- Chimera-users - RBVI Mailing Lists

Re: Chimera questions.
by Thomas Goddard 30 Jun '04

30 Jun '04

Hi Matt, Support for DCD trajectories is in our current Chimera development version, but is not in the most recent release, Chimera 1.1951. It is described in the development version of the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html If you like, I can give you the new Python code for DCD trajectories. I have not yet tested whether it will work in Chimera 1951, but I can test it. Otherwise, you can get it in our next release which is at least a few months away. To reposition a PDB model using Python code see the Programmer FAQ: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q4 Tom > Date: Wed, 30 Jun 2004 16:53:00 +0000 > From: Matthew Baker <mlbaker(a)gmail.com> > To: goddard(a)cgl.ucsf.edu > Subject: Chimera questions. > > Tom, > > Two quick questions: > 1. Is there a reader/display for DCD or netCDF trajectory files in > Chimera? I see that you can read AMBER trajectory files in the > Molecular Dynamics module. > > 2. How do you update a PDB file loaded into Chimera? I have a PDB file > and I want to apply a transformation to it and have the updated > coordinates applied in the viewer. > > Thanks, > > Matt

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Filled in/triangulated nucleotide base ring planes
by Pattanayek, Sabuj 28 Jun '04

28 Jun '04

Hi, I was wondering if I missed this feature in Chimera somewhere...a way to fill in nucleotide base rings/planes, this is what I mean: http://linegli.mc.vanderbilt.edu/~sabuj/1GQU_ribbons.png (using ribbons v3.2) http://linegli.mc.vanderbilt.edu/~sabuj/1GQU_vmd.png (using vmd 1.8.2) If you've ever used Ribbons you know it's a real pain to setup. I actually ended up using Chimera's selection methods to create separate pdb files for inputs into Ribbon's scripts, and it doesn't do multi-colored surfaces/transparency very well. VMD as you can see is filling in the ribose sugars (which I don't want) and is failing to fill in some of the bases. I tried recompiling it's code with some modifications but failed due to some header problems. Anyways I was wondering if this feature might be added, if it already isn't there, with the ability to choose colors for the base rings, or attribute certain colors to groups of bases, etc. Thanks, Sabuj

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Nice postscript output from chimera.
by J B Procter 26 Jun '04

26 Jun '04

Does anyone know of a way of generating postscript from chimera via a vector rendering of the structure, rather than simply embedding the rendered image ? What would be even more fun is if one could generate a molscript diagram from a chimera view. j.

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Re: Save options
by Eric Pettersen 24 Jun '04

24 Jun '04

On Jun 24, 2004, at 2:30 PM, Karl N. Kirschner wrote: > Hi, > We are looking at chimera to use in our department here at Hamilton. > I am currently evaluating it and I was wondering is there a way to save > a structure under a different format other than filename.py (ie PDB)? > From your website it appears that one should be able to do this. We > are > using the chimera-1.1951-linux.exe and chimera-1.1917-linux_x86_64.exe > versions of the program. Maybe it is a bug - or maybe I am not just > seeing something. > > Thanks, > Karl Hi Karl, You can write out structures in PDB format either using the "write PDB" button of the model panel (Favorites..Model Panel in the menus), or by using the "write" command in the command line ("help write" will provide details of using the write command). Both of these methods save the entirety of the models specified, displayed or not. To save parts of models, one can either delete the unwanted portions (Actions..Atoms/Bonds..delete in the menus or using the "delete" command), or (on UNIX-based systems) use the pdbrun command to output only the displayed portions ("help pdbrun" for details). Please feel free to ask about any other things that may not be obvious -- it helps us to refine the usability of Chimera's interface. I should note that usage-style questions like these should probably go to the chimera-users mailing list rather than chimera-bugs though. Thanks for giving Chimera a try! Eric Pettersen UCSF Computer Graphics Lab

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[Chimera-users] Chimera 1.1951 on OSX 10.3.4 fails to do much at all...
by Grant Jacobs 20 Jun '04

20 Jun '04

re: Chimera 1.1951 on OSX 10.3.4 fails to do much at all... I'm a first time user obviously! :-) Trying to open Side View or any of the Tools:Viewing Preferences fails. Many commands via the command interface likewise fail, e.g. surface #0 (no module msms), (no module webrowser). AFAICS from the error messages, the errors appear to be either Python modules missing or Tcl/TK errors. My download is the correct size. Q: Does Chimera require a Tcl/TK installation? - which doesn't show these up and they aren't hidden in one of the sbin's (I'm assuming that they are named tcl and tk - I've never had to work with them directly myself). If so is this tested on start up? There appears to be nothing about this in the docs AFAICS. The OSX installation instructions only say to drag the app. to the disk, nothing about other requirements. So naturally that's all I've done so far! If it does require more stuff, would someone be so kind as to tell me exactly what and where to get it? Two suggestions: It'd be good to have a simple test of what modules are present to "verify" an installation. (e.g. Tools:test:modules) It'd be good to have a test of the presence of Tcl/TK & let the user know it its not around. Grant E.g. of traceback: ImportError: No module named Lighting.controller (see reply log for Python traceback info) Traceback (most recent call last): File "/Applications/Science/Chimera-1.1951.app/Contents/Resources/share/__main__.py", line 56, in ? File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/share/chimeraInit.py", line 301, in init File "tkgui.py", line 2891, in eventLoop File "/usr/local/src/staff/chimera-build/Darwin-X11/foreign/Python-2.3.2/lib/python2.3/lib-tk/Tkinter.py", line 965, in mainloop File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__ File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ File "base.py", line 434, in activate File "base.py", line 80, in menuActivate File "ChimeraExtension.py", line 20, in activate File "base.py", line 102, in module ImportError: No module named Lighting.controller AttributeError: ViewerDialog instance has no attribute 'nb' (see reply log for Python traceback info) Traceback (most recent call last): File "/Applications/Science/Chimera-1.1951.app/Contents/Resources/share/__main__.py", line 56, in ? File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/share/chimeraInit.py", line 301, in init File "tkgui.py", line 2891, in eventLoop File "/usr/local/src/staff/chimera-build/Darwin-X11/foreign/Python-2.3.2/lib/python2.3/lib-tk/Tkinter.py", line 965, in mainloop File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__ File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ File "base.py", line 495, in activate File "base.py", line 80, in menuActivate File "StdTools.py", line 81, in activate File "StdTools.py", line 206, in raiseViewingTab AttributeError: ViewerDialog instance has no attribute 'nb' -- ------------------------------------------------------------------- Grant Jacobs Ph.D. BioinfoTools ph. +64 3 478 0095 (office, after 10am) PO Box 6129, or +64 25 601 5917 (mobile) Dunedin, gjacobs(a)bioinfotools.com NEW ZEALAND. Bioinformatics tools: deriving knowledge from biological data Bioinformatics tools - software development - consulting - training Check out the website for more details: http://www.bioinfotools.com The information contained in this mail message is confidential and may be legally privileged. Readers of this message who are not the intended recipient are hereby notified that any use, dissemination, distribution or reproduction of this message is prohibited. If you have received this message in error please notify the sender immed- iately and destroy the original message. This applies also to any attached documents.

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Re: chimera questions
by Thomas Goddard 11 Jun '04

11 Jun '04

Hi Wen, There is not a Chimera command to print the transformation of one model relative to another. But you can get it with some Python code. Below is some Python code to add two keyboard shortcuts that print the transform of model 0 relative to model 1 or model 1 relative to model 0. The model numbers are shown in the Model Panel dialog (Tools/Inspectors or Favorites menu), 0 being the first model you opened. To use the keyboard shortcuts copy the Python code below to a file, say accel.py. Show the accelerator dialog, Tools/Keyboard/Accelerator List, and enter the path to the accelerator file and press Load. Also click the "Accelerators on" switch. After loading two models you can type x0 or x1 in the Chimera graphics window and it will print out the transform to the Chimera reply log (Favorites/Reply Log). The accelerator file is remembered so you only need to do this setup once. To have the accelerators be on whenever you start Chimera, set Accelerators On to "auto start" in Favorites/Preferences/Category Tools. The transformation matrix is a 3 by 4 matrix. The first 3 columns give the rotation, and the 4th column is a translation. The rotation is applied first, then the translation. Tom def print_transform(model_id_1, model_id_2): '''Print transformation matrix of model 1 relative to model 2.''' import chimera m1 = chimera.openModels.list(id = model_id_1)[0] # returns a list m2 = chimera.openModels.list(id = model_id_2)[0] xf1 = m1.openState.xform xf2 = m2.openState.xform xf2.invert() xf1.multiply(xf2) print xf1 def register_accelerators(): from Accelerators import standard_accelerators, add_accelerator standard_accelerators.register_accelerators() add_accelerator('x0', 'Print model 0 transform relative to model 1', lambda: print_transform(0,1)) add_accelerator('x1', 'Print model 1 transform relative to model 0', lambda: print_transform(1,0))

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Re: chimera questions
by Thomas Goddard 10 Jun '04

10 Jun '04

Hi Wen You can write out coordinates of a PDB model relative to another model such volume you hand docked to, using Model Panel (under Favorites menu or Tools/Inspectors menu). Show the Model Panel dialog, click on the PDB model in the list, press the "Write PDB" button in the right column of the Model Panel. Then a Save file dialog comes up and at the bottom is a checkbutton that says "Save relative to model chosen in model panel when 'OK' is hit". You then click on the volume listed in the Model Panel that the PDB coordinates should be relative to. Then press OK in the Save dialog. A bit crazy. We'll probably improve this confusing interface in a future release. Tom > From: Wen Jiang <wjiang(a)bcm.tmc.edu> > Subject: Re: chimera questions > Date: Thu, 10 Jun 2004 17:06:28 -0500 > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Tom, > Is it possible to do manual fit of PDB to a density map in Chimera then > save the transformed PDB coordinates to a new PDB file? If it is not > possible, how to read out the transformations applied to the PDB model? > Thanks, > > Wen

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Re: save session/grasp surfaces
by Thomas Goddard 07 Jun '04

07 Jun '04

Hi Sabuj, We'll consider adding DelphiViewer session saving. It is a fair bit of work and we have been thinking of replacing DelphiViewer's surface coloring capabilities with something that works with volume data other than electrostatic potential maps. I'll discuss it with other Chimera developer's and get back to you. Tom > Date: Mon, 7 Jun 2004 11:49:00 -0500 > From: "Pattanayek, Sabuj" <sabuj.pattanayek(a)Vanderbilt.Edu> > To: goddard(a)cgl.ucsf.edu > Subject: save session/grasp surfaces > > Hi, > > Method 1 would be what I am looking for (reload potential file, grasp surface > file, recalculates colors according to saved preferences, and places the surface > where it was before saving). I accidentally deleted your message, but I think > that was the gist of choice #1. > > Thanks, > Sabuj Pattanayek

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[Chimera-users] v1.1951 save session not reopening grasp surfaces that were there before i saved session
by Pattanayek, Sabuj 04 Jun '04

04 Jun '04

Hi, I had to resort to using grasp surfaces because MSMS doesn't behave "nicely" when dealing with multiple free floating residues that come directly from a PDB file. Although grasp surfaces are lower in visual quality than MSMS, grasp rendered all the areas I wanted whereas the MSMS plugin could not. So, after I did save session and re-opened the session the grasp surfaces did not reappear. Is there anyway to add functionality so that the grasp surfaces, colors, and the corresponding locations can be recalled when I load the saved session file? This saves time especially when there are many grasp surface components each with different colors. One more minor detail/UI glitch I noticed?: Color Editor -> click opacity : the "A" row along with slider appears -> unclick opacity : the sliders disappear but the "A" along with row space remains ...don't know if that was done on purpose. Thanks for the great program!

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Re: [Chimera-users] non-GUI use of Chimera
by Charles Moad 25 May '04

25 May '04

Hi, I am working with Randy on this, and I think we have a web service type solution that will work using your suggestions. The one problem that remains is killing chimera after a request. The webdata facility is targeted to run on a client's machine where a user quits chimera, but we will be running it on the server. I tried adding the 'stop' command at the end of the chimerax file, but I received an error from chimera and it continued to run. Same story for 'sys.exit()' Running the chimera_send script a second time only opens a new instance of chimera which also remains open. Is there a way to attach chimera_send to an existing process of chimera, or have chimera quit at the end of a chimera_send call? Thanks, Charlie > -----Original Message----- > From: chimera-users-bounces(a)cgl.ucsf.edu > [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Thomas Goddard > Sent: Monday, May 24, 2004 6:20 PM > To: heiland(a)indiana.edju > Cc: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] non-GUI use of Chimera > > Hi Randy, > > If I understand correctly you want to be able to type some Chimera > Python > code or Chimera commands to a web browser, those get sent to the web > server > which sends them to Chimera running on the web server machine. Then you > capture the Chimera image and send it back to the web browser. > > I believe this can be done using the Chimera "Web Data" facility. > This > allows programs to send commands to Chimera. The intended use is for > displaying models in Chimera when the user clicks a link in a web > browser. > It works by having the *.chimerax file associated with the link lauch > helper application <chimera-install-location>/bin/chimera_send. > The same mechanism allows any program to send commands to Chimera. > The Chimera User's Guide describes this under Tools/Web Browser > Configuration. > Here's a URL: > > > http://www.cgl.ucsf.edu/chimera/1.1951/docs/ContributedSoftware/webdata/ > chimerax.html > > What you might do is have your web server create an appropriate > *.chimerax that executes the user's commands and then prints the > Chimera graphics window to a file. The web server than sends the > image (jpg) to the web client. There is a bunch of somewhat tricky > glue to make this work. As previous posts mentioned, Chimera will > need to pop up windows on some screen to render an image. For the web > server to know when Chimera has finished making an image, the > *.chimerax file might end in a command that writes to some secondary > status file after the image file is written. That will tell the web > server that the image is ready. > > We haven't tried this. And there are other pitfalls, like you are > likely to run into trouble if the web server starts 2 instances of > Chimera > and then tries to dispatch commands with the chimera_send program. > > Please let me know if you get this to work. Feel free to send > additional > questions. > > Tom > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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