Dear Chimera-user list, I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them. It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen) or sphgen_cpp. Radius and color information could then also be displayed. This might be a helpful new feature to be included in a future release of Chimera. Thank you, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
Dear Trent, If I remember correctly there was a utility program included with DOCK, "showsphere" to convert sphere format to PDB. It was pretty decent for display in Midas, but not so great in Chimera, so in 2008 I wrote a fortran program (yeah, yeah stop laughing) to convert sphere format for better display in Chimera. This is not to say your suggestion isn't valid (or has been taken care of), but in the meanwhile this program I wrote might be helpful. I will dig up that 2008 email with the program attached and more detailed information and forward it momentarily. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 2, 2011, at 9:09 AM, Trent E. Balius wrote:
Dear Chimera-user list,
I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them.
It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen) or sphgen_cpp. Radius and color information could then also be displayed.
This might be a helpful new feature to be included in a future release of Chimera.
Thank you,
Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
Hi Trent, Elaine's tool seems like a good start since it helps you visualize the various sphere clusters. You are right that it would be nice to have a tool more closely integrated with Chimera that would also allow you to delete spheres and rewrite your sphere file. I will open an enhancement-request ticket in our bug-tracking database with you and the other cc recipients on it so that you all will be notified when it gets implemented. I hope Elaine's program will be helpful enough until I have time to get to it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Nov 2, 2011, at 10:09 AM, Elaine Meng wrote:
Dear Trent, If I remember correctly there was a utility program included with DOCK, "showsphere" to convert sphere format to PDB. It was pretty decent for display in Midas, but not so great in Chimera, so in 2008 I wrote a fortran program (yeah, yeah stop laughing) to convert sphere format for better display in Chimera.
This is not to say your suggestion isn't valid (or has been taken care of), but in the meanwhile this program I wrote might be helpful.
I will dig up that 2008 email with the program attached and more detailed information and forward it momentarily. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 2, 2011, at 9:09 AM, Trent E. Balius wrote:
Dear Chimera-user list,
I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand ) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them.
It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen ) or sphgen_cpp. Radius and color information could then also be displayed.
This might be a helpful new feature to be included in a future release of Chimera.
Thank you,
Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
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Hi Elaine, I believe this program will be helpful to us and we will try it out and let you know. However, In the future, it might be useful to have a .sph reader and witter in chimera to eliminate the intermediate steps. Chimera is a very useful program especially for DOCKing preparation and this might add to this functionality. Thanks, Trent -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> To: Trent E. Balius <tbalius@aol.com> Cc: chimera-users <chimera-users@cgl.ucsf.edu>; sudipto.mukherjee <sudipto.mukherjee@gmail.com>; brianfochtman <brianfochtman@gmail.com>; rizzorc <rizzorc@gmail.com>; jianglilian68 <jianglilian68@gmail.com> Sent: Wed, Nov 2, 2011 1:09 pm Subject: Re: [Chimera-users] docking sphere visualization Dear Trent, If I remember correctly there was a utility program included with DOCK, "showsphere" to convert sphere format to PDB. It was pretty decent for display in Midas, but not so great in Chimera, so in 2008 I wrote a fortran program (yeah, yeah stop laughing) to convert sphere format for better display in Chimera. This is not to say your suggestion isn't valid (or has been taken care of), but in the meanwhile this program I wrote might be helpful. I will dig up that 2008 email with the program attached and more detailed information and forward it momentarily. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 2, 2011, at 9:09 AM, Trent E. Balius wrote:
Dear Chimera-user list,
I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them.
It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen) or sphgen_cpp. Radius and color information could then also be displayed.
This might be a helpful new feature to be included in a future release of Chimera.
Thank you,
Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
participants (3)
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Elaine Meng -
Eric Pettersen -
Trent E. Balius