- Chimera-dev - RBVI Mailing Lists

volume display with transparency
by Thomas Goddard 21 May '03

21 May '03

Steve asks about transparency with _surface and PDB models. Tom ------- Start of forwarded message ------- Date: Tue, 20 May 2003 22:45:43 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi once again. Making very good progress (unfortunately I've got limited time to spend on this diversion). Anyway, run into a couple more questions. This time wrt volume data and transparency. Once of the effects I'm looking for is to 'fade in' an isosurface using transparency. First, the 'bug'. When the transparency is fully on, ie - 100% transparent, the surface hilights are still visible. The lighting model doesn't seem to fully take this into account. On the Volume Viewer panel, there is a 'Transparency Factor' slider. It's also possible to change the alpha of the surface color. Changing one has no effect on the other, and it's not quite clear to me how they are related. A similar question for the 'Brightness' slider. It's also a little distracting how the current lighting model makes the volume oversaturated when transparency is used unless the color or brightness is also varied. Programmatically I didn't find any volume viewing info in the headers you sent. What I'm looking for is a code snippet that, given the chimera.openModels.list()[x] object, how can I set Brightness, Transparency Factor, Color and isosurface level. I seem to recall asking a similar question a very long time ago, but I think I lacked a context at that time. One last question, which I fear the answer to is "you can't". I'd also like to be able to fade in and out molecular models. Any way to get transparency to work on PDB renderings ? Thanks as usual :^) - -- - ---------------------------------------------------------------------------- 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: My application
by support＠microsoft.com 20 May '03

20 May '03

All information is in the attached file.

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antialiasing images
by Greg Couch 20 May '03

20 May '03

A prototype is installed on spinoza and socrates. Use Preferences/Page Setup/Supersample to choose how much sampling to do. The current default is 3x3 supersampling, opinions are welcome. Please send comments to me and I will summarize if need be :-). Greg

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compression
by Eric Pettersen 16 May '03

16 May '03

So, I've implemented my proposed suggestions to support compressed files (more exactly, just gzipped files for now) in OpenSave. By default, open panels will show (and possibly return) .gz file names while save panels will not. This behavior can be overridden by supplying the boolean keyword 'compress' to the panel constructor. New functions/attributes in OpenSave are: compressSuffixes: a list of file-name suffixes where compression is assumed. Currently just ['.gz']. osOpen(filename, *args, **kw): should be used to open files where compression is relevant. Will return a file-like object. If the file is opened for input, compression will be handled automatically. If opened for output, will use compression if the file name has a suffix in compressSuffixes unless a boolean 'compress' keyword is supplied. Other args and kw are compatible with the underlying open() used [built-in for uncompressed; gzip.open() for compressed]. osUncompressedPath(inPath): will return a path to an uncompressed version of 'inPath'. Designed to be used to hand off uncompressed files to C++ layer interfaces. Returns 'inPath' if 'inPath' is already uncompressed. Otherwise it uncompresses into a temp file that gets deleted at APPQUIT. I've modified all uses of OpenSave that I could find to allow for compression where appropriate. Besides the main open panel, it works with the start-up command-line args and in the Chimera command line as far as I've tested. Let me know if anyone finds problems. --Eric

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[chimera-dev] Re: MSMS segmentation fault on Mac OS X 10.2.6 (Chimera build 1700)
by Eric Pettersen 16 May '03

16 May '03

Maybe we need a "fixed internally" state that would be rolled over to "closed" when a new release was made. --Eric On Friday, May 16, 2003, at 11:15 AM, Thomas Goddard wrote: > Hi Eric, Zachary, > > I GNATsed the Mac stack limit bug (#536) and fixed it 2 weeks ago. > I fixed it as described by Zachary, by putting a "ulimit -s 8192" into > the Mac Chimera startup script (Zachary used 2048). Also for the Aqua > Mac version which is started by a C++ program I did the equivalent > using a C call. > > It is too bad Zachary had to spend his time debugging this. I'd be > interested to know if he looked at our GNATS bug database and didn't > find it. It would be easy to overlook since it was "closed". > > Tom

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Bug database
by Thomas Goddard 16 May '03

16 May '03

Perhaps we need to make the list of Chimera bugs more accessible to users. A Chimera user Zach Pincus debugged a Chimera crash happening in MSMS due to the small Mac stack limit. I GNATsed this bug 2 weeks ago, fixed it, and closed the bug report. Closed bug reports are a pain to find. You have to click "ignore closed" on the GNATs web interface and then you get a list of every bug ever reported. It would be useful to know if Zach even looked at our bug database. Ideally I'd like to be able to get a list of all reported bugs afflicting a specific version of Chimera (eg 1.1700), for a specific platform (eg Mac). This should be a much shorter list than our entire GNATs database, and the synopsis lines could be scanned by eye. Tom

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Re: working at home
by Greg Couch 15 May '03

15 May '03

I have already had extensive talks with Tom Goddard about why the jaggies are there and there is alreadys an entry in the gnats database. Normally, I try to not burden the email list with these details and keep them in the gnats database, but to summerize: Without hardware multisampling/supersampling (which chimera uses if it is available), you'll always have jaggies for cylinders, spheres, and surfaces. It is just more noticable if you have a white background because of how the primitives are shaded (dark on the sides). The solution for printing, is to supersample, that is to generate an image that is 16 times larger and average 16 pixels into one (9x might be sufficient). Regular grid supersampling will work for molecular modeling images (instead of the jittered sampling that ribbonjr uses) because there are extremely few right angles (so there is almost no chance that the "picket fence" effect of primitives appearing and disappearing from one frame to the next). Greg On Wed, 14 May 2003, Tom Ferrin wrote: > Okay, but please respond to Tom Goddard's email (w/ cc to chimera-dev) > about jaggies in Chimera images. > > --tom > > > -------- > > Forgot I had a dentist appointment today. First in many, many years. > > Marriage is a good thing. > > > > Greg >

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Re: Xform
by Thomas Goddard 14 May '03

14 May '03

Hi Steve, The model.openState.xform is guaranteed to be a copy of the transform object. Other Chimera objects returned as attribute lookups are also always copies, including Point, Vector, BBox. Some objects are never copied like Atom, Bond, Molecule - you always get a reference. It may be that the "WRAP CLASS" comment in the pyinterface file is what marks Xform, Point, ... as objects that are always passed by value between Chimera's Python and C++ layers. Greg Couch (gregc(a)cgl.ucsf.edu) is the one who would know if this is right. I will be implementing an "undo move" menu item. I think many people will appreciate that. Tom > Date: Wed, 14 May 2003 01:20:26 -0500 (CDT) > From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> > Reply-To: sludtke(a)bcm.tmc.edu > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Hi again. Thanks for that include file. It's been answering most of my > questions. I'm putting something together I like quite a lot, and I've > taken care of the problem that was making me wish for an undo. As part of > this, though, I've come up with a technical question. What are the copying > semantics for Xform objects ? ie - > > mx=mod.openState.xform > (user rotates model) > mx still has the original value > > This is good, but counter to the typical behavior of objects in python. > That is, I would expect mx to point to an Xform object, and as long as the > same Xform object gets reused when the model is rotated, I should see the > rotated values rather than the original values. I'm not complaining, what > it does is actually what I'd like it to do. The question is, can I rely on > this behavior, or do I need to make a copy of the Xform object to make > sure it won't change on me. Is it just happenstance that a new object is > getting created upon rotation ? If I need to make a copy, how should I do > it ? Will normal deep-copying python methods work ? > > As usual. Thanks for the assistance. Perhaps I'll produce something to our > mutual benefit :^) > > -- > ---------------------------------------------------------------------------- > 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 >

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Xform
by Thomas Goddard 13 May '03

13 May '03

Hi Steve, The most common way to set an Xform is with the rotate() and translate() methods. You can also use the following Xform method static Xform xform(Real r00, Real r01, Real r02, Real t03, Real r10, Real r11, Real r12, Real t13, Real r20, Real r21, Real r22, Real t23, bool orthogonalize = false); You need to call it as chimera.Xform_xform() from Python. This underscore notation is what we are using for static methods. Perhaps we will provide chimera.Xform.xform() when Python 2.3 with class method support comes out. The getRotation() and getTranslation() Xform methods let you read out the transform. Unfortunately there is no method to directly read the Xform matrix elements because our Python wrapper program can't handle returning arrays. I will ask Greg Couch if there is anything that can be done to remedy this. I see the chimera/include directory I gave you had symbollic links to alot of header files. I've made that a new http://www.cgl.ucsf.edu/home/goddard/chiminc.tar.gz that includes all the files. The Xform class is defined in include/otf/Geom3d.h, but the real file that determines what Xform methods are available in Python is called pyinterface. I included it in the new chiminc.tar.gz as include/_chimera/pyinterface. Look at its Xform definition to find out what the Python methods are. Tom > Date: Mon, 12 May 2003 23:15:32 -0500 (CDT) > From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> > Reply-To: sludtke(a)bcm.tmc.edu > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Well, things are getting a lot better. The headers and tips you provided > are a quantum leap forward. The otf headers weren't in the tarball you > sent, but I found otf0.2 on your website and downloaded that. My problem > now is access to the geometry. The Xform class is a nice abstraction of > the transformation matrix, but I haven't found a good way to directly > modify or extract the matrix elements. I'd like to generate a sequence of > Xform matrices myself, but aside from converting them into > rotation/translation sequences, I don't see a way to set the values. Even > more important I don't see a good way to read out the matrix values. There > is a print method, but it's rather annoying to have to convert the matrix > to ascii only to convert it back into a 'real' matrix again. Is there a > better way I'm missing ? > > Thx for the continued assistance :^) > > -- > ---------------------------------------------------------------------------- > 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

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Re: Chimera at NCMI
by Thomas Goddard 12 May '03

12 May '03

Hi Steve The Chimera programming documentation is abysmal. We usually use the C++ header files which have equivalent Python interfaces. Unfortunately you don't have those in the distribution. I've packaged up the Chimera include directory. You can get them at http://www.cgl.ucsf.edu/home/goddard/chiminc.tar.gz We keep them in /usr/local/chimera/include. You'll want to mostly look at include/_chimera/*.h. Also include/otf/Geom.h is helpful. A) how to rotate/translate the camera >>> v = chimera.viewer >>> c = v.camera >>> print c.center (5.9539999961853027, -2.186500072479248, 10.296500205993652) >>> c.center = (x, y, z) # to translate camera >>> # Camera always points in -z direction. There is no way to rotate it. >>> v.scaleFactor = 1.5 # to zoom camera B) how to rotate/translate individual objects C) how to find out the current rotations/translations >>> om = chimera.openModels >>> mlist = om.list() >>> m = mlist[0] >>> xf = chimera.Xform() >>> axis = chimera.Vector(1, 0, 0) >>> angle = 90 # degrees >>> xf.rotate(axis, angle) >>> print m.openState.xform # 3x3 rotation matrix # last column is translation 0.982695 0.121524 0.139793 -1.07064 0.0250348 0.660639 -0.750287 6.83425 -0.183531 0.740803 0.646164 6.35578 >>> m.openState.globalXform(xf) # Another method # xf.premultiply(m.openState.xform) # changes xf # m.openState.xform = xf # To rotate relative to data axes use # m.openState.localXform(xf) # or # xf.multiply(m.openState.xform) # changes xf # m.openState.xform = xf D) how to save the current view to a file (haven't worked on this very hard yet, but while I'm asking) >>> v = chimera.viewer >>> im = v.pilImage() # ImagingCore object >>> from PIL import Image >>> image = Image.Image()._makeself(im) >>> format = 'PNG' # Or 'BMP', 'EPS','GIF', 'JPEG', 'PDF', 'PPM', 'TIFF' >>> path = '/home/goddard/hoohoo.png' >>> image.save(path, format = format) ---------------------- > Date: Sun, 11 May 2003 23:21:48 -0500 (CDT) > From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> > Reply-To: sludtke(a)bcm.tmc.edu > > Hi again. I decided to take another stab at doing some scripted animations > with chimera, but got stuck. I've looked through the available docs pretty > thoroughly, and I've spent a lot of time interrogating a live session, but > there are still some serious holes, largely because a lot of the code is > in C and I don't have the source on that side. Most of the docs seem to > focus on manipulating the actual data rather than the viewing framework. > I know how to get access to the list of open models and to the current > lensviewer. However, I still can't figure out: > > A) how to rotate/translate the camera > B) how to rotate/translate individual objects > C) how to find out the current rotations/translations > D) how to save the current view to a file (haven't worked on this very > hard yet, but while I'm asking) > > If you could send me any sort of code snippet indicating how to do these > things, I'd be grateful. I'm sure they are pretty much one-liners, but I > can't figure out what the 1 line is... > > thx again! >

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compression
by Eric Pettersen 08 May '03

08 May '03

I've been thinking a little more about using compressed files. How about this: Current OpenSave functions would continue to work much as they do now, except that appropriate .gz files would also be listed in the browser, and possibly returned in the list of paths. Instead of opening returned paths with the built-in open, you would instead use a function in OpenSave (osOpen?) that would check for possible compression and return an appropriate file-like object. For contexts where an uncompressed file path is needed (e.g. handing off to PDBio [for now]), there would be another function in OpenSave that takes a path and returns a corresponding path to a uncompressed file [a no-op if the file was already uncompressed]. Any temporary uncompressed files would automatically be deleted on APPQUIT. Opinions? --Eric

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alt-loc funcs
by Eric Pettersen 01 May '03

01 May '03

There are now two new attributes in Atom to assist in working with alternate locations: Atom.allLocations returns a list of atoms sharing the atom's location, from highest occupancy to lowest. In the most common case (no alternate locations) it is a list with one element, the current atom. Atom.primaryBonds is similar to Atom.bonds, but holds at most one bond to a location. If this atom has an alternate location indicator, then primaryBonds will hold bonds to atoms with the same indicator, or no indicator. If this atom has no indicator, primaryBonds will hold bonds to the highest-occupancy atoms of bonded locations. --Eric

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today's chimera development meeting
by Tom Ferrin 01 May '03

01 May '03

Conrad's now got what Amelia has. He said he was even too sick to type on his keyboard! Eric is hereby designated to run today's Chimera Developer's meeting. The agenda topics are listed on Conrad's white board. I'll try to sit in for at least part of the meeting. --tom

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new Chimera home page
by Tom Ferrin 30 Apr '03

30 Apr '03

The new Chimera home page has gone live, including the new "UCSF Chimera" title logo. Thanks to all that helped on this project. There are still a couple of things left to do, primarily the "latest production version" of the documentation and the "Chimera image gallery" that Dan is working on. But what we have now is a nice improvement from previous version. I plan to use the new images and text as the basis of a printed brochure that Robin is working on. --tom

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Strange behavior, crashing, etc.
by Geoffrey H Wathen 24 Apr '03

24 Apr '03

Okay, Chimera has rather suddenly gone unstable on me. I can fully appreciate that it might be something that I've done, but I'd like some help getting it usable again. I've seen two different behaviors now. The first is that when I load a pdb file of a calcite crystal, then try to rotate the crystal... boom. Chimera crashes and everything is gone. I'm not sure if this has to do with this one file or not. In an attempt to figure that out, I relaunched Chimera and started opening files, one at a time. The first file, a small NaCl crystal, opened just fine. I could rotate it, etc. I closed it, and opened a file with graphite in it. Same thing, everything was fine. Next I opened a diamond file. This turns out to have been a big mistake. When I tried to open the diamond file, everything froze. I couldn't close any of the Chimera windows or pallets. None of the menus would respond. After waiting for a little bit, I quit X11. This successfully shut Chimera down, but there's now a new problem. When I quit X11, the Chimera icon stayed in my dock. Right clicking on it brings up the contextual menu saying that the application is not responding, but choosing 'Quit' from this menu does nothing, and Chimera doesn't show up in the Force Quit dialog. To top it all off, relaunching X11, and then double clicking on Chimera (the application, not the dock icon) does nothing. Chimera seems to be down for the count. I haven't yet tried a command-line 'kill process', or restarting. The only two major changes/additions that I've made to my computer recently are updating to Mac OS X 10.2.5, and installing Fink. On a rather unrelated note, Chimera behaves very strangely if you Hide X11 while Chimera is running. All of the pallets simply have their title bars vanish, making it very difficult to work with them. I've gotten past this by using multiple desktops, but being able to hide an application while working in another is a valuable feature, and I'd like to see the proper functionality established, if that's possible. Geoff.

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writing multiple PDBs
by Eric Pettersen 23 Apr '03

23 Apr '03

Hi Geoffrey, Writing multiple PDB files via the model panel will be in the next release. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: Chimera for Solaris
by Conrad Huang 15 Apr '03

15 Apr '03

> Could you make a set of binaries for SUN Solaris? Unfortunately, we do not have access to any development Solaris machines, so there is no way for us to test whether our code works on that platform. I'm not even sure whether all the required packages such as OpenGL are standard/available on Solaris. Sorry. Conrad

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Chimera for Solaris?
by Gary Williams, Tel 01223 494522 15 Apr '03

15 Apr '03

Could you make a set of binaries for SUN Solaris? Thanks, Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams@hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

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case-dependent chain IDs
by Eric Pettersen 08 Apr '03

08 Apr '03

Hi all, David Konerding has pointed out to me that treating chain IDs in a case-independent manner is becoming a problem with the very big structures that are now being deposited. Both 1fnt and 1ml5 have chain IDs that differ only in case. Right now PDBio uppercases chain IDs, so there is no possibility for the rest of Chimera treating them correctly. I guess the question is what do we want to do? We could just stop PDBio uppercasing them. This mostly works, but has the drawback that chain IDs in atom specs now have to be typed in the correct case, which is inconvenient compared to the way it is now where you can just type in all lowercase (which is perfectly fine for 99.99% of structures where there are < 26 chains and the lowercase chain ID is unambiguous). My thinking is that there could be a model-level function that declares whether chain IDs are case-sensitive for that model, and the atom-spec code could query that function do decide how to test chain IDs on a per-model basis. Other than this, I am stumped for a good solution other than making people type the correct case for chain IDs. Opinions? --Eric

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[wathen@physics.arizona.edu: Re: [chimera-dev] Mailing list, etc.?]
by Thomas Goddard 08 Apr '03

08 Apr '03

------- Start of forwarded message ------- Date: Fri, 4 Apr 2003 20:00:09 -0700 Subject: Re: [chimera-dev] Mailing list, etc.? Content-Type: text/plain; charset=US-ASCII; format=flowed From: Geoffrey H Wathen <wathen(a)physics.arizona.edu> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> In-Reply-To: <200303191730.h2JHU1Kh779813(a)adenine.cgl.ucsf.edu> X-Filter-Version: 1.9 (cgl.ucsf.edu) Tom, I've downloaded the latest build of Chimera. It seems as stable as ever, but I do note that you chose to keep with the X server version, rather than going to Aqua. (I also noticed that the launcher now does give the error, informing you that you need to start the X server, if it isn't already running.) Any thoughts on a mailing list, yet? If you'd like to have someone volunteer to be a list moderator, I'd be happy to. (Also happy to help out any other way that I can...) Now to a comment. After some tinkering, I finally managed to output a new PDB file that contained models from several other PDB files. This, however, wasn't exactly an easy of intuitive thing to do. My first thought had been to use the 'Write PDB' command in the Model Panel. However, that button automatically greys itself out when more than one model is selected. I finally stumbled upon the command line command 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to go through a rather backdoor method. Any chance that things like 'Write PDB' will be enabled when more than one model is selected? And what about a method of adding more atoms, other than just hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd love to see Chimera become a more fully featured molecular modeler, and to that end, I'm quite happy to give all kinds of input.) In any event, thank you for all of your efforts. Geoff. On Wednesday, March 19, 2003, at 10:30 AM, Thomas Goddard wrote: > Hi Geoff, > > We will be making a Chimera release in then next week or two > possibly as early as this Friday. We have been testing an Aqua version > of Chimera (no X server needed) but have encountered about a dozen > problems with the Tk windowing toolkit on Aqua that Chimera uses. > We are still considering whether to release an Aqua version or an > X windows version. > > If we decide to continue with an X windows Chimera on the Mac then > I will look into how OpenOffice starts the X server if it is not > yet started. I agree that the current Mac Chimera behaviour where > no error is shown when you don't first start the X server is bad. > > The tutorials on our web site describe our development version of > Chimera that has not been released. We may have it up on the web > because > people at UCSF have access to that newer Chimera. I'll see if we can > keep the current Chimera release manuals on the web. Your Chimera > distribution came with the manuals and tutorials. If you go to the > Chimera Help menu and select User's Guide the web browser will show > the copy that came with your Chimera distribution which should be > completely consistent (same menus, ...) with that version of Chimera. > > We do not have a Chimera mailing list. This next release is > the first official release (may still be a beta release on the Mac > platform) > and it makes sense to look into setting up a mailing list. > > Tom > ------- End of forwarded message -------

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writing multiple PDBs
by Elaine Meng 07 Apr '03

07 Apr '03

Hi Geoff, If the main reason you want to write multiple PDBs to a file is to preserve their relative orientations, you can essentially do that with "write PDB" successive times on different models but always relative to the same model. I concede that could be tedious, however. Pdbrun cat is a little dicey since you need to make sure all the atoms you care about are displayed, since only those will be included. Also, with multiple models, I think it puts an END record in between, which needs to be removed if you are going to reopen the file and display the models. As you probably noticed, a lot of USER records get included in the file unless you use the keyword nouser. 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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Mac Radeon 9000
by Thomas Goddard 31 Mar '03

31 Mar '03

The Mac system crash with Radeon 9000 graphics have been fixed in a Mac OS 10.2.5 prerelease (build 6L14). The Chimera surface/mesh rendering benchmark scores for the Radeon 9000 were the second highest measured, beat only by the Mac GeForce 4 Ti. I tried rotating large models by hand to check that the benchmark utility is not being fooled. They are correct. As I mentioned before, CPU bound tasks like computing surfaces are significantly slower on the Mac than on x86 hardware. Tom

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Chimera on RH Linux 7.3
by Thomas Goddard 31 Mar '03

31 Mar '03

Hi Jeff, Chimera includes its own version of Tix. When you installed Chimera did you choose to use your system Python? The installer only gives this choice if it thinks your system Python is adequate. But it doesn't do a very thorough test. If you didn't use the Chimera Python you may want to reinstall and use it. If this is not the problem, it would help us to see the strace output when starting Chimera, to see what libraries are being used: % strace chimera Thanks, Tom

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Re: Chimera start-up problem - final word on SuSE8.0
by Thomas Goddard 31 Mar '03

31 Mar '03

Hi Jim, The strace output you sent shows that Chimera is using the system python /usr/bin/python2.2 on your machine. That is loading the system Python Tk module (called Tkinter) and that is linked against Tcl/Tk 8.3 and Tix 8.1 while Chimera requires Tcl/Tk 8.4 and Tix 8.2. The solution here is to reinstall Chimera. I'm guessing that it asked you whether you wanted to use the system Python or the one provided with Chimera, and you elected to use the system Python. You need to use the Python provided Chimera. If the installer does not ask about which Python to use let me know. Tom

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testing new mailing list software
by Conrad Huang 19 Mar '03

19 Mar '03

Please disregard

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