December 2002 - Chimera-dev - RBVI Mailing Lists

delphi question
by Tom Ferrin 08 Dec '02

08 Dec '02

This email was sent to the "chimera" list, but it's definitely a question for the chimera-dev list instead... ------- Forwarded Message Date: Sun, 08 Dec 2002 12:07:35 +0400 From: "Wade Nasholds" <vesuvius(a)omantel.net.om> To: <chimera(a)cgl.ucsf.edu> Subject: Using output from DelPhi server on Chimera Hello, I have tried to use an output file from the Honig Lab DelPhi server http://lipid.bioc.columbia.edu/~xu/ with Chimera's DelPhi Viewer extension but I get memory/Python error messages. Is it possible to take output from that server and use it in Chimera to visuali ze electrostatic potential surfaces on .pdb files? Could you help me with this or at least put me in contact with someone who can? Thank you very much. Wade Nasholds ------- End of Forwarded Message

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Documentation missing in 1602 release
by Thomas Goddard 05 Dec '02

05 Dec '02

Documentation for several of the recent contributed Chimera extensions did not make it into the release. Some of the missing directories from ContributedSoftware are are: accelerators, benchmark, multalignviewer, phantom, scalebar, structuremeas. This list is from a quick glance and there may be others missing. The links from the Extensions index to these modules are broken. Maybe the 1602 distributions should be repackaged with the complete documentation. Tom

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Re: Chimera at NCMI
by Thomas Goddard 04 Dec '02

04 Dec '02

Hi Steve, Each Chimera model can be active or inactive. This terminology is a bit confusing. It really means movable or fixed. If you bring up the the Model Panel (under Controllers menu) there is a column of checkbuttons so you can activate or deactivate any of the models. Then mouse actions will only move the active ones. For interactive docking you have to switch back and forth alot between rotating all models and rotating just one. I wrote some Python code for another docker to make Chimera accelerators that do this. I include the python code below. It defines keyboard accelerators 0, 1, 2, 3, 4, 5 which activate model #0, #1, ... only. It also defines and accelerator "aa" that activates all models. To use these bring up the accelerator dialog, menu Extensions/Keyboard/Accelerator List. Then change the accelerator file entry field to give the path to the code below, and press the load button. This will be remembered for you next Chimera session so you won't have to do it again. Then turn on the accelerators with the switch on the accelerator dialog. You may want to use Extensions/Manager, click show start buttons, and click the button to autostart accelerators whenever you start Chimera. For more on Chimera accelerators press the Help button on the Accelerator dialog. It explains how to switch between using Midas commands and accelerators. Tom ---- activate_accel.py follows: # ----------------------------------------------------------------------------- # def register_accelerators(): from Accelerators import standard_accelerators, add_accelerator reload(standard_accelerators) standard_accelerators.register_accelerators() add_accelerator('0', 'Activate model 0 only', lambda: activate_model_n_only(0)) add_accelerator('1', 'Activate model 1 only', lambda: activate_model_n_only(1)) add_accelerator('2', 'Activate model 2 only', lambda: activate_model_n_only(2)) add_accelerator('3', 'Activate model 3 only', lambda: activate_model_n_only(3)) add_accelerator('4', 'Activate model 4 only', lambda: activate_model_n_only(4)) add_accelerator('5', 'Activate model 5 only', lambda: activate_model_n_only(5)) add_accelerator('aa', 'Activate all models', activate_all_models) # ----------------------------------------------------------------------------- # def activate_model_n_only(n): from chimera import openModels for m in openModels.list(all = 1): m.openState.active = (m.id == n) # ----------------------------------------------------------------------------- # def activate_all_models(): from chimera import openModels for m in openModels.list(all = 1): m.openState.active = 1

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Re: [chimera-dev] [stevel@blake.3dem.bioch.bcm.tmc.edu: Re: Chimera at NCMI]
by Elaine Meng 04 Dec '02

04 Dec '02

Hi Steve, Not a dumb question - it just takes a while to learn various details. Models can be activated/deactivated for motion in several ways. As long as you have the two things opened as two different model numbers, you can deactivate one of them so that only the other is responsive to interactive movement with the mouse and movement commands (move, turn, etc.). How to activate/deactivate a model for motion: on the Midas Emulator, check/uncheck the box next to the model number http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html#emulator OR choose the model in the Model Panel and use the buttons "activate" and "deactivate" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#activate OR toggle the active checkbox in the Molecule Model attributes panel http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/moleculeattrib.html Your mail has alerted me that I should probably also mention this issue in the "mouse manipulation" page. Hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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[stevel@blake.3dem.bioch.bcm.tmc.edu: Re: Chimera at NCMI]
by Thomas Goddard 04 Dec '02

04 Dec '02

------- Start of forwarded message ------- Date: Wed, 4 Dec 2002 09:48:48 -0600 (CST) From: Steven Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> X-X-Sender: stevel(a)id.3dem.bioch.bcm.tmc.edu Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.EDU> Subject: Re: Chimera at NCMI In-Reply-To: <200212030001.gB301Ull676766(a)adenine.cgl.ucsf.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.9 (cgl.ucsf.edu) Hi. I've got a dumb question, but I've been unable to find anything about it in the manual. Is there any way to interactively rotate/translate an individual model ? ie - the sort of thing you might do for manual docking. That is, I have two models loaded, or an isosurface and a model, and I want to change the relative orientation of the two components. The closest thing I could find was in the Midas emulation, with the 'rock' and 'roll' commands. Am I missing something ? cheers... - -- - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds ------- End of forwarded message -------

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Chimera-dev December 2002