Hi everybody, In a previous message I mentioned Pub3D as a useful source of 3D coordinates (SDF files) for many PubChem entries. The URL for that server is now http://www.chembiogrid.org/cheminfo/p3d Enjoy! Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html Begin forwarded message:
From: Rajarshi Guha <rguha@indiana.edu> Date: May 17, 2007 4:44:53 PM PDT To: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: Pub3D SDFs
I noticed that your Pub3D site has not been reachable for a while. ( http://rguha.ath.cx/~rguha/p3d/ )
Aah! My Apache redirect failed again :(
Actually, we have a new URL for it which should be constant (and is independent of my machine)
http://www.chembiogrid.org/cheminfo/p3d
------------------------------------------------------------------- Rajarshi Guha <rguha@indiana.edu> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE -------------------------------------------------------------------
Hi all. I'm trying to use chimera in order remove bad contacts in my crystal structure using the Minimize Structure under Tools -> Structure Editing. I have a Magnesium ion in the active site of my protein and I need to keep it for further calculations. When I attempt to minimize the structure I get the following message in the reply log: AttributeError: '_chimera.Atom' object has no attribute 'gaffType' (see reply log for Python traceback info) Dock Prep runs with no problems and I'm able to save the mol2 file in which everything is OK, including hydrogen atoms, charges and Mg atom type and charge. If I remove the Mg ion from the structure, then the minimization runs with no problems. I think it is a problem while assigning amber atom type for Mg, Can anybody help me???? Thanks in advance for any help Yunierkis __________________________________________________________________ Servicio de Correos del Grupo de Redes. UCLV Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu
Hi Yunierkis, Sorry - currently Minimize Structure does not work when a monatomic ion is present. We would like to improve the behavior in the future. However, for now, if the bad contacts you want to fix are not that close to the active site, I would probably use the following procedure: make sure the original structure is saved, add hydrogens and charges, delete the Mg++, minimize with the active site atoms frozen (make them the "Fixed atoms" during minimization), save another PDB, then text-edit the Mg++ from the original structure back in. It is a judgement call of how much of the structure should be frozen. If the bad contacts are fairly localized, you may want to allow only those few residues to move. Minimize Structure man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 18, 2007, at 9:42 AM, Yunierkis Perez Castillo wrote:
Hi all.
I'm trying to use chimera in order remove bad contacts in my crystal structure using the Minimize Structure under Tools -> Structure Editing.
I have a Magnesium ion in the active site of my protein and I need to keep it for further calculations. When I attempt to minimize the structure I get the following message in the reply log:
AttributeError: '_chimera.Atom' object has no attribute 'gaffType' (see reply log for Python traceback info)
Dock Prep runs with no problems and I'm able to save the mol2 file in which everything is OK, including hydrogen atoms, charges and Mg atom type and charge.
If I remove the Mg ion from the structure, then the minimization runs with no problems. I think it is a problem while assigning amber atom type for Mg,
Can anybody help me????
Thanks in advance for any help
Yunierkis
__________________________________________________________________ Servicio de Correos del Grupo de Redes. UCLV Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu
participants (2)
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Elaine Meng -
Yunierkis Perez Castillo