Hi all, is there an easy way to test and develop programs within Chimera? I always write python scripts and open these in Chimera… Would be much easier to have something like idle or similar to develop scripts and test them. Or is there a better way I did not found? Looking forward to any suggestions. Kind regards Mario
Hello Chimera-developers/users: Does someone have a script that can perform pairwise backbone RMSD calculations for a group of pdb structures in a file and write out the RMSD matrix? This may already be implemented in the clustering routine. Just need to get the RMSDs. Thanks, Austin-
Will you be running Chimera with a graphical interface? If so, then the Ensemble Cluster tool already prints the RMSD matrix to the Reply Log. If you want to get the RMSD in "nogui" mode, please let us know and we can figure something out. Conrad On 7/10/12 7:57 AM, Austin B. Yongye wrote:
Hello Chimera-developers/users: Does someone have a script that can perform pairwise backbone RMSD calculations for a group of pdb structures in a file and write out the RMSD matrix? This may already be implemented in the clustering routine. Just need to get the RMSDs. Thanks, Austin-
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Hi Dr. Huang, I would like to use the "nogui" mode. Thanks a lot! Austin- --- On Tue, 7/10/12, Conrad Huang <conrad@cgl.ucsf.edu> wrote:
From: Conrad Huang <conrad@cgl.ucsf.edu> Subject: Re: [Chimera-users] RMSD calculation To: "Austin B. Yongye" <ybausty@yahoo.com> Cc: chimera-users@cgl.ucsf.edu Date: Tuesday, July 10, 2012, 9:18 AM Will you be running Chimera with a graphical interface? If so, then the Ensemble Cluster tool already prints the RMSD matrix to the Reply Log. If you want to get the RMSD in "nogui" mode, please let us know and we can figure something out.
Conrad
On 7/10/12 7:57 AM, Austin B. Yongye wrote:
Hello Chimera-developers/users: Does someone have a script that can perform pairwise backbone RMSD calculations for a group of pdb structures in a file and write out the RMSD matrix? This may already be implemented in the clustering routine. Just need to get the RMSDs. Thanks, Austin-
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Here's a script that will print out the RMSD "distance" matrix for an ensemble (all models have exactly the same set of atoms). To use, just run: chimera --nogui --silent your_file.pdb dm.py > matrix The output in file "matrix" should be N lines, each with N tab-separated floating point numbers, where N is the number of structures in your_file.pdb. Please let me know if that's what you're looking for. Thanks. Conrad On 7/10/12 11:32 AM, Austin B. Yongye wrote:
Hi Dr. Huang, I would like to use the "nogui" mode. Thanks a lot! Austin-
--- On Tue, 7/10/12, Conrad Huang <conrad@cgl.ucsf.edu> wrote:
From: Conrad Huang <conrad@cgl.ucsf.edu> Subject: Re: [Chimera-users] RMSD calculation To: "Austin B. Yongye" <ybausty@yahoo.com> Cc: chimera-users@cgl.ucsf.edu Date: Tuesday, July 10, 2012, 9:18 AM Will you be running Chimera with a graphical interface? If so, then the Ensemble Cluster tool already prints the RMSD matrix to the Reply Log. If you want to get the RMSD in "nogui" mode, please let us know and we can figure something out.
Conrad
On 7/10/12 7:57 AM, Austin B. Yongye wrote:
Hello Chimera-developers/users: Does someone have a script that can perform pairwise backbone RMSD calculations for a group of pdb structures in a file and write out the RMSD matrix? This may already be implemented in the clustering routine. Just need to get the RMSDs. Thanks, Austin-
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Well, there is Idle :-) The menu item "Tools -> General Controls -> IDLE" will bring up an Idle window. I usually use Idle for testing out snippets of code but prefer to edit scripts outside of Chimera. Keeping the "Open File" dialog up by checking the "Keep dialog up after Open" box (above the Close button) helps a lot. The file you last opened remains selected, so you can repeatedly edit your script and hit the Open button to reload it. All a matter of preference... Conrad On 7/10/12 7:18 AM, Mario Dejung wrote:
Hi all, is there an easy way to test and develop programs within Chimera? I always write python scripts and open these in Chimera… Would be much easier to have something like idle or similar to develop scripts and test them. Or is there a better way I did not found? > Looking forward to any suggestions. Kind regards Mario _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Austin B. Yongye -
Conrad Huang -
Mario Dejung