- Chimera-users - RBVI Mailing Lists

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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