Rebecca

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 quickly.

Cheers

Nigel


On Tue, Nov 5, 2013 at 9:28 AM, Anshul Bhardwaj <Anshul.Bhardwaj@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@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@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Rebecca Oot [ootr@upstate.edu]
Sent: Monday, November 04, 2013 10:18 PM
To: phenixbb@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
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