- Chimera-users - RBVI Mailing Lists

netCDF trajectories?
by John R. Frank 24 Nov '04

24 Nov '04

Tom and other users, Based on this posting, I deduce that Chimera's Movie capability cannot yet display netCDF trajectories: http://www.cgl.ucsf.edu/pipermail/chimera-users/2004-June/000171.html MMTK generates netCDF trajectories. Can you recommend any already-built tools for converting them to multi-model PDBs? Or, perhaps you can direct me to the parts of Chimera where I could help add netCDF trajectory support? John -- ___________________________ John R. Frank <jrf(a)mit.edu> Physics Graduate Student mobile: 857-928-0614

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Re: [Chimera-users] Select Function
by Elaine Meng 23 Nov '04

23 Nov '04

Dear Dr. Molnar, All chains present in structures open in Chimera should be listed. If two chains have the same ID, however, they will not have separate listings in Select/Chain. Another thing that might be confusing is that residues can be assigned to chains named "het" or "water": Any HETATM residue that does not already have a chain identifier is assigned to chain HET, unless the residue is named WAT or HOH, in which case it is assigned to chain WATER. Additional possibilities are a bug or something strange with the input files. If you have some input files that demonstrate the problem (and don't mind sharing them), you could send them to me or to chimera-bugs(a)cgl.ucsf.edu along with a short explanation of how to duplicate the problem (how files were opened, what order). Best, 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

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Select Function
by Stephen P. Molnar, Ph.D. 23 Nov '04

23 Nov '04

I want to load two files, one for the protein and the other for the ligand. This is, of course, not a problem. The question is how do I get both files to be present as choices in Select/Chain? Some times both of them are there, but at other times only the first one that I loade. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://www.geocities.com/FoundationForChemistry

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Chimera / APBS
by Thomas Goddard 23 Nov '04

23 Nov '04

Hi Miguel, Eric Pettersen passed to me your question about Chimera reading APBS electrostatic potential maps. It looks easy to add -- probably only take me a couple hours if it is the OpenDX file format described in the APBS documentation. Could you provide me an small example file? I'll be on vacation this week starting this afternoon but I can probably do it early next week and send you the Python code for use in your current version of Chimera. Tom

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orientation matrix
by Miguel Ortiz Lombardía 18 Nov '04

18 Nov '04

Hi all, Sorry, this question may be very simple, but I didn't manage to find an answer in the documentation. Is it possible to read a transformation (rotation + translation) matrix so that the molecule is displayed exactly in the orientation you wish? Thank you! Miguel -- University of York Structural Biology Lab email: mol1(a)york.ac.uk http://www.ysbl.york.ac.uk/~mol ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées

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orientation matrix
by Miguel Ortiz Lombardía 31 Oct '04

31 Oct '04

Hi all, Sorry, this question may be very simple, but I didn't manage to find an answer in the documentation. Is it possible to read a transformation (rotation + translation) matrix so that the molecule is displayed exactly in the orientation you wish? Thank you! Miguel -- University of York Structural Biology Lab email: mol1(a)york.ac.uk http://www.ysbl.york.ac.uk/~mol ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées

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Chimera production release
by Eric Pettersen 20 Oct '04

20 Oct '04

We have now made a production release, version 1.2038, that corrects a few problems in the 1.2029 snapshot and adds a tiny number of new features. The salient new features that weren't in the 1.2029 snapshot are: Actions...Label now allows much more flexible labeling of residues Per-Model Clipping now allows a model's clip plane to be aligned with the clip plane of another model, and allows a clip plane to be flipped 180 degrees. The 1.2029 bug fixes are explicitly listed in the 1.2038 release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2038.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [Chimera-users] Specifying residue color of residues with a text file
by Elaine Meng 20 Oct '04

20 Oct '04

Hi David, You can specify residues and corresponding R,G,B values using Define Attribute, which is included in our newer releases (snapshot 1.2029 and production release 1.2038, of which I recommend the latter). Basically, this tool reads a file that specifies the residues and the associated values. The manual page for Define Attribute can be viewed at: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… including three examples near the end: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… There are two general approaches you may want to consider: (1) the direct approach that you described. Just reassign R,G,B values to the existing attribute of atom color and/or residue ribbonColor. This is most like the third example, except that you would use residue specifications by number (e.g., :12.A) instead of name, and the color specifications would be in the form of R G B (e.g., 1.0 0.2 1.0) instead of color names. (2) a less direct approach but one that provides more flexibility in how you show the data. Create your own new attribute (as in the first example). Then, you can use Render by Attribute (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html) to show these values with colors, atom radii, and/or "worm" radii. The data will show as a histogram, and the mapping to colors and radii can be controlled with markers you place on the histogram. This may be a lot to digest, so please feel free to contact us with any further questions/issues. Thanks, 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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[Chimera-users] Specifying residue color of residues with a text file
by David Piper 20 Oct '04

20 Oct '04

Chimera, Is it possible to provide a color input file that would include a residue number and an [R,G,B] value to color each residue in a structure? Or does one simply have to select each residue seperately within the program and specify an [R,G,B] value? For example, I would like to map some experimentally measured, functional data onto a model structure by coding it into a color. Would be much easier to use a lookup table of values than click and set each one. Thanks, David

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new Chimera snapshot release
by Eric Pettersen 19 Oct '04

19 Oct '04

Hi all, A new Chimera snapshot release (version 1.2029) is now available for download. I've summarized the major changes since the last release (1.1951) below. A list of _all_ the changes since the last release is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2029.html Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu General changes --------------- The "web fetch" part of the "File...Open" dialog has been split off into its own "Fetch by ID" dialog. The Fetch dialog now supports fetching NDB IDs. Labels are now offset in the viewing coordinate system (rather than the model coordinate system), making them much less likely to be obscured. Moved C3' off of ribbon backbone so that the sugar ring isn't distorted. New Tools --------- Nucleotides (Graphics): create various nucleotide-specific depictions, such as stylized representations of base pairings or filled sugar rings Define Attribute (Utilities, Programming): assign values to new or existing attributes of atoms, residues, or models. Particularly useful in conjunction with the Render by Attribute tool. Tool Changes ------------ AddH improved to avoid steric clashes (and appears in model panel) Match -> Align can handle circular permutations in multiple alignments [formerly only in pairwise] Movie can read PSF/DCD files from CHARMM, NAMD, and X-PLOR; can read PDB-format trajectories (single concatenated file or one file per frame) Multalign Viewer can save a subset of an alignment to a file Multiscale Models includes the zone-selection options Near and Contacts PipesAndPlanks now connects the secondary structure elements with loops Web Data preference category renamed to Web Access and includes HTTP proxy options Render by Attribute implements Radii section (atom radius scales with attribute value) and Worms section ("worm" ribbon radius scales with attribute value) Ribbon Style Editor scalings are now treated similarly to cross sections (per-residue, no startup default except in New Molecules preferences); new "residue class" tab allows specification of which atoms should guide the ribbon, this generalizing ribbons to polymers other than standard peptides and nucleic acids ViewDock includes new interface for choosing compounds by descriptor values New Commands ------------ addaa: add amino acids to the C-terminus of a peptide/protein addh: add hydrogens (command implementation of AddH) bond/~bond: create and delete bonds chirality: report the R/S configuration of a chiral center (see User's Guide for caveats) defattr: define a new attribute and/or assign attribute values (command implementation of Define Attribute) rangecolor: color over a range according to attribute values rmsd: evaluate the RMSD between specified sets of atoms (without matching) Command Changes --------------- atom specification operators added for union (|) and negation (~) [previously just intersection (&) and operators for combining attributes] hbonds has "tilde version" (~hbonds) which removes the pseudobonds showing hydrogen bonds labelopt info has "res" or "residue" keyword indicating that only residue name and number should be shown (not atom name) rainbow can color by model (previously only by residue or chain); likewise for Rainbow tool select has "up" or "down" arguments which behave like up-arrow and down-arrow to broaden and narrow a pre-existing selection

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Help, chimera keeps crashing on startup
by Ann Mullin 19 Oct '04

19 Oct '04

Hi, I run Chimera on MacOS 10.3 with X11. Today I started having problems with Chimera crashing on startup. I deleted the programs and downloaded them again. No help. I reinstalled X11. Again no help. Thanks for all help. Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

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by Dr .Julio Ortiz 13 Oct '04

13 Oct '04

Dear Srs: I am a new user of Chimera, and I really like it! I would like to know if some of the developers could include a new format for density maps amongs those that are readable in Chimera: EM format. That would increase its use in our group, because now we need convert our density maps to mrc each time that we want to use Chimera. With my actual skills in programming, to write a plugin will take me like a year, and I think that should be relative easy for someone with experience. As attachment I am sending a text file with a procedure wrote in matlab to read EM format files. The syntax should not be so different from python. I could also provide you with test data. Thank you very much for your help, Dr. Julio Ortiz -- Max-Planck Institut für Biochemie Abteilung Molekulare Strukturbiologie Am Klopferspitz 18 D-82152 Martinsried Germany Tel: +49 (89) 8578 2034 fax: +49 (89) 8578 2641 --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux(a)biochem.mpg.de

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[Chimera-users] Re: streaks in Chimera image of virus electron density map
by Thomas Goddard 12 Oct '04

12 Oct '04

Hi Lu, The streaks on your Chimera density map display are very likely a driver bug specific to the Mac ATI Radeon 9600 Pro (RV350, 64 Mb). You don't see the streaks on a Mac with Radeon 9600 XT graphics (RV360, 128 Mb), and I don't see them with your data set on my Mac Radeon 9800 Pro (R350, 128 Mb). Setting the transparency to a non-zero value makes the streaks go away. When you use transparency Chimera does not use OpenGL display lists. This suggests that the graphics driver bug is related to display lists. OpenGL is an industry standard 3D graphics library that Chimera uses. We have had alot of graphics driver problems with Apple. We submit bug reports to them and sometimes visit them in Cupertino, but it is unlikely we could get this fixed since it appears to be limited to a graphics card they no longer sell. If the streaks do not bother you on-screen too much, a reasonable work-around might be to set transparency to 0.001 just when saving an image. This setting will substantially slow down rotation of the model so it is best to leave the transparency at 0 until you get the right orientation for image saving. Thanks for reporting the problem. Tom > Date: Tue, 12 Oct 2004 14:23:37 -0700 > From: Lu <lugan(a)scripps.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: streaks in Chimera image of virus electron density map > > Hi Tom, > I see definitely see streaks in the Chimera display, and they appear to be > parallel to the one of the crystal lattices. They remain even if I rotate > the particle. When I loaded a .pdb with axis coordinates, they appear > parallel with the Y-axis. Another phenotype is that if I make the > transparency non-zero, the streaks go away. > The graphics card is an ATI Radeon 9600 Pro, 64mb. We don't notice this > problem on our other G5, which has an ATI RV360 chip with 128MB of RAM. So > there's a possibility that either our video card is bad, or that specific > ATI model has some issues. > I've attached an example map (which is a low resolution crystal structure > by the way) of our virus particle. It's dsn6/omap formatted. > I hope the problem is just isolated to our video card. > Thanks. > > -Lu > > On Tue, 12 Oct 2004, Thomas Goddard wrote: > > > Hi Lu, > > > > I took a look at the virus EM map image you sent to Eric Pettersen. > > I haven't seen this bug in Chimera. Do you see the streaks in the > > Chimera graphics window? Or do they only appear in the saved image? > > If they appear in the graphics window are they features that persist > > when the model is rotated? Also are the streaks parallel the data set > > x, y, or z axis? You could see this by displaying the outline box > > around the map with volume viewer / options / show outline box. > > > > I have the same Mac as you only my RV350 has 128 Mb. Do you happen > > to know what model graphics card you have, for example, mine is Radeon > > 9800 Pro? I don't think you can find this out from Mac OS -- you just > > have to know from when the machine was purchased. > > > > I suspect our latest Chimera snapshot release 2029 that just came > > out will exhibit the same problem. But it might be worth trying it. > > > > Can you reproduce the streaks with any small data set that I could > > get from you (by web, ftp, or email)? > > > > Hopefully we'll be able to figure this out quickly. > > > > Tom > >

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Re: [Chimera-users] display vectors
by Eric Pettersen 11 Oct '04

11 Oct '04

On Oct 11, 2004, at 6:50 AM, Mingfeng Yang wrote: > I want to show motions of some atoms. Is it possible to draw vectors > origin from each atoms in Chimera? Specifically, I like to draw an > arrow, originning from each atom, with direction and length to > describe the motion. The answer is yes, though the process is a little involved. Can I ask you in what context you are doing this? Is it related to an MD trajectory? Perhaps in future releases we could make this easier if we know specifically what you want to do and what data you are working from. Anyway, there are two methods I can suggest: VRML and pseudobonds. You can show exactly what you want with VRML, but it may be more effort. Pseudobonds may be easier, but you can’t have arrowheads. For VRML, you just compose a VRML file using a cylinder and cone for each arrow. The cone is the “arrowhead” and you have the cylinder go from the atom to the base of the cone, and have the cone point in the right direction. If you don’t know how to use VRML, this page has a spec and examples: http://www.web3d.org/x3d/specifications/vrml/ISO_IEC_14772-All/ index.html For pseudobonds, you would make up a fake molecule where the “atoms” are at the ends of the vectors you want to show. If you make a PDB file, start it with a TER card and use HETATM records for each atom, with a different residue number for each. This will ensure that Chimera won’t connect any of the atoms in the fake molecule. You can then use the PBReader tool (in the Utilities category) to read in the pseudobonds to display (including colors and optional labels). You can use the pseudobond panel (under inspectors) to control if the pseudobonds are wires or sticks, if they are dashed [wire only], and so forth. Let me know if you need any more help getting started with this. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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[Chimera-users] streaks in Chimera image of virus electron density map
by Lu 11 Oct '04

11 Oct '04

Hello, I've been using Chimera to generate beautiful images of entire virus particle from an O-style map file. However, most of the images that I capture have a few black streaks in the image. The streaks appear as thin, parallel lines, like someone dragged a pen across a painting before it dried. Does anyone know how I can remove these streaks without having to resort to Photoshop? I can provide sample images too. Thanks in advance! -Lu Gan

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Problems in Windows XP
by Jutta J Roth 28 Sep '04

28 Sep '04

To whom it may concern: We have been trying to run chimera in Windows XP and unfortunately are not able to do so. The program runs great on the Mac machines though. The only problem obvious for us is, that the collaboratoryHub shortcut does not show up. We can start the program, but when we try to open a file the sequence window starts flickering and the structure does not load. We really like the program a lot and would like to cite it in a paper we are currently working on, but in order to do that we need to get it to work on the PCs. Therefore every advice would be highly appreciated. Thanks! Sincerely, Jutta Roth ''''''''''''''''''''''''''''''''''''''''''''''' Jutta Johanna Roth Department of Ecology and Evolutionary Biology Yale University 165 Prospect Street New Haven, CT 06511 Tel.: 203.432.9741 (w) 203.776.2364 (h) Fax: 203.432.3870

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display of single letter AA code?
by Mark Daniels 28 Sep '04

28 Sep '04

Hello Chimera administrator(s)- I was wondering if there is any way fior Chimera to display amino acid residue names in single-letter format, rather than the three-letter format one gets when selecting Actions-->Label-->residue-->name ? I have looked over all the documentation I can but have not found anything to answer this question. Thanks in advance- Mark Mark J Daniels Department of Cell Biology The Scripps Research Institute La Jolla, CA 92037

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Request info
by Negi, Surendra S. 22 Sep '04

22 Sep '04

Hi, How can i save some region of an EM data in Chimera. I can corp the region of my interest in EM map using chimera but I am unable to save the data in mrc format. How can i save this region of EM data in mrc file. Thanks for your help. Best, surnedra

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Fwd: [Chimera-users] Chimera, Python, WindowsXP or AMD64 conflict?
by David Piper 17 Sep '04

17 Sep '04

Unfortunately, there is not a suitable graphics driver update for the ATI Radeon card for the notebook I am using. David

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Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Pattanayek, Sabuj 17 Sep '04

17 Sep '04

Hi, I just tried this and it fixed the problem: Delete these directories: C:\Documents and Settings\All Users\Application Data\chimera C:\Documents and Settings\sabuj\Application Data\chimera (whatever your username may be) Then uninstall and reinstall chimera and file->open works again. Thanks, ...Sabuj Quoting "Pattanayek, Sabuj" <sabuj.pattanayek(a)vanderbilt.edu>: > Hi, > > I'm getting a strange error when I start chimera and do file->open. This is > the > reply log: > > ValueError: list.index(x): x not in list > (see reply log for Python traceback info) > Traceback (most recent call last): > File "C:\Program Files\Chimera\share\__main__.py", line 56, in ? > value = chimeraInit.init(sys.argv) > File "C:\Program Files\Chimera\share\chimeraInit.py", line 301, in init > tkgui.eventLoop() > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2891, in > eventLoop > app.mainloop() > File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 965, in > mainloop > self.tk.mainloop(n) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1751, > in > __call__ > _reporterror(self.func, args) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1814, > in > _reporterror > displayerror(msg) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1377, > in > displayerror > _errorReportFile.write(text + '\n') > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, > in > __call__ > return apply(self.func, args) > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 272, in > _importModel > clientSticky='ew') > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 178, in > __init__ > OpenModeless.__init__(self, **kw) > File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 185, in > __init__ > ModelessBase.__init__(self, **self.dialogKw) > File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 378, in > __init__ > BaseDialog.__init__(self, master, *args, **kw) > File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 220, in > __init__ > self.fillInUI(self.__top) > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 181, in > fillInUI > OpenModeless.fillInUI(self, parent) > File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 92, in > fillInUI > self.millerBrowser = MillerBrowser(parent, **self.millerKw) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 184, in > __init__ > self.makeMainColumn(initialdir, firstTime=1) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 509, in > makeMainColumn > titleMode=None, firstTime=firstTime) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 823, in > __init__ > index = normItems.index( > ValueError: list.index(x): x not in list > > I have also posted the screenshot here > http://linegli.mc.vanderbilt.edu/~sabuj/chimeraOpenError.jpg > > Also if I do "c:\Program Files\Chimera\bin\chimera.exe" file.pdb from the > command line, then do file -> open, it works again. I've tried running it > with > and without precompiling modules after installation, but get the same > result. > > I've downloaded the binary installation several times, done uninstall, then > install, but I'm still getting the same error. I have not been able to > re-create > the error on another winxp sp1 machine. > > Any help would be appreciated, > Thanks, > Sabuj Pattanayek > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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WinXP SP1 python error on File -> Open
by Pattanayek, Sabuj 17 Sep '04

17 Sep '04

Hi, I'm getting a strange error when I start chimera and do file->open. This is the reply log: ValueError: list.index(x): x not in list (see reply log for Python traceback info) Traceback (most recent call last): File "C:\Program Files\Chimera\share\__main__.py", line 56, in ? value = chimeraInit.init(sys.argv) File "C:\Program Files\Chimera\share\chimeraInit.py", line 301, in init tkgui.eventLoop() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2891, in eventLoop app.mainloop() File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1751, in __call__ _reporterror(self.func, args) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1814, in _reporterror displayerror(msg) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1377, in displayerror _errorReportFile.write(text + '\n') File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 272, in _importModel clientSticky='ew') File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 178, in __init__ OpenModeless.__init__(self, **kw) File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 185, in __init__ ModelessBase.__init__(self, **self.dialogKw) File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 378, in __init__ BaseDialog.__init__(self, master, *args, **kw) File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 220, in __init__ self.fillInUI(self.__top) File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 181, in fillInUI OpenModeless.fillInUI(self, parent) File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 92, in fillInUI self.millerBrowser = MillerBrowser(parent, **self.millerKw) File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 184, in __init__ self.makeMainColumn(initialdir, firstTime=1) File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 509, in makeMainColumn titleMode=None, firstTime=firstTime) File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 823, in __init__ index = normItems.index( ValueError: list.index(x): x not in list I have also posted the screenshot here http://linegli.mc.vanderbilt.edu/~sabuj/chimeraOpenError.jpg Also if I do "c:\Program Files\Chimera\bin\chimera.exe" file.pdb from the command line, then do file -> open, it works again. I've tried running it with and without precompiling modules after installation, but get the same result. I've downloaded the binary installation several times, done uninstall, then install, but I'm still getting the same error. I have not been able to re-create the error on another winxp sp1 machine. Any help would be appreciated, Thanks, Sabuj Pattanayek

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Chimera, Python, WindowsXP or AMD64 conflict?
by David Piper 16 Sep '04

16 Sep '04

Chimera, Wonderful software package!!! I am running successfully on my desktop (Intel P4 2.8 GHz; Windows XP Professional) at the lab. On my eMachines M6807 notebook (Mobile AMD Athlon 64 3000+, 800 MHz, Windows XP home edition) although I can start Chimera and open a PDB file, as soon as I try to do anything (say rotate the molecule) I get an error message: Assertion failed! Program: C:\Program Files\Chimera\pythonw.exe File: togl.c Line: 960 Expression: res == TRUE && "Togl_MakeCurrent: failed" I did not see anything on your website addressing such a conflict, but hoped you might have a suggestion for me. Thanks, David Piper

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3D viewing?
by Steven J Kolodziej 15 Sep '04

15 Sep '04

Hi; I was wondering if Chimera had an option for viewing files in 3D from a PC using glasses and if so what hardware is needed. Steve Kolodziej steven.j.kolodziej(a)uth.tmc.edu

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chimera in fink
by Ersatz Sophist 15 Sep '04

15 Sep '04

Hi, Have you considered distributing chimera through fink? Payam ------ "...who search the reason of things Are those who bring the most sorrow on themselves." --Euripides, The Medea ------ "...who search the reason of things Are those who bring the most sorrow on themselves." --Euripides, The Medea

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by Sheetal Patil 07 Sep '04

07 Sep '04

Hello, Iam trying to configure Phantom desktop with Chimera. I get the following error: "Couldnot load Chimers_phantomcursor library.Can you please tell me where I can find this piece of software? Thanks, Sheetal +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ " The future belongs to those, who believe in the beauty of their dreams "

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ribbons of nucleic acids
by Ann Mullin 01 Sep '04

01 Sep '04

Hello, I am wondering how to adjust the ribbons of nucleic acids so that they follow the path of the phosphates or the sugars, anything but the averaged path they have now. I want to show the backbone as a ribbon with bases projecting out, but now some bases float about the backbone. Thanks for any help. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

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Chimera and building molecules
by Elaine Meng 31 Aug '04

31 Aug '04

Dear Ben, We definitely agree that molecule-building would be a very useful addition to Chimera. Toward this functionality, Chimera includes hydrogen addition; also, the "bond" command has been implemented (and will be available in the next release). Chimera also includes the "swapaa" and "swapna" commands which "mutate" one sidechain or base to another, although they are not very sophisticated. I am not certain what you are referring to in MIDAS, which only had very rudimentary building capabilities and no ability to add hydrogens. The "addgrp" command did allow definition of new amino acid sidechains, but was quite unwieldy and not usable for building in general. Similarly, "addaa" could append one of the standard amino acids to the end of a peptide but was not generalizable to other types of molecules. If you could clarify how you were applying these tools, we might be able to prioritize developments accordingly. Thank you, 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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building molecules
by Ben Schuler 31 Aug '04

31 Aug '04

Dear Chimera developers, It seems to me that the manual formation of bonds and building of any type of molecules (not only proteins and nucleic acids), which was a strength of MIDAS, is not supported by Chimera. I would very much welcome an implementation of these features to make Chimera a real replacement for MIDAS. Ben __________________________________________________ Prof. Ben Schuler, PhD Biochemisches Institut, Universität Zürich Winterthurerstr. 190, CH-8057 Zürich Tel: +41 44 635 5535, Fax: +41 44 635 5907 Web: www.biochem.unizh.ch/schuler Email: schuler(a)bioc.unizh.ch

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chimera --send with multiple Chimeras
by Thomas Goddard 22 Jul '04

22 Jul '04

Hi Sandeep, If you have more than one Chimera running on a machine then "chimera --send" sends the file to the most recent one that is accepting connections. Each time you change the Favorites/Preferences/Web Data option to accept connections, that Chimera becomes the most recent. The way this works is there is a list of running Chimera instances that are accepting connections in file (on unix /tmp/chim_webinfo-<username> where <username> is your login name). This file lists the Chimera process id and port number it is listening on. The last line indicates the most recent Chimera that is accepting connections. I wouldn't recommend relying on info in this file since the implementation may change in the future. Tom

3 3

suggest OBJ export option
by Steven McQuinn 19 Jul '04

19 Jul '04

I'm really happy with Chimera, but vexed that every attempt to export a high resolution mesh via the VRML utility ends in a python failure. Have not tried exporting molecular models, only isosurfaces with 250,000+ polygons. What I use instead for export is VMD, which has an .stl export option, providing smaller file sizes than VRML. VMD is buggy on my XP system, requiring several attempts to export correctly. I use Chimera to get my isosurface settings right, then plug these values into VMD. SUGGESTION: If you provided an OBJ mesh export option, nearly every 3d application could utilize the product. The Wavefront OBJ format is the defacto universal exchange format, fairly small file sizes, retaining textures. Should be easy for you geniuses to program. Also, the stereo camera option never "takes." The walleye and crosseye cameras work OK but not the straight stereo pair, which I have to compose from the right and left images. Would like to send the development team some work samples. How do I do that? Please reply to my email address, as I don't read the list. Steven McQuinn _________________________________________________________________ MSN Toolbar provides one-click access to Hotmail from any Web page FREE download! http://toolbar.msn.click-url.com/go/onm00200413ave/direct/01/

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Re: [Chimera-users] PDB-file trajectories
by Eric Pettersen 16 Jul '04

16 Jul '04

I have PDB-file trajectory support working in Movie now. It's only in our internal development version, but I could make a custom snapshot release for anyone who wants to use it immediately. Otherwise, it will be in the next regular release, which will probably be in a month or two. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu > On Thursday, January 8, 2004, at 06:52 AM, amutha ramaswamy wrote: > >> It is possible to make movies with PDB structurers in chimera. this >> would really be helpfull in visualing the conformatinal changes. I >> know chimera has the option for movie with trajectory files. but i >> wish to kow the option with PDB files only. > > Hi Amutha, > I assume you're talking about the situation where you have one PDB > file for each "frame" of a trajectory (or a multi-MODEL PDB file of > the trajectory), rather than a starting and ending PDB file that you > want to "morph" between. Either way, unfortunately, we don't currently > support what you want. However, now that you have pointed out the > usefulness for plain-PDB support in Movie, I can probably add it in > the not-too-distant future. But given my other priorities (including > support for attribute coloring that you mentioned earlier!) the > "not-too-distant future" might still be a couple of months. I'll send > mail when there is at least a preliminary version available.

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How to send files to Chimera
by Thomas Goddard 02 Jul '04

02 Jul '04

Hi Sandeep, To open files in an already running Chimera from your program you can use the chimera --send option. For example, chimera --send myfile.mrc You need to tell Chimera to accept "web data" for this to work. You do this using Chimera menu entry Favorites/Preferences, category Web Data, set "Accept web data" to true. Press the Save button if you want this setting to apply to all future Chimera sessions (saved in ~/.chimera/preferences). If you don't set this preference, the --send command-line option will just start another copy of Chimera. This is described in the Chimera manual where command-line options are described: http://www.cgl.ucsf.edu/chimera/1.1951/docs/UsersGuide/options.html You can do fancier things, like send Python code (*.py files) or Chimera commands (*.cmd or *.com files) to Chimera to show your data in a certain way. You would still use the --send option to send the Python file. These remote control features were added to Chimera so that a web browser link can cause commands and files to be sent to Chimera and this is described in the Chimera manual: http://www.cgl.ucsf.edu/chimera/1.1951/docs/ContributedSoftware/webdata/chi… The hard part here is that volume data display options like threshold levels do not have simple Chimera commands to set them. Instead you have to dig around in the VolumeViewer Python code (in the share directory) in order to see what Python functions set these things. This is not easy to figure out. I can help you if you have specific questions about the Python functions for volume data display. Tom > Date: Fri, 2 Jul 2004 10:01:40 -0600 > From: Sandeep N Seshadri <sandeep(a)nmsu.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Re: [chimera-dev] regd error when opening a .mrc file > > Hi Tom, > sorry for being very confusing . i am trying to open up files generated from my > program . as of now all i do is chimera test1.mrc > > and next time i generate another file i would open it as chimera test2.mrc > > so it would open a new chimera window and show the next .mrc file . what i would > like to do is when i open the second file test2.mrc i would like to see it open > in the already opened chimera window for test1.mrc. > > do you think i can do this ? Please let me know > > Sandeep Seshadri

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[Chimera-users] Re: [chimera-dev] regd error when opening a .mrc file
by Thomas Goddard 01 Jul '04

01 Jul '04

Hi Sandeep, This error indicates that the mrc file data values are all zero. The error occured when making the histogram that is shown in the Volume Viewer dialog, when it was trying to scale it to fit the width of the dialog. Of course, our code should not generate an error in this case. I will fix it for the next release. If you will be opening mrc files that may be all zero you can change chimera/share/VolumeViewer/histogram.py line 26 hscale = float(cheight) / max_height to if max_height == 0: hscale = 1 else: hscale = float(cheight) / max_height Then you will not get any error and the histogram will display correctly. Thanks for pointing out this problem. I am not familiar with pdb2mrc so I do not know why it is generating a volume consisting of all zeros. Tom > Date: Wed, 30 Jun 2004 21:33:12 -0600 > From: Sandeep N Seshadri <sandeep(a)nmsu.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] regd error when opening a .mrc file > > i am getting the following error when i try to open a .mrc file . i generated a > .pdb file and use a pdb2mrc to generate a .mrc file . i tried opening the .pdb > file it works fine but when i try to open the .mrc file it gives the error. > > if anyone has any idea on why this error occurs please let me know > > thanks > sandeep > > > Error while processing test-helix.mrc: > ZeroDivisionError: float division > (see reply log for Python traceback info) > Traceback (most recent call last): > File "/home/sandeep/chimera/share/__main__.py", line 56, in ? > value = chimeraInit.init(sys.argv) > File "/home/sandeep/chimera/share/chimeraInit.py", line 275, in init > prefixableType=1) > File "/home/sandeep/chimera/share/chimera/__init__.py", line 886, in open > models = func(filename, *args, **kw) > File "/home/sandeep/chimera/share/VolumeViewer/ChimeraExtension.py", line 30, > in open_cb > d.add_data_sets([g]) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 175, in > add_data_sets > self.redisplay_cb() > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 459, in > redisplay_cb > self.show_using_dialog_settings(self.focus_region) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 380, in > show_using_dialog_settings > tp.update_histograms(data_region) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 1142, in > update_histograms > cw.update_histogram(data_region, read_matrix, self.dialog.message) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 1465, in > update_histogram > h.show_data(Numeric.log(s.counts + 1)) > File "/home/sandeep/chimera/share/VolumeViewer/histogram.py", line 26, in > show_data > hscale = float(cheight) / max_height > ZeroDivisionError: float division

2 2

Is it possible to undo an action?
by Lesheng Kong 30 Jun '04

30 Jun '04

Hi, Is it possible to undo an action in Chimera? I notice that some actions in Chimera can be undid, such as "undo selection" or "undo move". Can every action be undid in Chimera? For example, I colored a selection zone in a different color. But I want to undo this action and recover each atom's previous color. Thank you very much! With best regards, Lesheng

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

30 Jun '04

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

1 0

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

2 1

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

1 0

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

1 0

[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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