- Chimera-users - RBVI Mailing Lists

chimera on linux ia64 (sgi prism)
by Sabuj Pattanayek 14 Jul '06

14 Jul '06

Hi, I was wondering if there is a port for chimera to run on Linux IA64 (sgi prism)? The x86 version runs in emulation mode on the system, thus the graphics defaults to Mesa indirect glx (really slow). Would a dev be willing to port it for this system if given access to the system? I'm also working on getting pymol compiled for it. vmd already has a native port with good performance. Thanks, Sabuj Pattanayek

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matchmaker command
by Haas, Ryan Matthew 10 Jul '06

10 Jul '06

Dear Chimera Users, How does the matchmaker command perform its superposition? Is it a C-alpha superposition, or just backbone atoms, or all atoms? Is it appropriate to use these RMSD values obtained from "mmaker" in a manuscript? Help is greatly appreciated. Matthew Haas

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Re: [Chimera-users] script for residues w\in zone
by Eric Pettersen 06 Jul '06

06 Jul '06

On Jul 6, 2006, at 1:54 PM, Sorani, Marco wrote: > Thanks. I'm running Chimera and Python\IDLE on Windows XP. > > a) Can I still use the "script.com" you suggested? You could, by getting a UNIX-shell-like environment such as Cygwin (www.cygwin.com) or possibly just from the DOS prompt. If you don't care if Chimera's interface shows as the script runs, you could just run Chimera and then use File...Open to run the script. > b) When I try "script.py", I can't find the module "chimera" or > "chimera.py". Where should I look? script.py will only work if Chimera is the interpreter, rather than a stand-alone Python interpreter. So you need to either run "chimera -- nogui script.py" using methods like in the previous answer, or open the script using Chimera's main File...Open dialog. --Eric

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script for residues w\in zone
by Sorani, Marco 06 Jul '06

06 Jul '06

Hi, A question: For a given PDB structure (say, 1J4N) and a given point mutation (say, C104K), I want to find all residues within 5 angstroms. Manually, this is easy to do with 'Select' --> 'Zone...', but if I have 1000 mutations, is there a way to automate the process and send results to a file? ****************** soranim(a)pharmacy.ucsf.edu Marco Sorani Program in Biological & Medical Informatics University of California, San Francisco

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calculating charges for Dock
by Joshua D Campbell 28 Jun '06

28 Jun '06

Hello, My name is Josh Campbell and I'm trying to prepare a ligand for docking that is made up of non-standard residues using Chimera. The Dock Prep tool of course does not assign charges to non-standard atoms. I looked at your UserGuide and it said that there were other places to calculate non-standard residues using the Antechamber module, but I could not find any of these tools anywhere in the Chimera program. If you could give me some clarification as to adding charges on non-standard residues, I would be very greatful. I am working with "beta version 1 build 2199 2006/01/24". Thanks. Sincerely, Josh Campbell Harvard Medical School Laboratory of Structural Cell Biology

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select certain transformants of multiscale models.
by Jonathan Hilmer 27 Jun '06

27 Jun '06

Actually, it is possible to use the command line to select portions of a multiscale-models generated volume set: it's just not really efficient. Open your structure and apply the BIOMT with multiscale models. Then select all the surfaces of the multiscale structure. Hide the surface representation and then show a ribbon representation. You might have to wait awhile for this to finish on a large structure. This will generate a new model for each subunit that can be selected manually, via command line, or with the model panel. You can then use the multiscale models panel to make color adjustments, show surfaces etc using selections defined in the command line. However, I can say from experience that learning the Python code is worth the effort in the long run. Jonathan > Hi, > > I'm wondering if it is possible to select specific volumes generated > via the multiscale model tool via the command line? E.g., for a set > of 60 biomt matrices I'm interested in coloring the chains generated > with matrices 1-20 in one color, matrices 21-40 in another color, and > matrices 41-60 in yet another color. Any suggestions on how to > accomplish this would be appreciated. > > thanks! > > Cathy Lawson > > > > *****************************************************************' > Catherine Lawson > Laboratory for Structural Biology and Bioinformatics > Department of Chemistry and Chemical Biology > 610 Taylor Road > Piscataway, NJ 08854 USA > http://roma.rutgers.edu > http://rutchem.rutgers.edu/~lawson > ***************************************************************** > > > > ------------------------------ > > Message: 2 > Date: Mon, 26 Jun 2006 18:18:57 -0700 (PDT) > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] selecting multiscale model volumes > To: cathy.lawson(a)rutgers.edu > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <200606270118.k5R1IvGE1909532(a)guanine.cgl.ucsf.edu> > > Hi Cathy, > > Unfortunately no Chimera commands allow selecting or coloring > multiscale surfaces. The multiscale tool in general is not well > integrated with the other Chimera capabilities -- like the Actions > Color menu won't color chain surfaces that you select with the mouse. > We plan on fixing this in the future but it may take a while (6 months > or more). > > Everything is possible using Python code, although this can be quite > difficult to figure out. It is not documented and the best approach is > to ask for examples from us that you can then modify. Below is code > to color multiscale surfaces with specific matrix subunits and chain IDs. > If you open that file in Chimera (with File / Open..., or with the "open" > command) it will do the type of coloring you requested. When you modify > the code be careful not to change the indentation since this is important > in Python. > > We could easily do a little better and add a Chimera command so that > you would not have to edit a Python script to specify what residue > ranges and colors to use. > > I am going on vacation tomorrow until July 18 but can make that > command for you when I return. It just requires some additional > Python code that Chimera will load at startup. > > Tom > > ---- > Python file mmcolor.py follows: > > # ---------------------------------------------------------------------------- > # Color certain matrix subunits and chains of a multiscale model. > # > def color_multiscale(rgba, model_num, matrix_nums, chain_ids = None): > > import MultiScale > d = MultiScale.multiscale_model_dialog(True) > for cp in d.chain_pieces(): > g = cp.surface_group > if g.model().id == model_num: > mnum, chain_id = g.oslName.split('.') > if chain_ids == None or chain_id in chain_ids: > if int(mnum) in matrix_nums: > cp.set_color(rgba) > > # ---------------------------------------------------------------------------- > # > red = (1,0,0,1) # Red, green, blue, opacity > green = (0,1,0,1) > blue = (0,0,1,1) > cyan = (0,1,1,1) > > color_multiscale(blue, 1, range(1,21)) # Color matrix subunits 1-20 > color_multiscale(cyan, 1, range(21,41)) # Color matrix subunits 21-40 > color_multiscale(green, 1, range(41,61)) # Color matrix subunits 41-60 > > # Example coloring subunits 1-20, only chains 'A' and 'B'. > #color_multiscale(red, 1, range(1,21), ['A', 'B'])

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new snapshot release
by Eric Pettersen 26 Jun '06

26 Jun '06

We just put out another snapshot release (1.2255), principally to improve Antechamber reliability (particularly on Windows), but it nonetheless has a few other significant improvements: If you have Modeller installed, the Model Loops extension (very much under development) can fill in missing sections of structure. The defaults for Movie Recorder have been changed to improve playback performance and the ability to produce .avi files has been added. Multalign Viewer can add plain-text sequences to an existing alignment. Volume Viewer can display meshes as squares instead of just triangles. The "reset" command can interpolate between saved positions (i.e. positions in "savepos" commands) to ease creation of scripts involving motion. A new "Alignments" tutorial covers MatchMaker and Match->Align capabilities. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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selecting multiscale model volumes
by Cathy Lawson 26 Jun '06

26 Jun '06

Hi, I'm wondering if it is possible to select specific volumes generated via the multiscale model tool via the command line? E.g., for a set of 60 biomt matrices I'm interested in coloring the chains generated with matrices 1-20 in one color, matrices 21-40 in another color, and matrices 41-60 in yet another color. Any suggestions on how to accomplish this would be appreciated. thanks! Cathy Lawson *****************************************************************' Catherine Lawson Laboratory for Structural Biology and Bioinformatics Department of Chemistry and Chemical Biology 610 Taylor Road Piscataway, NJ 08854 USA http://roma.rutgers.edu http://rutchem.rutgers.edu/~lawson *****************************************************************

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Making aliases persist
by Jeramia J Ory 26 Jun '06

26 Jun '06

I have some students this summer who are using Chimera to check out ligand anomalies in the PDB, and have fallen in love with the 'alias' command, no surprise. Is there a way to have them persist between sessions, or save them in the preference file somewhere? I imagine piling them all into a file and then having them 'read' it each session would work, but I thought I would see if there is a better way. Thanks, Jeramia Ory

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question
by Jaya Bhatnagar 26 Jun '06

26 Jun '06

Hi, Is it possible in chimera to define a new amino acid residue? Also, what algorithms does it support involving docking of two proteins? And is there a limit on number of amino acids present in the protein? thanks a lot, Jaya

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Selecting from a surface area
by Miguel Ortiz-Lombardia 26 Jun '06

26 Jun '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'd like to pick an area of a (msms) surface (like with a "lasso" tool) and from that area, select the atoms/residues from which it is built. I haven't found anything like this in the documentation, so I'm afraid it's not possible. Or is it? Best regards, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Darwin) iD8DBQFElFsPF6oOrDvhbQIRAiLYAJ9NHoF7sHbXJnZijo9Gfv8z9HJatQCfb9XQ 9q3hYNVjsZjVslF3Hv9+8ZU= =5dnB -----END PGP SIGNATURE-----

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Re: [Chimera-users] question
by Goel, Manisha 26 Jun '06

26 Jun '06

Hi Elaine, I too have been looking for a good protein-protein docking program, so I am jumping on the bandwagon .. Just small question regarding point 2 in the mail .. Does chimera do any minimization/optimization of the complex after we manually dock the two protein together ? Thanks a lot for your help.. Regards, -Manisha -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Elaine Meng Sent: Monday, June 26, 2006 11:34 AM To: Jaya Bhatnagar Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] question Dear Jaya, (1) Chimera will display whatever coordinates and residue names are present in the input file. It does not matter if the residues or the atoms in them are standard or not. However, you cannot define new residues to be built by Chimera with the "swapaa" or "addaa" commands. We have recently added a Build Structure tool (Structure Editing category) that lets you add arbitrary atoms and bonds to structures interactively. It is in the early stages of development, however, and is likely to change in the future. If you use this, you may want to check the bond lengths and adjust them in the "Set Bond Length" section of the Build Structure tool. The man page for Build Structure: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html (2) Chimera does not do any automated docking. However, you can manually/interactively dock structures by moving one relative to the other (to freeze a structure and move only the others, you would uncheck its Active button in the Model Panel or its checkbox under the Command Line). The man page for the Model Panel: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html (3) I believe there is no limit on the number of amino acids present in the protein. There may be limitations due to the input file format (that is, the residue number column can only be a certain width in the input file format, usually PDB). However, in combination with use of different chain IDs this limit is quite high. For example, ribosome structures can be viewed in Chimera, although it may take a while for the structure to load. I hope this helps, Elaine On Jun 23, 2006, at 8:06 AM, Jaya Bhatnagar wrote: > Hi, > Is it possible in chimera to define a new amino acid residue? Also, > what > algorithms does it support involving docking of two proteins? And > is there > a limit on number of amino acids present in the protein? > > thanks a lot, > Jaya > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [Chimera-users] Chimera-users Digest, Vol 38, Issue 12
by Jonathan Hilmer 16 Jun '06

16 Jun '06

Thanks to all for the quick responses on interpolation. Here's a quick example showing what I was concerned about: arrows.bld ------------------ .color red .arrow 0 0 0 1 0 0 .color green .arrow 0 0 0 0 1 0 .color blue .arrow 0 0 0 0 0 1 ------------------ matrix2 ----------------- Model 0.0 0.505641 0.433743 -0.745785 -2.58211 -0.807506 0.542275 -0.232105 2.90884 0.303746 0.719587 0.624446 -0.194334 ----------------- matrix3 ---------------- Model 0.0 0.60158 -0.458982 0.653787 0.653219 0.190507 -0.712397 -0.675423 5.48737 0.775763 0.530872 -0.341124 0.0103466 ---------------- The first matrix is just unity. The 'reset'-based interpolation works great for going between 1 and 3 or 1 and 2 in both directions, as well as 3 to 2, but fails from 2 to 3. Since all this is new to me, I can't say for certain that this is due to gimbal lock, but that was my first guess. I haven't had the opportunity yet to try out Tom's axis-angle approach, but that should rule out any Euler problems. The other problem for me is that all my current methods are based upon a stepwise approach via commands (ungainly, but very functional when combined with shell scripts, imagemagick etc), and this is incompatible with the 'reset' interpolation. Perhaps it was misleading to mention the use of 'matrixset'. I appreciate that it is more trouble to deal with external files, but if it is not possible to easily implement the interpolation I'm looking for dynamically within Chimera's Python (due to required math libraries, etc) then I would have to hard-code the interpolation matrices into the .py script file anway, defeating the purpose. Thanks for the help: I'd love to hear about any future development in this area.

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Chimera paper virus models
by Thomas Goddard 16 Jun '06

16 Jun '06

Hi Ulrich, This week I made 5 paper virus models using the Chimera flatten icosahedron tool. You can have the images I created: http://www.cgl.ucsf.edu/home/goddard/temp/viper-gallery-jun2006/ The image files are named according to the Protein Data Bank (PDB) 4 letter id code. The page http://www.cgl.ucsf.edu/home/goddard/temp/viper-gallery-jun2006/vipergaller… shows images of the approximately 200 known virus capsids taken from the VIPER web site. http://viperdb.scripps.edu/ I added some comments to the flatten icosahedron documentation a few days ago describing "tiling" of the Chimera image to handle capsid proteins that are cut in half -- so they appear on both sides of the cut. http://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.h… I printed my images on standard photopaper. The images above will need to be scaled to fit on a piece of paper. I just asked my web browser to scale them to fit when I printed. One additional note about my images -- I turned on "silhouette edges" to give the black outlines around the proteins. This is done using Chimera menu entry Tools / Viewing Controls / Effects. Tom

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Chimera movies in PowerPoint
by Thomas Goddard 16 Jun '06

16 Jun '06

Hi Xinchao, Several people have asked exactly your question of how to get a Chimera movie to play in PowerPoint on Windows without being jerky. I don't have a Windows machine to test on today but I investigated on the web and have a theory. I believe the jerky playback is because Chimera is encoding the movie using the -qscale option to the ffmpeg encoder causing variable bit rate (VBR) encoding. When you play the movie it becomes jerky because the player software does not handle the variable bit rate well -- it doesn't buffer up enough data and then can't handle the passages when alot is changing in the video. Another issue is choosing a format that PowerPoint on Windows accepts. Here are two suggestions. The first is to reencode the movie using the ffmpeg program included in Chimera: chimera/bin/ffmpeg -i mymovie.qt -f avi -vcodec msmpeg4 -b 2000 mymovie.avi This command produces an AVI file using msmpeg4 encoding at a bit rate of 2000 Kbits / sec (about 12 Mbytes / minute) from a quicktime file created by Chimera. You can increase the bit rate to get better quality or lower it to get smaller file size and worse quality. From what I read on the web Windows XP will be happy with AVI format and msmpeg4 encoding. You may find it hard to run this command unless you are familiar with running command-line programs on Windows. You could use a Windows Command Prompt window or Run Command, but you may need to provide full paths to the ffmpeg program and movie file. An alternative is to modify the Chimera Movie Recorder code chimera/share/MovieRecorder/ffmpeg_encoder.py putting comment characters (#) in front of lines 106-111: arg_list.append('-qscale') qsc = param_dict['Q_SCALE'] if qsc: arg_list.append(str(qsc)) else: arg_list.append('1') so they become # arg_list.append('-qscale') # qsc = param_dict['Q_SCALE'] # if qsc: # arg_list.append(str(qsc)) # else: # arg_list.append('1') This change is eliminating the -qscale option when Chimera runs ffmpeg to encode your movie. Instead we will explicitly request the encoding bit rate with the -b ffmpeg option. Now restart Chimera and record a movie with the Movie Recorder using "Custom" video format to select bit rate (which controls movie quality and file size). The Custom video format settings are under the Movie Options panel, swich on "Use preset video format" and select "Custom" from the Presets menu. Then set the resolution to match your Chimera window size (shown in the upper right corner of the Movie Recorder dialog, choose the encoding format and set the bit rate (in kilobits per second). If you don't make these Custom settings then Movie Recorder will use ffmpeg's standard very low bit rate of 200 kbits/second making a very low quality and small file size movie. Let me know if you found either of these suggestions to produce usable movies for PowerPoint on Windows. Then I can change Chimera Movie Recorder to make it easy to use such settings. Tom > To: goddard(a)cgl.ucsf.edu > Subject: Chimera Movie format > Date: Fri, 16 Jun 2006 15:33:52 -0400 > From: Xinchao Yu <yxinchao(a)bu.edu> > > Dear Tom: > I am a graduate student working with Dr. Christopher Akey at Boston > University. Recently, I have been trying to make some movies for large > compplexes with multiple domains. My problem is that if I use MPEG as the > output movie format, the movement can get very jerky in the movie. While I > don't have this problem with .mov format (compressed to the same extent as > the .MPEG files). But .mov file is not readily incorporated into powerpoint > presentations. Did you have similar observations? Or do you have some > suggestions concenning this problem. Thanks a lot! > > > Xinchao Yu > Department of Physiology & Biophysics > Boston University, School of Medicine > 700 Albany Str., Boston, MA, 02118 >

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matrixget/set, keyframes, and interpolation
by Jonathan Hilmer 16 Jun '06

16 Jun '06

Does anyone have experience making movies in Chimera used more advanced motions, besides the standard roll, rock, etc? My general idea is to use matrixget to output a series of matrices, interpolate them in my standard Python environment (which is related to the question from Vol 38, Issue 10), and create as output a Chimera script composed of hundreds of 'matrixset' matrices. The Python Computer Graphics Kit (http://cgkit.sourceforge.net) will give me the functions for quaternions, as would ScientificPython or pythonOpenGL, but a quick review of their documentation suggests that in any package it will be necessary to interpolate the rotation separately from the translation: obviously it would be more convenient if there is a package that can transparently interpolate the matrices as provided by Chimera. Has anyone gone through this issue before, hopefully with some tips for me? Thanks, Jonathan

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how to tell chimera to use the local python installation
by Sabuj Pattanayek 15 Jun '06

15 Jun '06

Hi, With the release of xorg-7.1.1 and mesa-6.5 I finally have direct rendering for my i855gm/i810 intel video device under linux. However I get lots of flickering of an object inside of the chimera display window when I rotate or move the object. I don't have this issue with pymol (compiled against the system python) and vmd (compiled against C/C++ opengl bindings?) or even glxgears. Perhaps I can workaround this problem by telling Chimera to use the local python installation? How is this done? Thanks, Sabuj

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saved image discoloration
by Megan Grabenauer 13 Jun '06

13 Jun '06

I've successfully used Chimera in the past to make beautiful images for publication. However I recently installed v1.2199 for Mac OS X and now whenever I try to save an image I get discolored boxes throughout the saved image. (see attached) The position of the boxes varies slightly each time. I have the image width set to 1050 pixels, 300 pixels per unit, and supersample at 3x3. Any suggestions would be appreciated. I do have an older computer, is this possibly a hardware issue? Megan

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Dock PDB into low resolution EM map.
by Puey Ounjai 12 Jun '06

12 Jun '06

Dear all, I am trying to dock atomic coordinate of a protein derived from 3D X-ray crystal (PDB format) into lower resolution (about 20-25 A resolution) EM map (BRIX, XPLOR ASCII or SITUS format) from 2D crystal. 1. Does Chimera have this kind of fitting tool (PDB to volume) or I have to fit the coordinate by hand? If chimera can do this task, Which command should I use? 2. Does Chimera have any statistical evaluation for manual fitting? 3. How can you evaluate the % matching of 2 models in Chimera? Best regards, Puey Ounjai

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Fish-eye view
by Thomas Goddard 12 Jun '06

12 Jun '06

Hi Gabe, Fish-eye would be handy for presentation images. I submitted a request for this in 2003 to the Chimera bug/feature tracking system. Unfortunately it has not seen the light of day since. But I make fish-eye images once in while. I've attached one I just made for you as a test looking inside reovirus (1ej6). The trick is to bring up the Chimera Python shell, menu entry Tools / General Controls / IDLE and type a few things: >>> c = chimera.viewer.camera >>> c.viewDistance 30.0 >>> c.screenWidth 13.0 >>> c.viewDistance = 2 >>> The parameters that control the field of view are "viewDistance" (default 30) and "screenWidth" (default 13). I think view distance means how far your face is from your screen and screen width is how wide the Chimera window is -- maybe the defaults refer to centimeters. The defaults (narrow screen and far view) give a field of view of 25 degrees. Setting viewDistance = 2 gives a field of 150 degrees. Tom > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > From: Gabriel Lander <glander(a)scripps.edu> > Subject: odd request > Date: Fri, 9 Jun 2006 13:03:11 -0700 > > Hi Thom, > The P22 paper I presented at the biophysics conference in Salt Lake > City will be published on June 23rd in Science, so when that happens > I'll send the movie I made with Chimera your way. > We actually got the cover of the issue, and I worked with a graphics > artist here at scripps to put it together using his fancy graphics > software. One thing that really made the structure very visually > striking was the implementation of a fisheye lens. Although this > feature is not scientifically very useful, it would be a great artistic > addition to Chimera. I have no idea how difficult this would ever be > to implement or if it'd be worth it, but it's just a thought. I know > you get like a million suggestions a day, so obviously this would go > somewhere in the utmost bottom list of things to do. > I've attached the mockup we made for the cover to give you an idea of > what I'm talking about. > Cheers, > -gabe > > *** removed image ***

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Colored Rays
by Mark Cunningham 12 Jun '06

12 Jun '06

Elaine, thanks for your response to my question on the coordinate system problem. My problem, as you suggested, was not related to coordinate systems, rather there was a problem with GOLD writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine. But now I have another question. Occassionally, while visualizing and manipulating a protein structure (1XAP) with Chimera, I get colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear. Thanks. Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Sporadic Colored Rays Across Screen
by Mark Cunningham 11 Jun '06

11 Jun '06

Elaine and Eric, thanks for your responses to my question on the coordinate system problem. My problem, as you suggested, was not related to coordinate systems, rather there was a problem with GOLD writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine. But now I have another question. Occassionally, while visualizing and manipulating a protein structure (1XAP) with Chimera, I get colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear. Thanks. Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Reading Frame Problem
by markcunningham 10 Jun '06

10 Jun '06

Could someone please help with this. . Using Chimera, I am trying to calculate rmsd between an observed ligand versus GOLD docked ligand, however the problem is the ligands load into different reading frames. The format for both ligands is .mol2. How can I correct this problem, in other words load both ligands into the same reading frame so that I can then calculate their rmsd. Thanks. Mark

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Reading Frames
by Mark Cunningham 09 Jun '06

09 Jun '06

Hopefully someone can please respond to this before the weekend. I have Windows version of Chimera. I am using Chimera to run rmsd between observed ligands and GOLD calculated ligands. When I open both ligands ( with .mol2 format) with Chimera, they load in different reading frames, thus I can't make the rmds calculation. Please address this issue. The rmsd works fine otherwise, its just with the GOLD ligand files that I am getting the reading frame problems. Thanks very much. Mark Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Writing a .x3d file that other programs can read
by Esther Bullitt 07 Jun '06

07 Jun '06

Hi, I am having trouble exporting a .x3d file in a format which programs that convert .x3d data to VRML data can read. The error message for one of them is: Xj3D Version: 1_0 Device found: Mouse-0 Device found: Keyboard-0 Error: Unexpected Exception: Unknown field name: chimera:hither for node: org.web3d.vrml.renderer.ogl.nodes.navigation.OGLViewpoint@1080876 Error: Failed to load file -- The ultimate goal is to have a VRML file that includes both the EM surface map and the pdb subunit structure together in a file that can be read by one of the companies that laser etches the structure into a glass cube. Some companies can read the pdb, some the VRML, but none can read both. Chimera says the .x3d can be converted into .vrml if there are no clipping planes or perspective, which there are not. But I still get this error. Any suggestions, pls? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics, Room W302 Boston University School of Medicine 715 Albany Street (mail only; couriers use 700 Albany Street) Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041

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