[phenixbb] Restraints generation for TaBr

Nigel Moriarty nwmoriarty at lbl.gov
Tue Nov 5 10:01:42 PST 2013


Sorry for the delay in responding.

The reason I removed the ability to work with metal clusters is that the 3D
geometry generation is extremely complicated. You can still generate
restraints if you have the cartesian coordinates. The simplest way to do
this is using the Chemical Components.

phenix.elbow --chemical-component=TBR --final-geometry=TBR

I have attached the results.

Clearly I need to adjust the behaviour slightly so you can move forward



On Tue, Nov 5, 2013 at 9:28 AM, Anshul Bhardwaj <
Anshul.Bhardwaj at jefferson.edu> wrote:

>  Hello Rebecca,
> I was able to generate restraints for hexatantalum dodecabromide (TBR) on
> older PHENIX version 1.7.3-928. Attached is the .cif file.
> Nonetheless, I agree phenix.elbow run for ligand TBR in latest PHENIX
> version 1.8.4-1496 fails with error on linux (Ubuntu 12.04 64bit);
> PHENIX error: "eLBOW not suitable for metal clusters"
> Anshul
>  Anshul Bhardwaj, Ph.D.
> Faculty, Department of Biochemistry and Molecular Biology
> Manager, Kimmel Cancer Center X-ray Crystallography and Molecular
> Interactions
> Thomas Jefferson University
> 233 South 10th Street, BLSB suite 822
> Philadelphia, PA 19107
> Tel: (215) 503-4587
> anshul.bhardwaj at jefferson.edu
> http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/bhardwaj.html
> http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.htm
>    ------------------------------
> *From:* phenixbb-bounces at phenix-online.org [
> phenixbb-bounces at phenix-online.org] on behalf of Rebecca Oot [
> ootr at upstate.edu]
> *Sent:* Monday, November 04, 2013 10:18 PM
> *To:* phenixbb at phenix-online.org
> *Subject:* [phenixbb] Restraints generation for TaBr
>  Hello all,
> I am trying to create a restraints file for hexatantlum dodecabromide
> (TaBr or TBR) and using Elbow, I get an error message saying that the
> program does not deal with heavy atom clusters. Does anyone have any advice
> on which program would be suitable to use?
> Thanks very much in advance
> Rebecca
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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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