- Chimera-users - RBVI Mailing Lists

HELIX/SHEET/CONECT records for non-existent bonds/atoms are being inserted into file.pdb when pdbrun nouser cat > file.pdb is run
by Sabuj Pattanayek 07 Mar '05

07 Mar '05

Hi, If I load a pdb, display only selected atoms/bonds, then do pdbrun nouser cat > file.pdb, the outputted pdb file also has HELIX/SHEET/CONECT records for non-existent bonds/atoms (as if the pdb file in its entirety was written out). Is this a bug or a feature? Is there some way to completely turn off output of HELIX/SHEET/CONECT records? Thanks, Sabuj Pattanayek

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"add-vertex" button volume viewer
by Andrew Jewett 02 Mar '05

02 Mar '05

Please forgive and ignore my earlier post. I should have read the manual first. These features are already implemented. I'm sorry. However there are some user-interface issues... In particular, the method for adding and deleting points to the transfer function that determines voxel opacity and color could be more intuitive. (CTRL-click) This can have a big impact. I suggest putting small add-vertex, cut-vertex buttons near the histogram graph (see attatchment #1). (I stole these icons from xv) The results of using multiple vertices to control colors and or brightness-levels are strikingly better than using just two points. It would be good to make it obvious from the user interface that this option is available. Also, each time the user adds another vertex, a new color should be chosen, not the default white, in order to clue the user that the color can be changed. Similarly, it would be good to explicitly have an "add surface" "delete surface" buttons in solid or mesh mode. (No icon necessary, just write the names out in the buttons themselves itself). So go ahead and leave CTRL-Click in, but add buttons to make it explicit, and make the default color change each time a new vertex (or isosurface) is added. I've played with volume-viewer for quite a while, without realizing these options were available. (RTFM, I know...) And these features are _cool_. For example, attatchment#2 is an image of the same phage-T4 shown in the chimera image gallery using multiple colors. I like it a little better than the static grey image that Steve McQuinn made for the image gallery. http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/phageT4/phageT4c.jpg Again, I apologize for my earlier email. Anyway, cheers Andrew okay, back to work...

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colormap -and- opacity functions for voxels
by Andrew Jewett 01 Mar '05

01 Mar '05

Hi. I've asked a lot of questions, and I keep getting these long thoughtful and technical replies. Thanks. It's nice to get these replies However don't feel obligated to reply at all, at least when I post a question. The other features I mentioned are more important to me at least. I don't want you to be kept busy replying to emails. The question is: why not have a simultaneous independent opacity-map and color-maps for voxel-rendering? (...and I suppose, why do they have to be linear functions? Is piecewise linear hard to implement?) It seems unnecessary that the voxel values should only determine the opacity of the voxel. It seems reasonable to allow the color to be determined by the volxel value in addition to the opacity (for example, a cold-to-warm-to-hot color scheme). It looks like some kind of colormap user interface has been implemented in chimera. (Nice T4-phage slab image, by the way..) Would this be hard? This way, one could distinguish the DNA inside the T4 phage from the within capsid shell. Currently, 3-D volumetric rendering is cool, but it needs ...something. Since the demand for voxel rendering is probably low, I would understand if you choose to delay to ignore these issues. Andrew ------- That's the end of my question, but I included ------- some pictures at the end, for comparison. ------- You can skip this part. ------- They are not in color, but they do look ...pretty. ------- I wonder what they are doing? http://radiographics.rsnajnls.org/cgi/content/full/19/3/745/F5 http://radiographics.rsnajnls.org/cgi/content/full/19/3/745/F19 http://radiographics.rsnajnls.org/cgi/content/full/19/3/745/F13A http://radiographics.rsnajnls.org/cgi/content/full/19/3/745/F13B http://radiographics.rsnajnls.org/cgi/content/full/19/3/745/F8B http://radiographics.rsnajnls.org/cgi/content/full/19/3/745/F16A http://radiographics.rsnajnls.org/cgi/content/full/19/3/745/F17 Probably the main reason it looks so nice I think is because their data is manifestly much less bumpy than electron microscopy data. Also I'm suspect that increadibly expensive 3-D hardware doesn't hurt either. However there is something else interesting going on in these pictures. It seems that what appear to be fully opaque objects have a range of brightnesses/colors. In chimera, fully opaque objects are solid white (or blue or whatever color is set by the user) and they have no features except their somewhat fuzzy silhouette. The source of these pictures is a paper published at: http://radiographics.rsnajnls.org/cgi/content/full/19/3/745 One thing they talked about in the article was that they use separate brightness and opacity functions as a function of voxel value. They also use more general piecewise-linear functions instead of linear ones ("percentage classification"). The combination of those two features might explain something. Anyway, I wonder what they are doing. No need to reply. I'd rather you work on other stuff right now. Cheers! Andrew

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per-model-clipping needs "all models" option
by Andrew Jewett 01 Mar '05

01 Mar '05

Hi. Please forgive me for sending this message twice. In the first version, I forgot to include a subject line, so I'm sending it again. --------------- On Fri, 25 Feb 2005, Thomas Goddard wrote: > chimera-users(a)cgl.ucsf.edu When using the Per-Model-Clipping tool and selecting which model to apply the clipping to, there should be an option "All Models", and it should be the default option. Without this feature, some unintended results can happen. Suppose the user generates a surface either with MSMS or multiscale. If the user then uses the menu to select Tools->Graphics->Per-Model-Clipping The default model is the one with the atoms and bonds, not the surface model. When the user moves the clipping plane it will seem like nothing is hapenning. The user has to be quite attentive to realize that they have to select the surface model from the list. It would be better to have an "all models" option that is the default. Thanks Cheers! Andrew

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by Andrew Jewett 25 Feb '05

25 Feb '05

On Fri, 25 Feb 2005, Thomas Goddard wrote: > chimera-users(a)cgl.ucsf.edu When using the Per-Model-Clipping tool and selecting which model to apply the clipping to, there should be an option "All Models", and it should be the default option. Without this feature, some unintended results can happen. Suppose the user generates a surface either with MSMS or multiscale. If the user then uses the menu to select Tools->Graphics->Per-Model-Clipping The default model is the one with the atoms and bonds, not the surface model. When the user moves the clipping plane it will seem like nothing is hapenning. The user has to be quite attentive to realize that they have to select the surface model from the list. It would be better to have an "all models" option that is the default. Thanks Cheers! Andrew

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Re: pdb parsing problem-- hydrogen as mercury
by Josh Tasman 18 Feb '05

18 Feb '05

Eric and Greg, Thanks for your comments and help. Eric, thanks especially for the concise script. Dealing with the variety of non-standard-format PDB files is truly maddening, and I appreciate the help. Josh

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pdb parsing problem-- hydrogen as mercury
by Josh Tasman 18 Feb '05

18 Feb '05

I'm getting errors on reading PDB files containin hydrogens added by TRIPOS SYBYL. For example, the atoms 1677-1679 are parsed as Mercury (HG): ATOM 1674 HD11 ILE A 107 4.939 -2.338 17.094 1.00 0.00 ATOM 1675 HD12 ILE A 107 6.613 -2.979 16.971 1.00 0.00 ATOM 1676 HD13 ILE A 107 5.703 -3.133 18.512 1.00 0.00 ATOM 1677 HG21 ILE A 107 4.770 -2.095 20.141 1.00 0.00 ATOM 1678 HG22 ILE A 107 6.235 -1.314 20.827 1.00 0.00 ATOM 1679 HG23 ILE A 107 4.630 -0.527 21.006 1.00 0.00 ATOM 1680 H ILE A 107 5.291 0.799 16.773 1.00 0.00 ATOM 1681 N TYR A 108 3.267 1.810 19.498 1.00 21.63 Accoring to the table at http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl There are descrepencies between PDB-like file formats, and we see that the official PDB format would specify "1HG2" instead of "HG21". Does anyone know of a quick way to deal with this? I can write a perl search/replace script if need be. Thanks, Josh

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Re: [Chimera-users] Percent done
by Greg Couch 09 Feb '05

09 Feb '05

On February 7, 2005, David Belnap wrote: > It would be useful to have a percent done displayed when the image is being > rendered. I have a very large job that has been running for two days. I > think it is still progressing so I have not stopped it. For slower > machines or large jobs, it would be nice to know how far along jobs are. > > Thanks. I'm enjoying Chimera. I'm going to assume that you're having problems when you save images and you'd like an indication of how far along it is. That will slow down the image saving, but probably not very much. I'll look into it. I am really curious about how large a job you're running. The only way it could take two days is if you don't have enough physical memory and the system is paging memory to and from the disk. Some operating systems are better at handling programs that need more memory than is physically available than others (ie., BSD Unix and Linux), but all do poorly. Any system that doesn't exhaust memory, should be saveable in minutes. So, you should get some more physical memory for your computer if at all possible. We are working on making chimera more memory efficient, but that work won't be done until May or so. Thank you for using chimera, Greg Couch UCSF Computer Graphics Lab gregc(a)cgl.ucsf.edu

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Percent done
by David Belnap 07 Feb '05

07 Feb '05

It would be useful to have a percent done displayed when the image is being rendered. I have a very large job that has been running for two days. I think it is still progressing so I have not stopped it. For slower machines or large jobs, it would be nice to know how far along jobs are. Thanks. I'm enjoying Chimera. David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

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Re: [Chimera-users] Getting an extension handle
by Elaine Meng 07 Feb '05

07 Feb '05

> How would I get get a handle on a running instance of an extension? > Specifically, I want to be able to associate my own structures to > sequences in the MultAlignViewer. Hi Charlie, If I understand you correctly, this is something you can do this in the user interface (without dealing with code). Your structures should automatically associate with the sequences when opened in Chimera, if the structure's sequence and the sequence in the alignment match well enough. Even if they don't, you can "force" the structure to associate using Multalign Viewer's menu option Structure... Associations This option brings up a dialog in which you can specify which of the structures open in Chimera should be associated with a sequence in the alignment. I hope this helps, Elaine --- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Getting an extension handle
by Charles Moad 07 Feb '05

07 Feb '05

How would I get get a handle on a running instance of an extension? Specifically, I want to be able to associate my own structures to sequences in the MultAlignViewer. Thanks, Charlie

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re H-Bonds in ViewDock
by Vidana.Epa＠csiro.au 02 Feb '05

02 Feb '05

Hi Chimera users, I've started to use Chimera recently. When using ViewDock it struck me that it would be very useful, after loading a .mol2 file of ligands and computing H-bonds between them and the receptor, to be able to list the number of H-bonds as a column in the ViewDock ListBox. Or, is it somehow possible to do this already? (One way to fix this might be to have a script that will write the number of H-bonds computed for each molecule in a new .mol2 file, and then read in this modified .mol2 file .... Has anybody done something in this fashion?) Thanks very much. Cheers, Vidana. Vidana C. Epa CSIRO, Division of Health Sciences & Nutrition, 343 Royal Parade, Parkville, Victoria 3052, AUSTRALIA. tel.: (61) - 3 - 9662 - 7345 fax.: (61) - 3 - 9662 - 7347 email: Vidana.Epa(a)csiro.au

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Ribbon for a non-standard peptide
by Jagannadh Dr B, Scientist 01 Feb '05

01 Feb '05

Hi, I am new to Chimera Can any one suggest how one can draw a ribbon for a peptide which has non-standard residues Jagannadh

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[Chimera-users] Defining Attribute Color for Surface Independent of Atoms
by David Piper 25 Jan '05

25 Jan '05

Chimera Folks, I have set up a file to define a series of colors based on functional measurements for some residues in a PDB file. I would like to color the ball and stick atoms according to element type and a semi-transparent surface according to the colors defined by my text file. It seems like these two things are tied together; that the surface can either be colored by the model, the atoms, or a specific color. Can I color it according to a Defined Attribute but leave the atoms as CPK coloring? Thanks, David

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chimera --stereo crash
by Liu, Hao-Yang 24 Jan '05

24 Jan '05

Dear Sir/Madam, I am running chimera in IRIX, and when I am trying to run "chimera --stereo", I got this message: Unable to find hardware stereo support (Togl: couldn't get visual) and when I click ok, the program just quit. I can use the normal (mono) mode in chimera. and I think I had the hardware, because I use midas a lot, and never had problem in midas. Could you tell me how can I use the stereo mode in chimera? What am I missing? Thanks Hao-Yang Liu

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selecting
by John Nixon 18 Jan '05

18 Jan '05

Hi folks, I'm a newbie and am having trouble getting started. Sorry to be dense. Using the command line on a single protein chain O select :32-42,44-49.O or rep sphere :43:56:59:60:61:63:65:67:68:70:71:72:73:74:75:78:110:113.0 only seems to work on the last residue. Thus I'd have to write a separate command for each residue. Could you tell me what I've missed please! John

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[Chimera-users] FW: [PyMOL] Stereo-3D in a Window: Not in MacOS X Tiger?!!
by Warren DeLano 14 Jan '05

14 Jan '05

Greetings Fellow Vendors and Software Developers! Is stereo 3D graphics support on MacOS X something you would like to see soon? If so, then please take just 30 seconds to respond to the following petition. We've received more than 300 compelling responses over the past 18 hours about the importance of supporting stereo 3D graphics today -- but we will need more to convince Apple, so please consider participating. It is as easy as clicking this following link, adding a few words with your personal perspective on the issue, and then hitting send! mailto:warren@delsci.com&subject=Stereo%203D%20Matters%20to%20Me%21 Cheers, Warren -----Original Message----- From: pymol-users-admin(a)lists.sourceforge.net [mailto:pymol-users-admin@lists.sourceforge.net] On Behalf Of Warren DeLano Sent: Thursday, January 13, 2005 5:59 PM To: pymol-users(a)lists.sourceforge.net Subject: [PyMOL] Stereo-3D in a Window: Not in MacOS X Tiger?!! Fellow Visualization Software Users: My #1 gripe with MacOS X Panther has been the lack of support for industry-standard stereo-3D graphics (in a window). So far, I and others have been unable to convince Apple that this feature matters enough to their bottom line to merit implementation. Candid discussions this week at MacWorld confirmed that Tiger (OS X 10.4) will likewise ship without this essential capability at a time when the opportunity for Apple is at its peak in this market. I believe this would be a serious error, and that Apple must now hear from us on this issue. If you agree, then please reply directly to me, RIGHT NOW (mailto:warren@delsci.com) with the words: "Stereo 3D matters to me." Your response will be printed, and I will hand-deliver them to Apple management in nearby Cupertino at the end of the month. We need AS MANY responses as we can get (ideally 1,000+), so please forward this email to all of your visualization-oriented colleagues (in any sector), and ask them to submit individual emails to me as well. Here's why: Stereoscopic 3D visualization increasingly matters in science, medicine, and engineering. Though arguably the ultimate technical computing platform, the Mac remains hopelessly crippled in this key respect when compared to Sun, HP, Dell, or IBM workstations running Linux, Solaris, or even Windows. Dual-Xeon and dual-Opteron systems now ship stereo-3D-ready thanks to powerful nVidia/Quadro and ATI/FireGL graphics cards. Thus, the competition WILL OWN THIS MARKET if Apple doesn't support stereo-3D in a window on MacOS X, ASAP. The disruptive market opportunity created by the implosion of SGI and the stopgap adoption of "home brew" Linux systems is about to end. Professional-grade stereoscopic visualization is now a standard OpenGL capability, it is vendor-supported on a variety of hardware, and it is present on every platform EXCEPT THE MAC. None of those "amazing features" in Tiger matter one bit to technical users whose basic needs remain unmet. Stereo-3D inadequacy is a show-stopper for many scientists and engineers. The Mac will not have a fair shot at this market unless Apple quickly follows though on it's assumed responsibility to support all OpenGL features, including quad-buffered stereo-3D graphics in a window. Case in point: my company just spent $5k on a dual-Opteron Sun workstation instead of a dual-G5 Mac solely because stereo-3D in a window is absent from MacOS X. This pattern will surely be amplified many thousand-fold if Apple does not take immediate corrective action. Responding together, we can insure that Apple understands what this deficiency means for the future of MacOS X in scientific, medical, and technical visualization. I do not believe that Apple management has made an informed decision regarding stereo-3D, and I think this is our last best chance to change things before the issue becomes moot. Please share your concerns by responding to this email (mailto:warren@delsci.com). It will only take a second, but the benefits could last for years to come if Apple listens well and then acts decisively. Input from current Linux and Windows users is especially welcome, since Apple would love to sell you the visualization platform of your dreams if you're willing to help define it. Thank you for your time. Cheers, Warren Author of PyMOL: http://pymol.sf.net (Note that MacPyMOL is currently shown on http://apple.com/science under "The Tools" -- cool!) DeLano Scientific LLC company profile: http://delanoscientific.com/about.html PS. An alternate way to be heard is to post on the Apple SciTech or Sci-Vis mailing lists, but please CC me too to be sure that you're counted. http://lists.apple.com/mailman/listinfo/scitech http://lists.apple.com/mailman/listinfo/sci-vis -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren@delsci.com ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt _______________________________________________ PyMOL-users mailing list PyMOL-users(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users

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Re: [Chimera-users] Mol2 Trajectory Reader?
by Eric Pettersen 06 Jan '05

06 Jan '05

Hi Joshua, Given that what you really want to do is assemble a movie of your conformations rather than actually analyze them as a trajectory, what we've decided to do is write an extension that will allow you to record whatever is going on in Chimera as a series of frames (it will have a "Start" and a "Stop" button) and will assemble those frames into an mpeg. It will optionally allow you to keep the frames in case you want to assemble them into a format that is harder for us to support across all platforms (e.g. Quicktime), and may also support generating an animated GIF. A preliminary version will probably be done in a couple of weeks and we could send that to you if you want to be a guinea pig. Otherwise, it will be in the next release, which will probably be April or so. --Eric On Dec 25, 2004, at 8:15 PM, S Joshua Swamidass wrote: > Good point. > > I didn't notice the move menu. The ultimate goal of all this for me is > to literally make some movies, either with screen shots in sequence or > ideally if chimera can output an avi automatically. So i guess, > viewdock should work IF there is a way to capture all the images to > disk rather than just play them to the screen. > > S Joshua Swamidass > > > On Sat, 25 Dec 2004 09:29:55 -0800, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: >> Hi Joshua, >> Implementing the Mol2 trajectory format looks perfectly doable >> with >> the data file you provided. Before proceeding with the work, I guess >> I >> have a question as to why you want to use the molecular-dynamics Movie >> tool on the file rather than ViewDock tool. You do know that the >> ViewDock tool has a "Movie" menu >> (http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ >> viewdock/viewdock.html#movmenu) that allows you to step through docked >> conformers one by one? I guess I'm trying to determine if I should >> really be adding this fomat to the Movie tool or if we should somehow >> be improving the capabilities of ViewDock instead. >> >> --Eric

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Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Li Wang 04 Jan '05

04 Jan '05

Dear all, I forgot to attach the python code in my previous email. Please let me know if there is anything wrong with the code. By the way, I am using the Chimera beta version 1, build 1917, 2004/03/08. Should I download the newer version, version 1 build 2065? Thank you so much for your help in advance. Li

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Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Li Wang 04 Jan '05

04 Jan '05

Dear Eric, I just join the Chimera-users discussion group and haven't got reply email. However I checked the archive and found your reply email related to the WinXP SP1 python error on File -> Open. I have been using Chimera to generate the colorful ribbon picture for the pdb file using command line. Now I am tring to figure out the general way of defining the bfactor range corresponding to the different colors. I found the flexible python code for making the rainbow color by bfactor and tried it out. But it ended up with the file/open error message as I didn't see any problem in the code. Attached please find the copy of the python code. I did replace bo and b1 by min and max of bfactors in the pdb file. Your help and suggestion are greatly appreciated. Li Wang Biomedical Informatics of OSU Columbus, OH (w) (614)688-3236

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Mol2 Trajectory Reader?
by S Joshua Swamidass 21 Dec '04

21 Dec '04

Hello, How hard would it be to write an extension to chimera that read a multimolecule mol2 file into chimera as a trajectory? That would be really useful for me. Please let me know if you can do it or some advice on how to procede. S Joshua Swamidass

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Chimera Guassian Cube Extension
by S Joshua Swamidass 20 Dec '04

20 Dec '04

Hello, I have a bit of code to contribute. It allows chimera to read grid files in the GUASSIAN ascii grid format described here: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html It ignores any bond information. Who should i send it to so it will be incorporated into future releases? S Joshua Swamidass

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production release
by Eric Pettersen 17 Dec '04

17 Dec '04

Hail fellow Chimerians, We just put out a production release (version 1.2065). It is basically the same as the preceding release candidate (1.2056) except for a lot of bug fixes. The only new features are support for saving scenes in X3D format [but see the release notes for caveats], and some changes in how the label/rlabel commands interact. The release notes are at: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2065.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Chimera Multiscale using VRML?
by Thomas Goddard 13 Dec '04

13 Dec '04

Hi Dong, Here is an example VRML file that contains a virus particle model. It uses a cone as the icosahedral asymmetric unit. You could change the definition of the asymmetric unit at the top of the VRML. This file will display in Chimera 1.2056. Tom ----- File icos.vrml follows: #VRML V2.0 utf8 Transform { children [ DEF asymmetric_unit Transform { translation 0 5 0 children [ Shape { geometry Cone {} } ] } Transform { rotation 0.00000000 0.00000000 1.00000000 0.00000000 children USE asymmetric_unit } Transform { rotation -0.30901699 0.80901699 -0.50000000 3.14159265 children USE asymmetric_unit } Transform { rotation 0.57735027 0.57735027 -0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation 0.93417236 -0.35682209 -0.00000000 2.09439510 children USE asymmetric_unit } Transform { rotation 0.85065081 0.00000000 -0.52573111 2.51327412 children USE asymmetric_unit } Transform { rotation 0.52573111 -0.85065081 0.00000000 2.51327412 children USE asymmetric_unit } Transform { rotation 0.30901699 0.80901699 -0.50000000 3.14159265 children USE asymmetric_unit } Transform { rotation -0.00000000 -0.52573111 0.85065081 2.51327412 children USE asymmetric_unit } Transform { rotation 0.35682209 0.00000000 -0.93417236 2.09439510 children USE asymmetric_unit } Transform { rotation 0.52573111 -0.85065081 0.00000000 1.25663706 children USE asymmetric_unit } Transform { rotation 0.57735027 -0.57735027 -0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation 0.00000000 -0.93417236 0.35682209 2.09439510 children USE asymmetric_unit } Transform { rotation -0.50000000 -0.30901699 0.80901699 3.14159265 children USE asymmetric_unit } Transform { rotation -0.35682209 0.00000000 0.93417236 2.09439510 children USE asymmetric_unit } Transform { rotation 0.00000000 -0.52573111 -0.85065081 2.51327412 children USE asymmetric_unit } Transform { rotation -0.52573111 -0.85065081 -0.00000000 1.25663706 children USE asymmetric_unit } Transform { rotation 0.00000000 -0.93417236 -0.35682209 2.09439510 children USE asymmetric_unit } Transform { rotation -0.57735027 -0.57735027 0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation -0.50000000 0.30901699 0.80901699 3.14159265 children USE asymmetric_unit } Transform { rotation -0.57735027 0.57735027 0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation 0.30901699 0.80901699 0.50000000 3.14159265 children USE asymmetric_unit } Transform { rotation -0.93417236 -0.35682209 0.00000000 2.09439510 children USE asymmetric_unit } Transform { rotation -0.52573111 -0.85065081 0.00000000 2.51327412 children USE asymmetric_unit } Transform { rotation -0.85065081 0.00000000 0.52573111 2.51327412 children USE asymmetric_unit } Transform { rotation -0.30901699 0.80901699 0.50000000 3.14159265 children USE asymmetric_unit } Transform { rotation -0.52573111 0.85065081 0.00000000 2.51327412 children USE asymmetric_unit } Transform { rotation 0.52573111 0.85065081 0.00000000 2.51327412 children USE asymmetric_unit } Transform { rotation 1.00000000 0.00000000 0.00000000 3.14159265 children USE asymmetric_unit } Transform { rotation 0.80901699 0.50000000 -0.30901699 3.14159265 children USE asymmetric_unit } Transform { rotation 0.80901699 -0.50000000 -0.30901699 3.14159265 children USE asymmetric_unit } Transform { rotation 0.00000000 1.00000000 0.00000000 3.14159265 children USE asymmetric_unit } Transform { rotation 0.85065081 -0.00000000 -0.52573111 1.25663706 children USE asymmetric_unit } Transform { rotation 0.57735027 -0.57735027 0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation -0.00000000 0.52573111 -0.85065081 2.51327412 children USE asymmetric_unit } Transform { rotation 0.50000000 -0.30901699 0.80901699 3.14159265 children USE asymmetric_unit } Transform { rotation 0.00000000 0.52573111 -0.85065081 1.25663706 children USE asymmetric_unit } Transform { rotation 0.85065081 0.00000000 0.52573111 1.25663706 children USE asymmetric_unit } Transform { rotation 0.93417236 0.35682209 0.00000000 2.09439510 children USE asymmetric_unit } Transform { rotation 0.80901699 -0.50000000 0.30901699 3.14159265 children USE asymmetric_unit } Transform { rotation 0.00000000 0.93417236 -0.35682209 2.09439510 children USE asymmetric_unit } Transform { rotation -0.57735027 0.57735027 -0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation 0.52573111 0.85065081 -0.00000000 1.25663706 children USE asymmetric_unit } Transform { rotation 0.85065081 0.00000000 0.52573111 2.51327412 children USE asymmetric_unit } Transform { rotation 0.80901699 0.50000000 0.30901699 3.14159265 children USE asymmetric_unit } Transform { rotation -0.93417236 0.35682209 -0.00000000 2.09439510 children USE asymmetric_unit } Transform { rotation 0.00000000 0.93417236 0.35682209 2.09439510 children USE asymmetric_unit } Transform { rotation -0.52573111 0.85065081 0.00000000 1.25663706 children USE asymmetric_unit } Transform { rotation 0.57735027 0.57735027 0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation -0.85065081 0.00000000 -0.52573111 2.51327412 children USE asymmetric_unit } Transform { rotation -0.57735027 -0.57735027 -0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation -0.85065081 -0.00000000 0.52573111 1.25663706 children USE asymmetric_unit } Transform { rotation 0.00000000 0.52573111 0.85065081 2.51327412 children USE asymmetric_unit } Transform { rotation -0.00000000 0.52573111 0.85065081 1.25663706 children USE asymmetric_unit } Transform { rotation 0.50000000 0.30901699 0.80901699 3.14159265 children USE asymmetric_unit } Transform { rotation -0.85065081 0.00000000 -0.52573111 1.25663706 children USE asymmetric_unit } Transform { rotation -0.00000000 -0.52573111 -0.85065081 1.25663706 children USE asymmetric_unit } Transform { rotation 0.00000000 -0.52573111 0.85065081 1.25663706 children USE asymmetric_unit } Transform { rotation 0.00000000 0.00000000 1.00000000 3.14159265 children USE asymmetric_unit } Transform { rotation 0.35682209 0.00000000 0.93417236 2.09439510 children USE asymmetric_unit } Transform { rotation -0.35682209 0.00000000 -0.93417236 2.09439510 children USE asymmetric_unit } ] }

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Chimera export surfaces as VRML questions
by Thomas Goddard 10 Dec '04

10 Dec '04

Hi Dong, I have fixed the grayed out "Open" button in Chimera 1.2056 "Export surfaces as VRML" extenstion and that fix will be in our upcoming release (a few weeks). We are working on being able to export molecules (ribbons, ball and stick, ...) as well. We have written code that exports X3D format which is a successor to VRML format. There is no Chimera user interface for writing an X3D file yet. Few programs are able to read X3D so we may need to find a way to convert the X3D to VRML. Greg Couch on the Chimera development team is working on the X3D output. I don't know if it will be available in our next release. You mention that you had to eliminate the outermost part of the VRML code that Chimera exports Transform { children [ ] } in order to get some programs to read it. The Transform node is very common. I'm surprised it is causing trouble. What program is unable to read the unedited version of the Chimera VRML output? The Transform node usually positions the enclosing model (rotating and translating). Our current VRML output doesn't specify any rotation or translation so the VRML output does not preserve the orientation you have in the Chimera graphics window. It should. So instead of removing the Transform node I think the next step will be to add the correct rotation and translation information. I'll respond to your Multiscale questions in a separate email. Tom > Dear my concern > > Thank you for the distribution of this nice program, Chimera! > > Recently I downloaded new version of Chimera for Win32, 2056 build. > > Most of all function is fine but when I tried to export surface as VRML, the > button for "save" is not activated. > > Instead of "save" there is "open" button. This button could be activated > only by clicking "present file". > > If user clicks that activated button, the original file has gone and > replaced with new content's keeping its name. > > Is there any way to export other model, like ribbon or space fill model as > VRML? > > I think it will be very helpful. > > I tried lots of program, but the other programs are not good as Chimera at > least in terms of VRML export. > > My main purpose of using this program is "Multiscale modeling" ; I am so > interested in virus capsid model. > > It is so fabulous!!. > > I have never seen this function before and I love this.. > > However is it possible to make multiscale model from other format like VRML? > > I don't know exactly how chimera makes multiscale model, but I think chimera > may use the matrix. > > If then, I can guess we can make model from any format file whatever it is. > > Would you help me how to do this work? > > > And one more thing... > > The exported surface file VRML format from chimera starts with > > #VRML V2.0 utf8 > > Transform { > > children [ > > Shape { > > .... > > And ended with ]} > > > However without > > > Transform { > > Children [ > > > > ] } > > Sentence there is no problem to view this file. > > Moreover, some program which can import VRML file does not recognize > original exported file. > > After delete above sentence they could import VRML file. > > > Thank you > > > Dong Hoon Chung

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