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
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 [email protected] http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/... http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.h... ________________________________ From: [email protected] [[email protected]] on behalf of Rebecca Oot [[email protected]] Sent: Monday, November 04, 2013 10:18 PM To: [email protected] 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 The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.
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 < [email protected]> 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 [email protected]
http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/...
http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.h... ------------------------------ *From:* [email protected] [ [email protected]] on behalf of Rebecca Oot [ [email protected]] *Sent:* Monday, November 04, 2013 10:18 PM *To:* [email protected] *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
The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
*CAUTION*: Intended recipients should NOT use email communication for emergent or urgent health care matters.
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participants (3)
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Anshul Bhardwaj -
Nigel Moriarty -
Rebecca Oot