatic 1.412 0.020
> GYC C1 N3 aromatic 1.304 0.020
> GYC N2 CA2 aromatic 1.505 0.020 **
> GYC N3 C2 aromatic 1.349 0.020
> GYC N3 CA3 single 1.423 0.020
> GYC C2 O2 double 1.370 0.020
> GYC C2 CA2 aromatic 1.509 0.020
> GYC CA2 CB2 single 1.532 0.020
> GYC CA3 C single 1.496 0.020
> It's strange to me when comparing * and **
> and if I run AM1
> GYC CB1 CA1 single 1.533 0.035
> GYC CA3 C single 1.564 0.035
> as I know, the C-C single bond should be about 1.51.
> Does anyone get a problem like me?
> I wonder if I didn't do properly or some thing else, or any suggestion for
> my case.
> One more questions is that afterward I found cif file (seemly mmcif file) of
> my ligand in phenix-1.7-650/chem_data/chemical_components
> And I'm wondering that How the program use these cif file, or I can use them
> in which way?
> Thank you in advance.
> Best regards,
> Ngan Nguyen Bich
> KULeuven
> Belgium
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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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