- 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 06 Dec '02

06 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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About the DMS program in chimera
by Ming Lei 26 Nov '02

26 Nov '02

Dear Sir: I am using the chimera. And I knew it is a updated version of mediaplus. I wonder if there still is dms program to generate the ms input file for docking(SPHEN). If yes, can you tell me how to use it in chimera? Your immediately reply is much appreciated! Best, Ming ___________________________________ Ming Lei Ph.D Postdoctoral Research Associate Department of Chemistry Clark University Worcester, MA 01610 Tel: 1-508-421-3742 (Lab ) 1-508-831-9851 (Apt ) Email: milei(a)clarku.edu

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dms, Chimera
by Elaine Meng 26 Nov '02

26 Nov '02

[I forgot to cc chimera-dev so have enclosed the message to Ming Lei below] Dear Ming, Currently there is no dms program that comes with Chimera. It is something we want to have in the future, however. If you already have MidasPlus, you can continue to use the dms that comes with MidasPlus for making SPHGEN input. Best regards, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, R.Ph., 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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Help
by Srinivasan, Mythily 25 Nov '02

25 Nov '02

Hi, I am using Chimera (Windows 2000) operating system. I have a protein complex with two distinct chains. I would like to find the intersections of groups of atoms between the two chains. As I understand from the tutorials for Midas, the & operator should help me. However, I get a syntax error message. Can you please tell me the correct command? Thanking you, Sincerely, Mythily Indiana University School of Dentistry

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[stevel@blake.3dem.bioch.bcm.tmc.edu: Re: Chimera at NCMI]
by Thomas Goddard 25 Nov '02

25 Nov '02

------- Start of forwarded message ------- Date: Mon, 25 Nov 2002 13:37:43 -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: <200211251932.gAPJWPdN690278(a)adenine.cgl.ucsf.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.9 (cgl.ucsf.edu) On Mon, 25 Nov 2002, Thomas Goddard wrote: > I don't understand why the installer failed when installing in > /home/stevel/chimera. I just tried the linux installer from the web > in my home directory and it worked. If it works as root for you, that seems > to indicate it is a permissions problem. Can you send me the permissions > on your home directory, "ls -l /home/stevel"? It should also work if > you create the chimera directory first. I tested that and it also > worked. The installer no longer removes an old Chimera. If you try > to install where a Chimera already exists, it will ask you to move it > or delete it yourself (from another shell) before proceeding. Found the problem. Stupidity on my part (as ususal). One machine uses /homes/stevel, the other uses /home/stevel, and I got them backwards. > I agree that the web page should say next to the download link > the date and version of the last release. Currently you have to > follow the release notes link from the home page to check this. > If you already have Chimera running, the Help/Software Updates > menu entry will tell you if you have the most recent version. Good tip. > The Puppet extension for remote controlling chimera uses the Tcl socket > command to listen for socket connections. When a new connection is made > a Tcl event appears in the event loop. I couldn't get that behaviour with > the Python socket module, and I didn't try a separate thread. Using Tcl > socket worked ok, but I don't know if it handles unix domain sockets. > I was using INET domain sockets and Puppet just checks that the connection > is being made from the machine chimera is running on. That is obviously > inadequate security on a multi-user machine. The Puppet extension is not > distributed with Chimera because of this security problem. I think I gave > you a copy several months ago. If you can't find it, I can provide you > another copy of the Puppet Python code. Yeah, I've still got it. I sort of wanted to avoid doing any explicit TCL stuff. I hadn't checked to see how you handle that. Anyway, that answers my question Thx, and sorry to waste your time on the installer thing... - -- - ---------------------------------------------------------------------------- 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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Re: Chimera at NCMI
by Thomas Goddard 25 Nov '02

25 Nov '02

Hi Steve, I don't understand why the installer failed when installing in /home/stevel/chimera. I just tried the linux installer from the web in my home directory and it worked. If it works as root for you, that seems to indicate it is a permissions problem. Can you send me the permissions on your home directory, "ls -l /home/stevel"? It should also work if you create the chimera directory first. I tested that and it also worked. The installer no longer removes an old Chimera. If you try to install where a Chimera already exists, it will ask you to move it or delete it yourself (from another shell) before proceeding. I agree that the web page should say next to the download link the date and version of the last release. Currently you have to follow the release notes link from the home page to check this. If you already have Chimera running, the Help/Software Updates menu entry will tell you if you have the most recent version. If chimera is installed as root, users can still add their own directory of extensions using Extensions/Manager/Directories tab. Chimera will definitely remain free for academic users. The Puppet extension for remote controlling chimera uses the Tcl socket command to listen for socket connections. When a new connection is made a Tcl event appears in the event loop. I couldn't get that behaviour with the Python socket module, and I didn't try a separate thread. Using Tcl socket worked ok, but I don't know if it handles unix domain sockets. I was using INET domain sockets and Puppet just checks that the connection is being made from the machine chimera is running on. That is obviously inadequate security on a multi-user machine. The Puppet extension is not distributed with Chimera because of this security problem. I think I gave you a copy several months ago. If you can't find it, I can provide you another copy of the Puppet Python code. Tom

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