- Chimera-users - RBVI Mailing Lists

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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vrml 2.0 export of pdb representation
by Pattanayek, Sabuj 25 May '04

25 May '04

Hi, Is there anyway to export a pdb model into vrml once I have it just the way I want it (ribbon & atom sizes, colors, etc)? I tried a pdb2vrml converter from http://www.pc.chemie.tu-darmstadt.de/research/vrml/pdb2vrml_right.shtml but freewrl crashes when loading the output (I think pdb2vrml might be outputting vrml 1.0), it's also not very versatile as far as what I want to display into vrml from the pdb. Thanks

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non-GUI use of Chimera
by Thomas Goddard 24 May '04

24 May '04

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/chi… 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

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Re: [Chimera-users] vrml 2.0 export of pdb representation
by Pattanayek, Sabuj 22 May '04

22 May '04

imho, 3DS is currently more widely supported than X3D by expensive, cheap, and free 3d modellers. Most 3D format translators can convert from 3DS to other types (DXF, iv, etc). However it looks like from web3d.org that X3D is much more versatile and feature rich than old 3ds... Quoting Greg Couch <gregc(a)cgl.ucsf.edu>: > We currently only support VRML export of volume isosurfaces and multiscale > surfaces. So the answer is no, not yet. > > Exporting to a 3D graphics file format is definately something we would > like to do. However, it is unclear what format would be best to generate. > VRML 2.0 will never support transparency like chimera does. VRML's > successor, X3D, looks promising, but there aren't many users yet. Other > possiblities include the Renderman format, popular with animation studios; > the .3DS format, popular on PCs; and many others. > > So, a question for everyone reading this, if you had to pick one format, > would it be VRML97? And if so, why? And if not, why not? We are leaning > torwards outputing X3D, but would appreciate comments from people who > would actually be using the output. > > Greg Couch > UCSF Computer Graphics Lab > gregc(a)cgl.ucsf.edu > > > On Fri, 21 May 2004, Pattanayek, Sabuj wrote: > > > Is there anyway to export a pdb model into vrml once I have it just the way > I > > want it (ribbon & atom sizes, colors, etc)? I tried a pdb2vrml converter > from > > http://www.pc.chemie.tu-darmstadt.de/research/vrml/pdb2vrml_right.shtml > but > > freewrl crashes when loading the output (I think pdb2vrml might be > outputting > > vrml 1.0), it's also not very versatile as far as what I want to display > into > > vrml from the pdb. >

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Color blending on ribbons
by Emma Hill 20 May '04

20 May '04

Hi, I wondered if there is any easy way to blend colors from one residue to the next on a ribbon chain (as in the rainbow facility.) I want to be able to precisely define where this takes place (ie whenever I switch from one color to another) - more specifically I am coloring different regions of a superimposed pair to show where is aligned and where is not, and the drastic switch from one color to the next would definitely look better more blended. Thanks in advance Emma -- Emma Hill Brenner Research Lab U.C. Berkeley

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non-GUI use of Chimera
by Randy Heiland 20 May '04

20 May '04

I am evaluating Chimera as a tool for providing (pseudo-interactive) vis functionality from a web server and therefore would like to use it in a non-gui mode. I saw the earlier post/reply to this list (May 4) on this topic, and Eric indicated that one way to do this was to put all your cmds in a file then run "chimera --nogui <cmd-file>". Obviously this isn't ideal for my purposes. So, I'm wondering what the alternatives are? I'm a newbie to Chimera, but I've read how it was based on Midas, and so I decided to see how far I could get in reading in a pdb file and... I didn't get very far: (after install Chimera (Linux, beta 1 build 1951), plus dependent Python pkgs) %python >>> import chimera >>> import Midas >>> f=Midas.open('foo.pdb') and I get an error about 'missing default material' and realize I'm doing the wrong thing anyway. Basic question: can I, from the Python interpreter, use Chimera/Midas to read in a pdb file and do basic Chimera functionality? For now, I don't even care if it assumes X is running and pops up windows. Thanks, Randy

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rainbow command with sub-models
by Jarrod Smith 19 May '04

19 May '04

Hello all, Is it possible to add a new "level" to the rainbow command such that each submodel of a multi-model PDB file (MODEL/ENDMDL records) can be visited separately by the rainbow command? I have some pdb files with several tens to hundreds of submodels in them. Separating them by chain ID (so I can use the rainbow chains command) has proven to be impractical for other reasons, so this would be useful in such a case. Thanks for the great software. Jarrod Smith -- Jarrod A. Smith, Ph.D. Asst. Director, Center for Structural Biology Research Asst. Professor, Biochemistry Vanderbilt University 203 processes: 140 sleeping, 63 running

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new Chimera production release
by Eric Pettersen 14 May '04

14 May '04

Hi all, A new Chimera production release (version 1.1951) is now available for download. I've summarized the major additions since the last snapshot (1.1917) below. A list of all the changes since the last production release (1.1872) is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.1951.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu Changes since 1.1917: General changes --------------- Newly opened models are shown larger (as well as models after a 'window' or 'focus' command) Selections can be written out as parsable text files (Actions->Write... or from the Selection Inspector) New residue attributes: kdHydrophobicity (Kyte-Doolittle hydropathy, amino acids only) mavPercentConserved (% conserved in a sequence alignment open in Multalign Viewer) above for use with Render/Select by attribute tools Double-picking a bond brings up a menu with Rotate Bond and Select Bonded (the latter is new and selects the atoms); double-picking a pseudobond bring up a menu with just Select Bonded; "select bonded" also now in Pseudobond Panel As much as possible, can handle PDB files with 100000+ atoms (e.g. AMBER output). Some PDB records (e.g. CONECT records) have no room for 6-digit atom serial numbers, so only can be used for the first 99,999 atoms. A new tutorial describing preparing images for publication Select by Attribute Value... in Selection menu and Model Panel New Tools --------- Lighting (Viewing Parameters): change and save lighting parameters Color Secondary Structure (Graphics): color peptides/proteins by secondary structure Render Attributes (Graphics): color or otherwise change atom, residue, or model displays based on attribute values; was in 1.1917 release but several changes have been made and documentation added Demo (its own category; entries are individual demos): create/replay demos in Chimera; example demo included (Cyclooxygenase) Tool Changes ------------ Adjust Torsions now allows a bond to be rotated with mouse motions in the graphics window Movie has File->Save PDB for writing out either the current frame or all frames that have been viewed Multalign Viewer: ClustalX-style residue letter coloring added and made the default; can save alignment depiction as an EPS file; can hide Consensus and/or Conservation lines RibbonStyleEditor now has two panels in which scalings and cross-sections can be defined and named; named cross-section are analogous to the built-in cross-sections (flat, edged, round) and can be accessed from the Actions menu or with ribrepr; nucleic acids are now treated separately in the scalings panel New "Graphics" category; Per-Model Clipping, PipesAndPlanks, ResProp, and Ribbon Style Editor moved into it SimpleSession saves lighting, ribbon scaling and cross-section(s), B-factor and occupancy values Web Data asks for confirmation before accepting certain files; associated option in Preferences Command Changes --------------- alias: $1, $2, $3, ... may be used to indicate the first, second, third... arguments of the alias conic: works on Windows, and the -s flag now works on Linux (besides Mac, SGI) write: has "trajectory" keyword to write all frames that have been viewed (loaded) [analogous option added to Model Panel's "write PDB" dialog] ribbackbone: now applies to nucleic acids also

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by riccardodesantis＠fastwebnet.it 05 May '04

05 May '04

Hallo, my name is Riccardo De Santis and I'm a new user of CHIMERA. I'd like to know how run the program from the command line. I've tryed with the command NOGUI but the program doesn't start. Another question is: how can I use matchmaker (in the graphic menu) to match the molecules from the command line? Which is the istruction to type? Thank you in advance, Riccardo De Santis.

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by riccardodesantis＠fastwebnet.it 04 May '04

04 May '04

Hallo, my name is Riccardo De Santis, and I'm a new user of CHIMERA. I'd like to know how to use the program in command line mode. I noticed that there is a NOGUI option, I tryed it but unsuccessfully. Cuold you help me , please? Thank you in advance, Riccardo De Santis.

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Coloring by bfactor
by Thomas Goddard 23 Apr '04

23 Apr '04

Hi Padma, We have developed a Chimera tool to color by bfactor or other attributes but it is not yet released. We expect to have a new release in the middle of May. Here are a couple approaches you could use now. You can use the color command like the following to color all atoms with bfactor between 10 and 15 green. color green @/bfactor>=10 and bfactor<=15 You could put a series of these commmands in a file to color several intervals different colors to get a rainbow effect. Use the "open" command to run the file of coloring commands. A more flexible route is to use some Python code. Putting the code shown below in a file bcolor.py and then opening this file will make a rainbow coloring by bfactor for the selected atoms. A fancier version of this could have a dialog popup to specify bfactor range and colors. If you make a molecular surface with Actions/Surface/Show the default coloring of this surface is to use the atom colors. So coloring the atoms by any of the above means will allow you to get the same coloring on a surface. Tom ----- code bcolor.py follows: # ----------------------------------------------------------------------------- # def color_atoms_by_bfactor(atoms, b0, rgb0, b1, rgb1): for a in atoms: if hasattr(a, 'bfactor'): b = a.bfactor if b < b0: f = 0 elif b < b1: f = (b - b0) / (b1 - b0) else: f = 1 r,g,b = ((1-f)*rgb0[0] + f*rgb1[0], (1-f)*rgb0[1] + f*rgb1[1], (1-f)*rgb0[2] + f*rgb1[2]) import chimera a.color = chimera.MaterialColor(r,g,b) # ----------------------------------------------------------------------------- # from chimera import selection atoms = selection.currentAtoms() # currently selected atoms b0 = 5 rgb0 = (0,0,1) # blue b1 = 20 rgb1 = (1,0,0) # red color_atoms_by_bfactor(atoms, b0, rgb0, b1, rgb1) > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: One more Chimera question! > From: Padmaja Natarajan <nataraja(a)scripps.edu> > Date: Fri, 23 Apr 2004 13:31:38 -0700 > > Hi Tom, > > Is it possible to make a molecular surface based on PDB coordinates > and be able to view this surface colored (as a spectrum going from blue > for smallest to red for largest value), > depending on values stored in say B-factor column of the PDB file. > (as shown in figure below created using AVS) > > thanks again > regards > Padma

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Re: [Chimera-users] CHIMERA help - coloring density maps
by Thomas Goddard 23 Apr '04

23 Apr '04

Hi Padma, There is a Chimera command called "longbond" described in the Chimera User's Guide / Basic Functions / Commands / longbond http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html that removes long bonds. There is currently no radial masking tool. But using the Isosurface Colorizer extension from EMAN you can set the color to transparent black outside or inside a certain radius. That will make it invisible. For example you can make the color blue at radius 10 nm, and transparent black at 10.01 nm. You will also want to turn on the Volume Viewer / Options / Dim transparent surface mesh switch to get rid of the specular highlights on the transparent black part of the surface. This trick for masking does not "cap" the isosurface at the radius where it is cut. So you see the inside of the isosurface. Turning off two sided lighting in Volume Viewer / Options will make the interior of the surface dark. To cut and cap the isosurface at a specific radius you really want to the display to act as if the volume data were zero outside a specified radius. I don't have any way to do that, although it probably would not be too hard to hack something into surface.py that copied the 3-d matrix and made it zero outside a specified radius. By the way, the modification I described to Chimera surface.py to make the Isosurface Colorizer from EMAN work is not needed in Chimera 1917. That change was included in Chimera 1917. I you are looking at models of virus particles you might be interested in the Chimera Multiscale extension. Here are some example images: http://www.cgl.ucsf.edu/home/goddard/viper/ The images at the bottom of that page show the RNA in satellite tobacco mosaic virus. Tom > From: Padmaja Natarajan <nataraja(a)scripps.edu> > Subject: Re: [Chimera-users] CHIMERA help - coloring density maps > Date: Fri, 23 Apr 2004 13:08:02 -0700 > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Hi Tom, > > Thank you very much for the details you had given me earlier in > making the radial coloring work for surfaces. > I , with the help of my colleague Jeff who made the changes in the > chimera (version 1917) script, am > able to produce radial coloring for my density map! > > Can ask more questions?? > > 1) I have coordinates for an icosahedron, but when I read it into > chimera, > several un-wanted connections are made (probably because of the way the > PDB file is written - for use in the graphics program O). I do not see > any distance cut off > criterion command that would help (probably) remove some of those > connections! > > 2) density map: I would like a radial masking tool, that can be used to > choose > minimum and maximum values for radius and be able to see the map only > within this > radius range. For example, this helps in looking at the inner (RNA) > density in a virus structure. > > thanks again! > regards > Padma > ______________________________ > Padmaja Natarajan, Ph.D > The Scripps Research Institute > La Jolla, California, USA.

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install question
by Randy Heiland 23 Apr '04

23 Apr '04

Greetings from a newbie to Chimera, Is there a searchable archive? (I found the archive, but no associated search engine) I'd really like to be able to install Chimera without blowing away my current Python installation - is this possible? (I'll be using both Windows and Linux) Thanks, Randy

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Viewing orbitals and charge distributions
by João Otávio 23 Apr '04

23 Apr '04

Hello All! I am a CHIMERA newbie and I would like to know how could I create a module in order to read orbitals and/or charge distributions from molecular orbitals programs such as GAUSSIAN, GAMESS, etc. Thanks in advance, .................................................................João -- ___________________________________________________________ Sign-up for Ads Free at Mail.com http://promo.mail.com/adsfreejump.htm

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save session error in Chimera 1892
by Juha Huiskonen 22 Apr '04

22 Apr '04

Hi, when trying to save session in chimera 1892 I get an error: Error processing trigger "save session": ValueError: Can't convert type <type 'bool'> (see reply log for Python traceback info) Reply log: Traceback (most recent call last): File "/usr/local/chimera1892/share/__main__.py", line 56, in ? value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 285, in init tkgui.eventLoop() File "/usr/local/chimera/share/chimera/tkgui.py", line 2809, in eventLoop app.mainloop() File "/usr/local/chimera/lib/python2.3/lib-tk/Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "/usr/local/chimera/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera/share/chimera/baseDialog.py", line 409, in OK self.Apply() File "/usr/local/chimera/share/OpenSave/__init__.py", line 141, in Apply self.command(1, self) File "/usr/local/chimera/share/SimpleSession/gui.py", line 24, in _saveCB saveSession(paths[0]) File "/usr/local/chimera/share/SimpleSession/save.py", line 269, in saveSession chimera.triggers.activateTrigger(SAVE_SESSION, buf) File "/usr/local/chimera/share/chimera/triggerSet.py", line 214, in activateTrigger self._triggerDict[name].activate(data) File "/usr/local/chimera/share/chimera/triggerSet.py", line 127, in activate ret = handler.invoke(self._name, triggerData) File "/usr/local/chimera/share/chimera/triggerSet.py", line 82, in invoke self._funcData, triggerData) File "/usr/local/chimera/share/VolumeViewer/__init__.py", line 138, in save_session_cb session.save_volume_state(self, file) File "/usr/local/chimera/share/VolumeViewer/session.py", line 22, in save_volume_state t = objecttree.instance_tree_to_basic_tree(s) File "/usr/local/chimera/share/SessionUtil/objecttree.py", line 69, in instance_tree_to_basic_tree d[k] = it2bt(getattr(itree, attr)) File "/usr/local/chimera/share/SessionUtil/objecttree.py", line 37, in it2bt return instance_tree_to_basic_tree(it, c, a) File "/usr/local/chimera/share/SessionUtil/objecttree.py", line 72, in instance_tree_to_basic_tree raise ValueError, "Can't convert type " + str(t) ValueError: Can't convert type <type 'bool'> -- The session file is written, but it doesn't contain the files I have read into chimera. Cheers, Juha Huiskonen

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Re: [Chimera-users] chimera and hydrophobic potentials
by Thomas Goddard 12 Apr '04

12 Apr '04

Hi Miguel, If GRID computes the hydrophobic potential on a surface, it seems like a bad strategy to save it in a volume format. If you interpolate onto a slightly different surface, you will get values interpolated with zeros in the volume because the hydrophobicity wasn't computed at most grid vertices. It seems it would be better to render the hydrophobicity values with exactly the GRID surface. Can GRID output the triangulated surface with hydrophobicity values? I looked at the MSMS library. It does not look like it provides a triangulated version of the solvent accessible service needed by Chimera. It can give you the surface area contributed by each atom to the solvent accessible surface. Tom > Date: Sun, 11 Apr 2004 22:39:40 +0100 > From: Miguel Ortiz <mol(a)ysbl.york.ac.uk> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] chimera and hydrophobic potentials > > Dear Tom, > > I've tested your cns2delphi script and, as expected, it works wonderful- > ly. The problem with colouring the surface using these maps actually > comes from the fact that for the hydrophobic probe, grid only calculates > the potential on what it's called the "solvent accessible surface" and > not on the whole volume (as delphi does for electrostatics and grid for > other probes). Being this the case, the best solution would be to > render in chimera this surface (at present, msms renders the "solvent > excluded surface" defined as you said in your email) > > I will try to find out how msms renders its surfaces, because the only > difference between "solvent accessible " and "solvent excluded" is that > the first is the "surface" defined by the center of the probe, while > the second (msms one) is the contact surface between the surface of the > probe and that of the protein (as defined by the Van der Waals radii of > its atoms). And it seems to me that it shouldn't be difficult to convert > from one to the other. Or perhaps I'm wrong and it's more tricky... > > Thank you again for all your help. It has been not only useful but > also instructive. > > Best regards, > > Miguel

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Re: [Chimera-users] chimera and hydrophobic potentials
by Thomas Goddard 09 Apr '04

09 Apr '04

Hi Miguel, I wrote a conversion program cns2delphi.py that takes the k2f output and produces a delphi file and tried it on the data you sent. The delphi file is read properly by Chimera DelphiViewer and can be used to color an MSMS surface. A problem with the data you sent is that the hydrophobicity map is zero over the entire MSMS surface. There are blobs of hydrophobicity a few angstroms away from the surface but they don't touch the surface. I observed this by showing the map with the Chimera volume viewer (just use File/Open...). You can change the probe radius for generating the MSMS surface by going to Favorites/Model Panel, selecting the MSMS surface, clicking the Attributes button, changing the probe radius setting, and pressing Enter. (You need to set the surface color to a solid color before changing the radius or an error message is generated.) Unfortunately that does not push the molecular surface out uniformly -- only the surface in the cavities is pushed further from the molecule. Apparently the probe radius is the radius of a ball rolled over the molecule with standard atom radii. The MSMS surface is the surface of the region that cannot be touched by the ball. So a bigger ball does not change the surface location at protrusions. Maybe a better approach is to specify larger atom radii. Below is the cns2delphi.py Python program. It requires the Numeric Python module which is not a standard part of Python. The Python that comes with Chimera includes Numeric. You can convert k2f output to delphi format as follows. % /usr/local/chimera/bin/python2.3 cns2delphi.py 1ltlA.k2f 1ltlA.phi This creates the 1ltlA.phi file. To use the Chimera DelphiViewer extension, start Chimera, open 1ltlA.pdb, make a molecular surface with Actions/Surface/Show, start Extensions/Delphi/DelphiViewer, enter Potential File 1ltlA.phi, click the Browse button next to MSMS Surface in the Molecular surface pane so the surface is listed, then press Apply in the Molecular surface pane. This will color the surface. You can also just use File/Open... on 1ltlA.phi to see an isosurface of the hydrophobicity map. You can drag the vertical bar on the histogram shown in the volume viewer dialog to change the isosurface threshold level. Tom ----- cns2delphi.py follows. Preserve indentation since it is important in Python. #!/usr/bin/env python # ---------------------------------------------------------------------------- # Convert CNS volume to Delphi format. # # ---------------------------------------------------------------------------- # Returns matrix, xyz_origin, and xyz_step # def read_cns_file(path): f = open(path, 'r') f.readline() # First line is blank ntitle_line = f.readline() # integer number of comment lines try: ntitle = int(ntitle_line.split()[0]) except ValueError: raise SyntaxError, ('Invalid CNS comment line count on line 2: %s' % ntitle_line[:80]) for t in range(ntitle): f.readline() extent_line = f.readline() extent = split_fields(extent_line, 8, 9) try: na, amin, amax, nb, bmin, bmax, nc, cmin, cmax = map(int, extent) except ValueError: raise SyntaxError, 'Invalid CNS grid size line: %s' % extent_line[:80] cell_line = f.readline() cell = split_fields(cell_line, 12, 6) try: cell_params = map(float, cell) except ValueError: raise SyntaxError, ('Invalid CNS cell parameters line: %s' % cell_line[:80]) cell_size = cell_params[0:3] cell_angles = cell_params[3:6] axis_order_line = f.readline() # Must be ZYX asize, bsize, csize = (amax - amin + 1, bmax - bmin + 1, cmax - cmin + 1) if asize <= 0 or bsize <= 0 or csize <=0: raise SyntaxError, ('Bad CNS grid size (%d,%d,%d)' % (asize, bsize, csize)) import Numeric data = Numeric.zeros((csize, bsize, asize), Numeric.Float32) for c in range(csize): read_floats(f, 1) # c section number values = read_floats(f, asize * bsize) array = Numeric.array(values, Numeric.Float32) plane = Numeric.reshape(array, (bsize, asize)) data[c,:,:] = plane f.readline() # footer - int value must be -9999 f.readline() # density average and standard dev f.close() xyz_step = (cell_size[0]/na, cell_size[1]/nb, cell_size[2]/nc) xyz_origin = map(lambda gmin, step: gmin * step, (amin, bmin, cmin), xyz_step) return data, xyz_origin, xyz_step # ----------------------------------------------------------------------------- # Read ascii float values on as many lines as needed to get count values. # def read_floats(f, count): values = [0.0] * count c = 0 while c < count: line = f.readline() if line == '': raise FileFormatError('File is shorter than expected') fields = split_fields(line, 12, 6) if c + len(fields) > count: fields = fields[:count-c] for v in map(float, fields): values[c] = v c = c + 1 return values # ----------------------------------------------------------------------------- # def split_fields(line, field_size, max_fields): fields = [] for k in range(0, len(line), field_size): f = line[k:k+field_size].strip() if f: fields.append(f) else: break return fields[:max_fields] # ---------------------------------------------------------------------------- # def write_delphi_file(path, matrix, xyz_center, scale): zsize, ysize, xsize = matrix.shape if xsize != ysize or xsize != zsize: raise ValueError, "Matrix size (%d,%d,%d) has to be the same in all 3 dimensions" % (zsize, ysize, xsize) size = xsize uplbl = delphi_record('Converted from ' + path) morelabels = delphi_record('%70s' % '') import Numeric data_flat = Numeric.ravel(matrix) data = delphi_record(floats_as_string(data_flat)) botlbl = delphi_record('') params = delphi_record(floats_as_string((scale,) + tuple(xyz_center)) + integer_as_string(size)) f = open(path, 'wb') f.write(uplbl + morelabels + data + botlbl + params) f.close() # ---------------------------------------------------------------------------- # def delphi_record(data): size_str = integer_as_string(len(data)) r = size_str + data + size_str return r # ---------------------------------------------------------------------------- # def integer_as_string(i): import Numeric return Numeric.array((i,), Numeric.Int32).tostring() # ---------------------------------------------------------------------------- # def floats_as_string(f): import Numeric return Numeric.array(f, Numeric.Float32).tostring() # ---------------------------------------------------------------------------- # def cns_to_delphi_file(cns_path, delphi_path): data, xyz_origin, xyz_step = read_cns_file(cns_path) if xyz_step[0] != xyz_step[1] or xyz_step[0] != xyz_step[2]: raise Value_Error, 'Step sizes (%.2g, %.2g, %.2g) are not the same along all axes' % xyz_step scale = 1.0 / xyz_step[0] size = list(data.shape) size.reverse() xyz_center = map(lambda o, st, sz: o + st * ((sz-1)/2), xyz_origin, xyz_step, size) write_delphi_file(delphi_path, data, xyz_center, scale) # ---------------------------------------------------------------------------- # if __name__ == '__main__': import sys if len(sys.argv) != 3: sys.stderr.write('Syntax: cns2delphi <cnsfile> <delphifile>\n') sys.exit(1) cns_path = sys.argv[1] delphi_path = sys.argv[2] cns_to_delphi_file(cns_path, delphi_path)

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