- Chimera-users - RBVI Mailing Lists

Resize a molecule
by Thomas Goddard 27 Apr '05

27 Apr '05

Here is some code to scale a molecule size by a given factor. That is all atoms have their coordinates multiplied by a factor. Tom ------- Start of forwarded message ------- Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi Jinghua, By "virus cage pdb file" I guess you mean you placed atoms at icosahedral positions, and want to show them connected up to show some icosahedral pattern. I think the easiest approach is to open your old session, run a command to change the diameter of the cage, then save a new session. Below is some Python code that provides a "scalemol" Chimera command. Make a directory chimera/share/scalemol in your Chimera distribution and put the code below in file chimera/share/scalemol/ChimeraExtension.py. Then start Chimera, open the cage PDB model, use menu entry Favorites/Command line, and type a command: scalemol 0 1.5 to make model number 0 bigger by a factor of 1.5. If you have more than one model open you can see the model numbers using Favorites / Model Panel, the model number is shown in the left hand column. Tom - ---- scalemol/ChimeraExtension.py code follows: # ----------------------------------------------------------------------------- # def scale_molecule(cmdname, args): from Midas.midas_text import error fields = args.split() try: model_num = int(fields[0]) factor = float(fields[1]) except: error('Syntax error: scalemol <model-number> <factor>') return import chimera mlist = chimera.openModels.list(id = model_num) if len(mlist) == 0: error('scalemol: No model number %d' % model_num) return for model in mlist: for a in model.atoms: x, y, z = a.coord().xyz.data() c = chimera.Coord() c.x, c.y, c.z = (factor*x, factor*y, factor*z) a.setCoord(c) # ----------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('scalemol', scale_molecule) ------- End of forwarded message -------

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get to lighting adjustment
by jinghua＠ucsd.edu 26 Apr '05

26 Apr '05

to whom it may concern, How could I get to the adcanced feature of lighting adjustment? Can I add more lights with different directions? Thanks! Jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>< Jinghua Tang, Ph.D. Phone: 858-534-5852(o) 4107 Natural Sciences Bldg, MC-0378 858-597-2056(h) Department of Chemistry & Biochemistry Fax: 858-534-5846 University of California, San Diego E-mail: jinghua(a)ucsd.edu La Jolla, CA 92093-0378 http://jinghua.ucsd.edu <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><

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Writing the selection
by Charles Moad 19 Apr '05

19 Apr '05

How can I write the current selection to a file from a script? "write sel filename.pdb" does not work. Thanks, Charlie

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v1.2105 for amd64 (x86_64)
by Sabuj Pattanayek 18 Apr '05

18 Apr '05

Hi, I don't know if this has been asked before (couldn't find anything on searches) but will there be a native amd64/emt64 (x86_64) build of chimera v1.2105? Thanks, Sabuj Pattanayek

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Problem with Large Molecules
by Private 14 Apr '05

14 Apr '05

Dear Chimera Team: I think your work on Chimera has been of very high quality. In fact, I've used it to produce print quality images for an upcoming book of mine. However, I've had some problems with displaying some large molecules, for example, 1AYM and 1P5Y. I use the PDB file for the molecule, but specifically the assumed biological model file, not the the asymmetric unit file. I've been able to open the file in programs like Deepview and Raswin, but I can't open the file in Chimera. I'm running Windows 98 with about 256MB of RAM, and what happens when I attempt to open the assumed biological model file Chimera runs for over an hour trying to open the file and then crashes with a page fault message. I certainly would like to use the image capabilities provided by Chimera, so can you help me with this? Or is this simply a limitation of Chimera?

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Thanks for the movie recorder
by Ann Mullin 08 Apr '05

08 Apr '05

I just tried out the movie recorder and I am very pleased. Thanks very much to the programmers who contributed to the addition of this tool to my favorite molecular graphics program. 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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yet another snapshot
by Eric Pettersen 05 Apr '05

05 Apr '05

A new snapshot release (1.2106) is available for Windows only, which fixes several issues the 1.2105 release had on that platform, namely: Movie Recorder movie encoding now works documentation searching fixed unreadable highlighted text in certain widgets fixed Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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how were the virus images generated?
by Thomas Goddard 05 Apr '05

05 Apr '05

Hi Dieter, To make virus capsid images in Chimera like those on the VIPERdb web site, http://viperdb.scripps.edu/ or like those on our web site http://www.cgl.ucsf.edu/Research/virus/ http://www.cgl.ucsf.edu/chimera/ImageGallery/ you use the Chimera Multiscale tool, menu entry Tools / Multiscale / Multiscale Models. I'm guessing you tried making solvent excluded molecular surfaces with menu entry Actions / Surface / Show. That makes much higher resolution surfaces and tends to crash for large molecules or complexes. (We are working on replacing that third party code.) If your virus capsid PDB file header contains sixty REMARK 350 BIOMT matrices then you can just press the "Make Models" button at the bottom of the Multiscale dialog. This uses the matrices to make sixty copies of the asymmetric unit. You don't need a file containing coordinates for the full capsid with this tool. If your virus capsid PDB doesn't have the BIOMT matrices, but uses the coordinate system defined by the VIPER site (eg a PDB downloaded from VIPER), then you can instead choose Multimer Type: Icosahedral Symmetry, VIPER Z(2)35X(2) from the menu at the bottom of the Multiscale dialog, and then press the "Make Models" button. Once you have displayed the capsid model, you can color, hide, or display capsomeres at atomic resolution or with ribbons using the other buttons in the Multiscale dialog. For the full details look at the Tools section of the Chimera User's guide for Multiscale. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… You can show this documentation in a web browser by just pressing the Help button at the bottom of the Multiscale dialog. Let me know if you have additional questions, Tom > From: "Dieter Blaas" > To: goddard(a)cgl.ucsf.edu > Date: Tue, 05 Apr 2005 12:38:20 +0200 > Subject: how were the virus images generated? > > Dear Tom, > Vijay referred my question to you: As far as I > understand were the virus images in VIPER generated > with Chimera. I have tried hard to generate similar > surface renderings with this software on a win2k 2 GB > machine but Chimera always crashes upon trying to > make the surface! Are there any particular parameters > which must be set? What is the limit of atoms, > coordinates, surface resolution, RAM? Many thanks for > any hints. > > Regards, Dieter Blaas > ------------------------------------------------------------------------ > Dieter Blaas, > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > ------------------------------------------------------------------------ >

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HAVING TROUBLE W/ PROGRAM!
by Desmond McMahon 05 Apr '05

05 Apr '05

I downloaded Chimera and I tried to understand the help section. I'm a high school student and i'm using this for a report. CAN YOU PLEASE PLEASE PLEASE tell me how to START a DNA/Double helix structure and I can't find out. Can you help me??? Desmond __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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by Andreas Linden 31 Mar '05

31 Mar '05

Hi, maybe you can incorporate drag and drop into chimera? It's a bit of a hassle having to go through file>open> and then go through directories to get at the pdb file! Otherwise an excellent program, thanks for making it available! Cheers Andy (University of Sheffield, UK)

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new snapshot
by Eric Pettersen 29 Mar '05

29 Mar '05

We've put out a new snapshot (version 1.2105) which is basically the same as the 1.2104 snapshot but has the zone-selection crash bug fixed. --Eric

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Mac OS X stereo
by David Belnap 27 Mar '05

27 Mar '05

As a follow-up to the discussion about stereo by Virginia and Sabuj, will Chimera currently, or in the future, work in stereo on a Mac running OS X? David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

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Fwd: [Chimera-users] Zones to create inspector list of "contacts"
by Elaine Meng 23 Mar '05

23 Mar '05

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: Wed Mar 23, 2005 9:39:41 AM US/Pacific > To: Grant Jacobs <gjacobs(a)bioinfotools.com> > Subject: Re: [Chimera-users] Zones to create inspector list of > "contacts" > > Hi Grant, > You can write out the contents of the current selection with > Actions... Write. More details can be viewed at: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#writespec > > However, the resulting text file will simply list all selection > contents (i.e., not in pairs of what is contacting what). I don't > know if that is sufficient for your purposes. > > If you are specifically looking at H-bond interactions, however, > FindHBond includes an option to write out all the H-bonded atom pairs > and the distances between them. Man pages: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ > findhbond.html > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html > Best, > Elaine > ----- > 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 > > On Wednesday, March 23, 2005, at 02:55 AM, Grant Jacobs wrote: >> >> I am trying to achieve something with this effect: >> >> Generate a list of all the atoms in other molecules of a >> multi-protein complex that are within a specific "contact" distance >> of atoms a molecule of interest in the complex, with them presented >> in the same way that H-honds or distances are illustrated. >> >> You can use Select:Zones to get the atoms that lie within a set >> distance of a molecule. All that seems to be needed is for the >> Select:Zones operation to optionally generate a list of atom pairs >> that the inspection things present. >> >> So far I can't seem a simple way of doing this without hacking code >> or doing it manually. Is there a way of doing this currently, or >> should this be looked at as future possible feature? >> >> Obviously, there are other useful "neighbour" operations you can do >> also, e.g. neighbours within the current selected molecule, >> neighbours by atom/residue type. >> >> Grant >

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1.2104 snapshot release available
by Eric Pettersen 17 Mar '05

17 Mar '05

Hi all, A new Chimera snapshot release (1.2104) is available. As usual, we recommend you download a snapshot release only if you need features not found in the preceding production release (in this case version 1.2065) since snapshot releases don't get the same level of testing as production releases. Also, in this snapshot the Collaboratory feature doesn't work on Windows. That said, here's the major things that are new: GENERAL: local documentation searching added (Help... Search Documentation) nucleic acid ambiguity codes (R = A/G, Y = C/T/U, N = A/C/G/T/U) can be used in subsequence searching (Select...Sequence... and Sequence Panel) new residue attribute "isHet" (whether the residue is in HETATM records in the input PDB file) NEW TOOLS: Attribute Calculator (Utilities) - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute Demo Editor (Demos) - graphical interface for creating demos Movie Recorder (Utilities) - capture image frames from Chimera and assemble them into a movie file Surface Capper (Graphics) - cap surfaces where they intersect a clipping plane (the cap is maintained interactively) Surface Color (Volumes) - color surfaces according to volume data 2D Labels (Graphics) - create arbitrary text labels and place them in 2D [really a preliminary version; will be improved in the production release] TOOL CHANGES: Demos - changes in demo dialog buttons/menu; demo source file format changed to XML (see new Demo Editor); older format can still be played MD Movie (formerly Movie) - added step size option for playing the movie; RMSD map calculation faster; added option to automatically recolor the RMSD map for contrast; new prefix for metafiles ("md:") Multalign Viewer - Region Browser acts upon chosen region(s) (not necessarily the active region) and includes checkboxes to control which is active and which are shown in the sequence window ViewDock - H-bond statistics can be included in the sortable columns of ligand descriptors Volume Viewer - support added for UHBD electrostatic potential (binary only) NEW COMMANDS: movie - capture image frames and assemble them into a movie file; command-line implementation of Movie Recorder writesel - write a parsable text file containing specifications of the currently selected (or unselected) items; command-line implementation of Actions... Write Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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how save cyclooxygenase demo
by J. David Rawn 16 Mar '05

16 Mar '05

Sir: I would like to save the cyclooxygenase demo to show my class in a classroom without a unix based system. How is that done? J. David Rawn

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hardware stereo question
by Virginia B. Pett 16 Mar '05

16 Mar '05

I am interested in computer visualization, computer modeling, and crystallographic software for teaching and research at The College of Wooster. We are going to replace our five-year old cluster of Silicon Graphics machines in the near future. We are considering a cluster of PCs with either Windows or Linux, or Macs with OS X. The big stumbling block for us has been figuring out what is the best hardware platform for three-dimensional stereo viewing. Our current Silicon Graphics machines have the Stereographics Crystal Eyes viewing system. Is there something newer, better, or less expensive than the Stereograhics Crystal Eyes viewing system that is compatible with PC or Mac? Or is the Crystal Eyes still the best system for Chimera and other molecular modeling and computer visualization software? Stereographics sells a CrystalEyes Workstation (either Windows/Linux or Mac) that looks attractive. I would appreciate any advice you can offer. ________________________________________ Virginia B. Pett Professor of Chemistry Department of Chemistry, The College of Wooster 943 College Mall, Wooster, OH 44691 Telephone: 330-263-2114 Fax: 330-263-2386

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Re: [Chimera-users] Intersurf, protein interface display
by Thomas Goddard 14 Mar '05

14 Mar '05

Miguel suggests another coloring for protein interface surfaces based on surface complementarity judged by looking at surface normals. Tom ------- Start of forwarded message ------- Date: Sat, 12 Mar 2005 17:25:29 +0000 From: =?ISO-8859-15?Q?Miguel_Ortiz_Lombard=EDa?= <mol1(a)york.ac.uk> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Intersurf, protein interface display - -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Tom, With regard to your very interesting message, I would like to add another useful way of studying the surfaces of protein-protein (or protein-whatever) interactions. This way involves the concept of "surface complementarity", where the buried surfaces are scanned to see how parallel are the normals to them at every point (in a grid). It is shown that specific or high-affinity interactions have usually higher complementarity. There is a paper by Lawrence and Colman (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=A…) and a program by the same authors in the CCP4 suite called "sc" that performs such calculation. The "sc" program is also able to add the "surface complementarity value" to the vertexes of the interacting surfaces calculated in GRASP. I currently have a little program (modified by me from a Raster3D jiffy) to colour such a modified surface according to those values and render it with the render program from Raster3D. But I don't like GRASP and would like to have this analysis as a possibility in chimera. Such analysis have been very useful for me in the past, especially to study protein-protein interactions. If this is also interesting for you I would be glad to be of help. Cheers, Miguel Thomas Goddard wrote: > Hi Conrad, > > I read the paper > > Intersurf: dynamic interface between proteins > Nicolas Ray, Xavier Cavin, Jean-Claude Paul, Bernard Maigret > Journal of Molecular Graphics and Modelling, 23 (205) 347-354 > > It addresses 3 problems: how to find a surface interface between 2 proteins, > ways to color such a surface, and how to flatten that surface into two > dimensions. > > The surface calculation was a neat algorithm -- take the > Delauney tetrahedralization of all atom positions from both proteins, > then find tetrehedra with vertices from both proteins and cut those > tetrahedra in half. The tetrahedra are cut in half with one or 2 > triangles using vertices on tetrahedron edges that connect an atom > in one protein to an atom in the other protein. The vertices are > placed midway between the atoms moved in by their vdw radii. > > They proposed 2 ways of coloring the surface. One colored vertices > by how far apart the atoms were in the two proteins that were used to > create that vertex. Red to blue shows short to long distances. The > other coloring shows types of possible interactions between the two > residues associated with the two atoms for the tetrahedron edge that > the surface vertex splits. They gave different colors for predicted > hydrogen bonding, hydrophobic packing, pi ... X, pi ... pi, same charges, > opposite charges. Not sure what the pi bonding notation means. > > They also described how to flatten the 3-dimensional to a 2-dimensional > surface with one to one correspondence between vertices and edges. > Their method tried to come as close as possible to a conformal map. > Conformal means the angles of the triangles stay the same to the extent > possible. > > These calculations took a few seconds on 2000-5000 atom proteins. > > Here's my assessment. I think the concept of showing a protein interaction > interface and coloring it to show interactions sounds useful for protein- > protein interaction people. I think the flattening into 2 dimensions > is probably not useful. Conformal maps greatly distort the area of > the surface if it has curvature (you've seen the maps where Greenland > is bigger than Africa, Americas, Asia and Europe combined). So the flattened > surface is going to be hard to recognize as the interface, unless it > is already pretty flat. If it is already pretty flat you might as > weill just look at the 3-d surface. > > If we wanted to do something with interface surfaces I would suggest > talking to Tanya Korteme. We already have all the infra-structure to > create the surfaces. I would not use the Delauney surfaces, instead > just use MSMS surfaces on both proteins showing only the parts associated > with atoms in one protein that are within 5 angstroms of atoms in the > other protein. The zone calculation code I wrote for multiscale could > do that fast. We could offer a range of atom colorings that map onto > the surface (hydrogen bonds, distance to nearest atom in other protein, > charge complementarity, etc...). > > I don't have time or enough interest to work on this project. But > perhaps someone else will. We have talked about collaborating with > Tanya Korteme in the past and this would be a good opportunity. > > Tom > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users - - -- correo-e: 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 - -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.0 (MingW32) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFCMyYJF6oOrDvhbQIRAttkAJ0frREWIEA7IYDE2LY38jdcyfuRoACgkHLn M9VEY8TEz8HnR3F763pws0A= =zoYa - -----END PGP SIGNATURE----- ------- End of forwarded message -------

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Intersurf, protein interface display
by Thomas Goddard 09 Mar '05

09 Mar '05

Hi Conrad, I read the paper Intersurf: dynamic interface between proteins Nicolas Ray, Xavier Cavin, Jean-Claude Paul, Bernard Maigret Journal of Molecular Graphics and Modelling, 23 (205) 347-354 It addresses 3 problems: how to find a surface interface between 2 proteins, ways to color such a surface, and how to flatten that surface into two dimensions. The surface calculation was a neat algorithm -- take the Delauney tetrahedralization of all atom positions from both proteins, then find tetrehedra with vertices from both proteins and cut those tetrahedra in half. The tetrahedra are cut in half with one or 2 triangles using vertices on tetrahedron edges that connect an atom in one protein to an atom in the other protein. The vertices are placed midway between the atoms moved in by their vdw radii. They proposed 2 ways of coloring the surface. One colored vertices by how far apart the atoms were in the two proteins that were used to create that vertex. Red to blue shows short to long distances. The other coloring shows types of possible interactions between the two residues associated with the two atoms for the tetrahedron edge that the surface vertex splits. They gave different colors for predicted hydrogen bonding, hydrophobic packing, pi ... X, pi ... pi, same charges, opposite charges. Not sure what the pi bonding notation means. They also described how to flatten the 3-dimensional to a 2-dimensional surface with one to one correspondence between vertices and edges. Their method tried to come as close as possible to a conformal map. Conformal means the angles of the triangles stay the same to the extent possible. These calculations took a few seconds on 2000-5000 atom proteins. Here's my assessment. I think the concept of showing a protein interaction interface and coloring it to show interactions sounds useful for protein- protein interaction people. I think the flattening into 2 dimensions is probably not useful. Conformal maps greatly distort the area of the surface if it has curvature (you've seen the maps where Greenland is bigger than Africa, Americas, Asia and Europe combined). So the flattened surface is going to be hard to recognize as the interface, unless it is already pretty flat. If it is already pretty flat you might as weill just look at the 3-d surface. If we wanted to do something with interface surfaces I would suggest talking to Tanya Korteme. We already have all the infra-structure to create the surfaces. I would not use the Delauney surfaces, instead just use MSMS surfaces on both proteins showing only the parts associated with atoms in one protein that are within 5 angstroms of atoms in the other protein. The zone calculation code I wrote for multiscale could do that fast. We could offer a range of atom colorings that map onto the surface (hydrogen bonds, distance to nearest atom in other protein, charge complementarity, etc...). I don't have time or enough interest to work on this project. But perhaps someone else will. We have talked about collaborating with Tanya Korteme in the past and this would be a good opportunity. Tom

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Re: mdmovie/1508: instantaneous segmentation fault after clicking OK to multiple PDB molecular dynamics movie
by Sabuj Pattanayek 09 Mar '05

09 Mar '05

Hi, Thanks for looking into the problem. It would be nice to be able to read trr/xtc trajectories, but then would you also need to add functionality to read the gro file as well? Perhaps other Chimera users would also find these features useful. Thanks, Sabuj Pattanayek Eric Pettersen wrote: > Hi Sabuj, > I understand the problem now. My code is not expecting the > individual PDB files to have MODEL/ENDMDL records in them (the code is > placing these records around each file as it collates them). The > result is a mess. I will work on making my code more robust in this > regard. > There is a fairly easy workaround for you though: don't give the > -sep flag to trjconv. You will get a single file containing the > frames bracketed by MODEL/ENDMDL records (which is what Chimera would > have had to assemble anyhow), which you can read by using the "single > file" option of the PDB format trajectory reader. One caveat is that > the MD code expects the model numbers to start at 1, not 0, so you > will either have to renumber the MODEL records somehow, or delete > MODEL 0 from the file. I will also work on handling files where the > numbering starts at zero. > Do you work with Gromacs trajectories a lot? If you do, I could > put reading Gromacs trajectories directly on my to-do list. > > --Eric >

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Registration and VRML output for molecules
by Thomas Goddard 09 Mar '05

09 Mar '05

Julio Ortiz asks about registration behind a fire wall, and VRML output for molecules (ribbons, sticks, spheres). Tom ------- Start of forwarded message ------- Date: Wed, 09 Mar 2005 09:09:04 +0100 From: Julio Otiz <ortiz(a)biochem.mpg.de> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Registration-VRML-Chimera Hi Thomas: A couple of question: 1) Chimera registration: When I try to register from our institute, behind a firewall, I can not register, I received an error message as there were not internet connection. For my personal computer is not a problem. I can do it from home, but for other computers at the institute, it could be a problem. I would like to update all our versions from chimera, so..how to deal with the registration problem afterwards? 2) VRML export of pdb file representations: As far as I know Chimera can export surfaces of density maps to VRML format. It is possible to export some representation of a pdb files, like ribbons, sphere or sticks also to VRML?. There are some programs that do it, so maybe could be a nice feature to introduce in Chimera (if is not already possible). Greetings, Julio ------- End of forwarded message -------

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Combining ribbons and ball-n-stick using neon
by Todd Weaver 09 Mar '05

09 Mar '05

Dear Chimera- Wondering if there is a way to combine ball-n-stick rendered with neon and displaying distances as dashed lines with ribbons for other parts of the protein. I have attached an image captured with save, all looks good except the distances are not displayed as black lines because it has not gone through neon. If I run neon the ribbons do not show up. I would like to have both in the final image. Warmest regards, TOdd -- Todd M. Weaver, Ph.D. UW-La Crosse 1725 State Street Chemistry Department 4020 Cowley Hall La Crosse, WI 54601 Ph. (608)785-8269 Fax (608)785-8281

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suggestion
by Esther Garcia-Rodriguez 07 Mar '05

07 Mar '05

Hi, I am working with structure superposition and I have noticed that labelling relevant residues when two structures or more are superimposed is a bit of a nightmare. As the labels go to C-alpha in all cases it is very difficult to see anything. I would suggest to allow the user to change the default and be able to establish particular positions for labels, as well as the distance from the relevant atom. For example, label all selected residues in one chain at 0.1 angstroms from the CG atom and all of the second chain at 0.2 (in X or Y). Or maybe just been able to change the minimum distance between labels in all directions. Thanks, Esther Esther Garcia Rodriguez Henry Wellcome Building for Biocatalysis University of Exeter Stocker Road Exeter EX4 4QD United Kingdom

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

07 Mar '05

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

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

02 Mar '05

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

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

01 Mar '05

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

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

01 Mar '05

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

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by Andrew Jewett 25 Feb '05

25 Feb '05

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

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

18 Feb '05

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

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

18 Feb '05

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

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

09 Feb '05

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

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Percent done
by David Belnap 07 Feb '05

07 Feb '05

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

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

07 Feb '05

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

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Getting an extension handle
by Charles Moad 07 Feb '05

07 Feb '05

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

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

02 Feb '05

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

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

01 Feb '05

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

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

25 Jan '05

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

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

24 Jan '05

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

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selecting
by John Nixon 18 Jan '05

18 Jan '05

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

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

14 Jan '05

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

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

06 Jan '05

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

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

04 Jan '05

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

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

04 Jan '05

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

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

21 Dec '04

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

2 1

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

20 Dec '04

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

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production release
by Eric Pettersen 17 Dec '04

17 Dec '04

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

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

13 Dec '04

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

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

10 Dec '04

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

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Chimera Multiscale using VRML?
by Thomas Goddard 10 Dec '04

10 Dec '04

Hi Dong, The Chimera Multiscale extension is described in the Chimera User's Guide in the Tools section. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… It currently calculates surfaces for PDB models and positions multiple copies of those surfaces using matrices, like the BIOMT (biological unit) matrices in PDB file headers. If I understand your question correctly, you want multiscale to use your own VRML model for individual proteins instead of the surfaces it normally calculates. It won't do that, and it is not a simple change to make. If you want a VRML model of a virus and you have the positioning matrices and a VRML surface for one asymmetric unit, you could create a new VRML file in an editor using the Transform VRML node to position each of the subunits. But such a model would not be interactive like the Multiscale models -- you would not be able to change to ribbon display, look at atomic contacts, .... Tom > Dear my concern > > Thank you for the distribution of this nice program, Chimera! > > Recently I downloaded new version of Chimera for Win32, 2056 build. > > Most of all function is fine but when I tried to export surface as VRML, the > button for "save" is not activated. > > Instead of "save" there is "open" button. This button could be activated > only by clicking "present file". > > If user clicks that activated button, the original file has gone and > replaced with new content's keeping its name. > > Is there any way to export other model, like ribbon or space fill model as > VRML? > > I think it will be very helpful. > > I tried lots of program, but the other programs are not good as Chimera at > least in terms of VRML export. > > My main purpose of using this program is "Multiscale modeling" ; I am so > interested in virus capsid model. > > It is so fabulous!!. > > I have never seen this function before and I love this.. > > However is it possible to make multiscale model from other format like VRML? > > I don't know exactly how chimera makes multiscale model, but I think chimera > may use the matrix. > > If then, I can guess we can make model from any format file whatever it is. > > Would you help me how to do this work? > > > And one more thing... > > The exported surface file VRML format from chimera starts with > > #VRML V2.0 utf8 > > Transform { > > children [ > > Shape { > > .... > > And ended with ]} > > > However without > > > Transform { > > Children [ > > > > ] } > > Sentence there is no problem to view this file. > > Moreover, some program which can import VRML file does not recognize > original exported file. > > After delete above sentence they could import VRML file. > > > Thank you > > > Dong Hoon Chung

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Re: [chimera-dev] add h
by Elaine Meng 08 Dec '04

08 Dec '04

On Dec 7, 2004, at 4:17 PM, Virginie Lafont wrote: > > I am a new user of chimera and I already have a question. > I have an protonated aspartic acid in my protein and I was wondering, > is it possible to add hydrogen atom to aspartic acid with chimera? > Thanks > > Virginie Hello Virginie, It is possible, with a few steps. As you already noticed, if you just use "addh" the aspartic and glutamic acid carboxylate groups will not get protonated. In the definitions of these residues, the carboxylate oxygen atoms are type O2-, which would not get protonated. You can use Define Attribute to change the types of these atoms. First you need to know the residue number of the aspartic acid you want to protonate and which of the oxygens (OD1 or OD2) you want to receive the proton. Next, create a define attribute input file in which you specify these two atoms and change type of the oxygen you want protonated to O3 and the one you don't want protonated to type O2 (example attached). There is a file description and more examples in the manual page for Define Attribute, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html In Chimera: open your PDB file of interest run addh (note the aspartic acid is not protonated in this step) Tools... Utilities... Define Attribute (open the previously prepared input file) now run addh again (note the aspartic acid will be protonated) The proton may not be pointing the direction you want, so you will probably then want to rotate the OH to the proper position, as described in http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/ structuremeas.html#adjust My define attribute example file (attached) works with the PDB file 1zik. The define attribute file tells Chimera to change the atom types of Asp residue number 7 in chain B so that the side chain will be neutralized when AddH is run. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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release candidate
by Eric Pettersen 06 Dec '04

06 Dec '04

Hi, We've put out a "release candidate" for download (version 1.2056). We're hoping people will download it and try it and report any problems they find before we make a production release version in early January. The production release candidate will be functionally identical to the production release, except that we will fix any bugs reported between then and now. There are some new features in the 1.2056 release, and if you are interested in those you should really try it out so that if you find any problems they will be fixed in the production release. Here's a synopsis of the major new features since the 1.2038 release: NEW TOOLS: Surface Area/Volume (Utilities) - calculate surface areas and Voronoi volumes with the StrucTools server at http://molbio.info.nih.gov/structbio/basic.html TOOL CHANGES: Movie - support added for MMTK/NetCDF trajectory format - RMSD maps containing all-by-all comparisons among specified frames can be calculated (for all atoms or selected atoms) Volume Viewer - support added for APBS electrostatic potential format and TOM toolbox EM density map format sequence panel (opened from Model Panel) - secondary structure shown with color NEW COMMANDS: matrixget - write the current transformation matrices to a file matrixset - read and apply the transformation matrices from a file mmaker (matchmaker) - command implementation of MatchMaker; generates a sequence alignment for two structures and then superimposes the structures accordingly BUGS FIXED: large structures without HELIX/SHEET records now much faster to open (fixed bug in secondary-structure computation) non-default ribbon scalings from pre-1.2038 versions no longer cause bombing on startup (1.2038 would die at startup for such) Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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Command-line MatchMaker
by Eric Pettersen 01 Dec '04

01 Dec '04

> On May 5th 2004, Eric Pettersen wrote: > As for MatchMaker, right now it is too closely tied to the GUI > dialog > to be called from nogui mode. I will work on disassociating the > underlying computation from the graphical interface so that it can > become a command-line command. The hydrogen-bond finder has recently > been given this kind of treatment and is callable from the command line > in the release we will be making later this week. I'll send mail when > the same is true for MatchMaker. The command-line version of MatchMaker will be in our upcoming release-candidate snapshot, which will be out at the end of this week. --Eric

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Labeling Residues
by Stephen P. Molnar, Ph.D. 01 Dec '04

01 Dec '04

I have to admit to being completly flumoxed [sic] by this one! How do I label an individual residue: According to help the format is: wt %(1-letter code)s%(number)s Now I have an enzyme, 1QTI.pdb in which I wish to label the SER200 label. I have tried every combination of the example on the help page that I can think of without success. What is the exact format for creating that label? Thanks in advance. -- 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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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

1 0

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

2 1

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

2 1

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 "

2 1

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

2 1

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 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

2 1

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

1 0

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.

1 0

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

1 0

[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.

2 2

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

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Re: save session/grasp surfaces
by Thomas Goddard 07 Jun '04

07 Jun '04

Hi Sabuj, We'll consider adding DelphiViewer session saving. It is a fair bit of work and we have been thinking of replacing DelphiViewer's surface coloring capabilities with something that works with volume data other than electrostatic potential maps. I'll discuss it with other Chimera developer's and get back to you. Tom > Date: Mon, 7 Jun 2004 11:49:00 -0500 > From: "Pattanayek, Sabuj" <sabuj.pattanayek(a)Vanderbilt.Edu> > To: goddard(a)cgl.ucsf.edu > Subject: save session/grasp surfaces > > Hi, > > Method 1 would be what I am looking for (reload potential file, grasp surface > file, recalculates colors according to saved preferences, and places the surface > where it was before saving). I accidentally deleted your message, but I think > that was the gist of choice #1. > > Thanks, > Sabuj Pattanayek

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[Chimera-users] v1.1951 save session not reopening grasp surfaces that were there before i saved session
by Pattanayek, Sabuj 04 Jun '04

04 Jun '04

Hi, I had to resort to using grasp surfaces because MSMS doesn't behave "nicely" when dealing with multiple free floating residues that come directly from a PDB file. Although grasp surfaces are lower in visual quality than MSMS, grasp rendered all the areas I wanted whereas the MSMS plugin could not. So, after I did save session and re-opened the session the grasp surfaces did not reappear. Is there anyway to add functionality so that the grasp surfaces, colors, and the corresponding locations can be recalled when I load the saved session file? This saves time especially when there are many grasp surface components each with different colors. One more minor detail/UI glitch I noticed?: Color Editor -> click opacity : the "A" row along with slider appears -> unclick opacity : the sliders disappear but the "A" along with row space remains ...don't know if that was done on purpose. Thanks for the great program!

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Re: [Chimera-users] non-GUI use of Chimera
by Charles Moad 25 May '04

25 May '04

Hi, I am working with Randy on this, and I think we have a web service type solution that will work using your suggestions. The one problem that remains is killing chimera after a request. The webdata facility is targeted to run on a client's machine where a user quits chimera, but we will be running it on the server. I tried adding the 'stop' command at the end of the chimerax file, but I received an error from chimera and it continued to run. Same story for 'sys.exit()' Running the chimera_send script a second time only opens a new instance of chimera which also remains open. Is there a way to attach chimera_send to an existing process of chimera, or have chimera quit at the end of a chimera_send call? Thanks, Charlie > -----Original Message----- > From: chimera-users-bounces(a)cgl.ucsf.edu > [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Thomas Goddard > Sent: Monday, May 24, 2004 6:20 PM > To: heiland(a)indiana.edju > Cc: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] non-GUI use of Chimera > > Hi Randy, > > If I understand correctly you want to be able to type some Chimera > Python > code or Chimera commands to a web browser, those get sent to the web > server > which sends them to Chimera running on the web server machine. Then you > capture the Chimera image and send it back to the web browser. > > I believe this can be done using the Chimera "Web Data" facility. > This > allows programs to send commands to Chimera. The intended use is for > displaying models in Chimera when the user clicks a link in a web > browser. > It works by having the *.chimerax file associated with the link lauch > helper application <chimera-install-location>/bin/chimera_send. > The same mechanism allows any program to send commands to Chimera. > The Chimera User's Guide describes this under Tools/Web Browser > Configuration. > Here's a URL: > > > http://www.cgl.ucsf.edu/chimera/1.1951/docs/ContributedSoftware/webdata/ > chimerax.html > > What you might do is have your web server create an appropriate > *.chimerax that executes the user's commands and then prints the > Chimera graphics window to a file. The web server than sends the > image (jpg) to the web client. There is a bunch of somewhat tricky > glue to make this work. As previous posts mentioned, Chimera will > need to pop up windows on some screen to render an image. For the web > server to know when Chimera has finished making an image, the > *.chimerax file might end in a command that writes to some secondary > status file after the image file is written. That will tell the web > server that the image is ready. > > We haven't tried this. And there are other pitfalls, like you are > likely to run into trouble if the web server starts 2 instances of > Chimera > and then tries to dispatch commands with the chimera_send program. > > Please let me know if you get this to work. Feel free to send > additional > questions. > > Tom > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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vrml 2.0 export of pdb representation
by Pattanayek, Sabuj 25 May '04

25 May '04

Hi, Is there anyway to export a pdb model into vrml once I have it just the way I want it (ribbon & atom sizes, colors, etc)? I tried a pdb2vrml converter from http://www.pc.chemie.tu-darmstadt.de/research/vrml/pdb2vrml_right.shtml but freewrl crashes when loading the output (I think pdb2vrml might be outputting vrml 1.0), it's also not very versatile as far as what I want to display into vrml from the pdb. Thanks

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non-GUI use of Chimera
by Thomas Goddard 24 May '04

24 May '04

Hi Randy, If I understand correctly you want to be able to type some Chimera Python code or Chimera commands to a web browser, those get sent to the web server which sends them to Chimera running on the web server machine. Then you capture the Chimera image and send it back to the web browser. I believe this can be done using the Chimera "Web Data" facility. This allows programs to send commands to Chimera. The intended use is for displaying models in Chimera when the user clicks a link in a web browser. It works by having the *.chimerax file associated with the link lauch helper application <chimera-install-location>/bin/chimera_send. The same mechanism allows any program to send commands to Chimera. The Chimera User's Guide describes this under Tools/Web Browser Configuration. Here's a URL: http://www.cgl.ucsf.edu/chimera/1.1951/docs/ContributedSoftware/webdata/chi… What you might do is have your web server create an appropriate *.chimerax that executes the user's commands and then prints the Chimera graphics window to a file. The web server than sends the image (jpg) to the web client. There is a bunch of somewhat tricky glue to make this work. As previous posts mentioned, Chimera will need to pop up windows on some screen to render an image. For the web server to know when Chimera has finished making an image, the *.chimerax file might end in a command that writes to some secondary status file after the image file is written. That will tell the web server that the image is ready. We haven't tried this. And there are other pitfalls, like you are likely to run into trouble if the web server starts 2 instances of Chimera and then tries to dispatch commands with the chimera_send program. Please let me know if you get this to work. Feel free to send additional questions. Tom

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Re: [Chimera-users] vrml 2.0 export of pdb representation
by Pattanayek, Sabuj 22 May '04

22 May '04

imho, 3DS is currently more widely supported than X3D by expensive, cheap, and free 3d modellers. Most 3D format translators can convert from 3DS to other types (DXF, iv, etc). However it looks like from web3d.org that X3D is much more versatile and feature rich than old 3ds... Quoting Greg Couch <gregc(a)cgl.ucsf.edu>: > We currently only support VRML export of volume isosurfaces and multiscale > surfaces. So the answer is no, not yet. > > Exporting to a 3D graphics file format is definately something we would > like to do. However, it is unclear what format would be best to generate. > VRML 2.0 will never support transparency like chimera does. VRML's > successor, X3D, looks promising, but there aren't many users yet. Other > possiblities include the Renderman format, popular with animation studios; > the .3DS format, popular on PCs; and many others. > > So, a question for everyone reading this, if you had to pick one format, > would it be VRML97? And if so, why? And if not, why not? We are leaning > torwards outputing X3D, but would appreciate comments from people who > would actually be using the output. > > Greg Couch > UCSF Computer Graphics Lab > gregc(a)cgl.ucsf.edu > > > On Fri, 21 May 2004, Pattanayek, Sabuj wrote: > > > Is there anyway to export a pdb model into vrml once I have it just the way > I > > want it (ribbon & atom sizes, colors, etc)? I tried a pdb2vrml converter > from > > http://www.pc.chemie.tu-darmstadt.de/research/vrml/pdb2vrml_right.shtml > but > > freewrl crashes when loading the output (I think pdb2vrml might be > outputting > > vrml 1.0), it's also not very versatile as far as what I want to display > into > > vrml from the pdb. >

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Color blending on ribbons
by Emma Hill 20 May '04

20 May '04

Hi, I wondered if there is any easy way to blend colors from one residue to the next on a ribbon chain (as in the rainbow facility.) I want to be able to precisely define where this takes place (ie whenever I switch from one color to another) - more specifically I am coloring different regions of a superimposed pair to show where is aligned and where is not, and the drastic switch from one color to the next would definitely look better more blended. Thanks in advance Emma -- Emma Hill Brenner Research Lab U.C. Berkeley

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non-GUI use of Chimera
by Randy Heiland 20 May '04

20 May '04

I am evaluating Chimera as a tool for providing (pseudo-interactive) vis functionality from a web server and therefore would like to use it in a non-gui mode. I saw the earlier post/reply to this list (May 4) on this topic, and Eric indicated that one way to do this was to put all your cmds in a file then run "chimera --nogui <cmd-file>". Obviously this isn't ideal for my purposes. So, I'm wondering what the alternatives are? I'm a newbie to Chimera, but I've read how it was based on Midas, and so I decided to see how far I could get in reading in a pdb file and... I didn't get very far: (after install Chimera (Linux, beta 1 build 1951), plus dependent Python pkgs) %python >>> import chimera >>> import Midas >>> f=Midas.open('foo.pdb') and I get an error about 'missing default material' and realize I'm doing the wrong thing anyway. Basic question: can I, from the Python interpreter, use Chimera/Midas to read in a pdb file and do basic Chimera functionality? For now, I don't even care if it assumes X is running and pops up windows. Thanks, Randy

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rainbow command with sub-models
by Jarrod Smith 19 May '04

19 May '04

Hello all, Is it possible to add a new "level" to the rainbow command such that each submodel of a multi-model PDB file (MODEL/ENDMDL records) can be visited separately by the rainbow command? I have some pdb files with several tens to hundreds of submodels in them. Separating them by chain ID (so I can use the rainbow chains command) has proven to be impractical for other reasons, so this would be useful in such a case. Thanks for the great software. Jarrod Smith -- Jarrod A. Smith, Ph.D. Asst. Director, Center for Structural Biology Research Asst. Professor, Biochemistry Vanderbilt University 203 processes: 140 sleeping, 63 running

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new Chimera production release
by Eric Pettersen 14 May '04

14 May '04

Hi all, A new Chimera production release (version 1.1951) is now available for download. I've summarized the major additions since the last snapshot (1.1917) below. A list of all the changes since the last production release (1.1872) is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.1951.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu Changes since 1.1917: General changes --------------- Newly opened models are shown larger (as well as models after a 'window' or 'focus' command) Selections can be written out as parsable text files (Actions->Write... or from the Selection Inspector) New residue attributes: kdHydrophobicity (Kyte-Doolittle hydropathy, amino acids only) mavPercentConserved (% conserved in a sequence alignment open in Multalign Viewer) above for use with Render/Select by attribute tools Double-picking a bond brings up a menu with Rotate Bond and Select Bonded (the latter is new and selects the atoms); double-picking a pseudobond bring up a menu with just Select Bonded; "select bonded" also now in Pseudobond Panel As much as possible, can handle PDB files with 100000+ atoms (e.g. AMBER output). Some PDB records (e.g. CONECT records) have no room for 6-digit atom serial numbers, so only can be used for the first 99,999 atoms. A new tutorial describing preparing images for publication Select by Attribute Value... in Selection menu and Model Panel New Tools --------- Lighting (Viewing Parameters): change and save lighting parameters Color Secondary Structure (Graphics): color peptides/proteins by secondary structure Render Attributes (Graphics): color or otherwise change atom, residue, or model displays based on attribute values; was in 1.1917 release but several changes have been made and documentation added Demo (its own category; entries are individual demos): create/replay demos in Chimera; example demo included (Cyclooxygenase) Tool Changes ------------ Adjust Torsions now allows a bond to be rotated with mouse motions in the graphics window Movie has File->Save PDB for writing out either the current frame or all frames that have been viewed Multalign Viewer: ClustalX-style residue letter coloring added and made the default; can save alignment depiction as an EPS file; can hide Consensus and/or Conservation lines RibbonStyleEditor now has two panels in which scalings and cross-sections can be defined and named; named cross-section are analogous to the built-in cross-sections (flat, edged, round) and can be accessed from the Actions menu or with ribrepr; nucleic acids are now treated separately in the scalings panel New "Graphics" category; Per-Model Clipping, PipesAndPlanks, ResProp, and Ribbon Style Editor moved into it SimpleSession saves lighting, ribbon scaling and cross-section(s), B-factor and occupancy values Web Data asks for confirmation before accepting certain files; associated option in Preferences Command Changes --------------- alias: $1, $2, $3, ... may be used to indicate the first, second, third... arguments of the alias conic: works on Windows, and the -s flag now works on Linux (besides Mac, SGI) write: has "trajectory" keyword to write all frames that have been viewed (loaded) [analogous option added to Model Panel's "write PDB" dialog] ribbackbone: now applies to nucleic acids also

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by riccardodesantis＠fastwebnet.it 05 May '04

05 May '04

Hallo, my name is Riccardo De Santis and I'm a new user of CHIMERA. I'd like to know how run the program from the command line. I've tryed with the command NOGUI but the program doesn't start. Another question is: how can I use matchmaker (in the graphic menu) to match the molecules from the command line? Which is the istruction to type? Thank you in advance, Riccardo De Santis.

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by riccardodesantis＠fastwebnet.it 04 May '04

04 May '04

Hallo, my name is Riccardo De Santis, and I'm a new user of CHIMERA. I'd like to know how to use the program in command line mode. I noticed that there is a NOGUI option, I tryed it but unsuccessfully. Cuold you help me , please? Thank you in advance, Riccardo De Santis.

1 0

Coloring by bfactor
by Thomas Goddard 23 Apr '04

23 Apr '04

Hi Padma, We have developed a Chimera tool to color by bfactor or other attributes but it is not yet released. We expect to have a new release in the middle of May. Here are a couple approaches you could use now. You can use the color command like the following to color all atoms with bfactor between 10 and 15 green. color green @/bfactor>=10 and bfactor<=15 You could put a series of these commmands in a file to color several intervals different colors to get a rainbow effect. Use the "open" command to run the file of coloring commands. A more flexible route is to use some Python code. Putting the code shown below in a file bcolor.py and then opening this file will make a rainbow coloring by bfactor for the selected atoms. A fancier version of this could have a dialog popup to specify bfactor range and colors. If you make a molecular surface with Actions/Surface/Show the default coloring of this surface is to use the atom colors. So coloring the atoms by any of the above means will allow you to get the same coloring on a surface. Tom ----- code bcolor.py follows: # ----------------------------------------------------------------------------- # def color_atoms_by_bfactor(atoms, b0, rgb0, b1, rgb1): for a in atoms: if hasattr(a, 'bfactor'): b = a.bfactor if b < b0: f = 0 elif b < b1: f = (b - b0) / (b1 - b0) else: f = 1 r,g,b = ((1-f)*rgb0[0] + f*rgb1[0], (1-f)*rgb0[1] + f*rgb1[1], (1-f)*rgb0[2] + f*rgb1[2]) import chimera a.color = chimera.MaterialColor(r,g,b) # ----------------------------------------------------------------------------- # from chimera import selection atoms = selection.currentAtoms() # currently selected atoms b0 = 5 rgb0 = (0,0,1) # blue b1 = 20 rgb1 = (1,0,0) # red color_atoms_by_bfactor(atoms, b0, rgb0, b1, rgb1) > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: One more Chimera question! > From: Padmaja Natarajan <nataraja(a)scripps.edu> > Date: Fri, 23 Apr 2004 13:31:38 -0700 > > Hi Tom, > > Is it possible to make a molecular surface based on PDB coordinates > and be able to view this surface colored (as a spectrum going from blue > for smallest to red for largest value), > depending on values stored in say B-factor column of the PDB file. > (as shown in figure below created using AVS) > > thanks again > regards > Padma

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Re: [Chimera-users] CHIMERA help - coloring density maps
by Thomas Goddard 23 Apr '04

23 Apr '04

Hi Padma, There is a Chimera command called "longbond" described in the Chimera User's Guide / Basic Functions / Commands / longbond http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html that removes long bonds. There is currently no radial masking tool. But using the Isosurface Colorizer extension from EMAN you can set the color to transparent black outside or inside a certain radius. That will make it invisible. For example you can make the color blue at radius 10 nm, and transparent black at 10.01 nm. You will also want to turn on the Volume Viewer / Options / Dim transparent surface mesh switch to get rid of the specular highlights on the transparent black part of the surface. This trick for masking does not "cap" the isosurface at the radius where it is cut. So you see the inside of the isosurface. Turning off two sided lighting in Volume Viewer / Options will make the interior of the surface dark. To cut and cap the isosurface at a specific radius you really want to the display to act as if the volume data were zero outside a specified radius. I don't have any way to do that, although it probably would not be too hard to hack something into surface.py that copied the 3-d matrix and made it zero outside a specified radius. By the way, the modification I described to Chimera surface.py to make the Isosurface Colorizer from EMAN work is not needed in Chimera 1917. That change was included in Chimera 1917. I you are looking at models of virus particles you might be interested in the Chimera Multiscale extension. Here are some example images: http://www.cgl.ucsf.edu/home/goddard/viper/ The images at the bottom of that page show the RNA in satellite tobacco mosaic virus. Tom > From: Padmaja Natarajan <nataraja(a)scripps.edu> > Subject: Re: [Chimera-users] CHIMERA help - coloring density maps > Date: Fri, 23 Apr 2004 13:08:02 -0700 > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Hi Tom, > > Thank you very much for the details you had given me earlier in > making the radial coloring work for surfaces. > I , with the help of my colleague Jeff who made the changes in the > chimera (version 1917) script, am > able to produce radial coloring for my density map! > > Can ask more questions?? > > 1) I have coordinates for an icosahedron, but when I read it into > chimera, > several un-wanted connections are made (probably because of the way the > PDB file is written - for use in the graphics program O). I do not see > any distance cut off > criterion command that would help (probably) remove some of those > connections! > > 2) density map: I would like a radial masking tool, that can be used to > choose > minimum and maximum values for radius and be able to see the map only > within this > radius range. For example, this helps in looking at the inner (RNA) > density in a virus structure. > > thanks again! > regards > Padma > ______________________________ > Padmaja Natarajan, Ph.D > The Scripps Research Institute > La Jolla, California, USA.

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install question
by Randy Heiland 23 Apr '04

23 Apr '04

Greetings from a newbie to Chimera, Is there a searchable archive? (I found the archive, but no associated search engine) I'd really like to be able to install Chimera without blowing away my current Python installation - is this possible? (I'll be using both Windows and Linux) Thanks, Randy

2 1

Viewing orbitals and charge distributions
by João Otávio 23 Apr '04

23 Apr '04

Hello All! I am a CHIMERA newbie and I would like to know how could I create a module in order to read orbitals and/or charge distributions from molecular orbitals programs such as GAUSSIAN, GAMESS, etc. Thanks in advance, .................................................................João -- ___________________________________________________________ Sign-up for Ads Free at Mail.com http://promo.mail.com/adsfreejump.htm

2 1

save session error in Chimera 1892
by Juha Huiskonen 22 Apr '04

22 Apr '04

Hi, when trying to save session in chimera 1892 I get an error: Error processing trigger "save session": ValueError: Can't convert type <type 'bool'> (see reply log for Python traceback info) Reply log: Traceback (most recent call last): File "/usr/local/chimera1892/share/__main__.py", line 56, in ? value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 285, in init tkgui.eventLoop() File "/usr/local/chimera/share/chimera/tkgui.py", line 2809, in eventLoop app.mainloop() File "/usr/local/chimera/lib/python2.3/lib-tk/Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "/usr/local/chimera/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera/share/chimera/baseDialog.py", line 409, in OK self.Apply() File "/usr/local/chimera/share/OpenSave/__init__.py", line 141, in Apply self.command(1, self) File "/usr/local/chimera/share/SimpleSession/gui.py", line 24, in _saveCB saveSession(paths[0]) File "/usr/local/chimera/share/SimpleSession/save.py", line 269, in saveSession chimera.triggers.activateTrigger(SAVE_SESSION, buf) File "/usr/local/chimera/share/chimera/triggerSet.py", line 214, in activateTrigger self._triggerDict[name].activate(data) File "/usr/local/chimera/share/chimera/triggerSet.py", line 127, in activate ret = handler.invoke(self._name, triggerData) File "/usr/local/chimera/share/chimera/triggerSet.py", line 82, in invoke self._funcData, triggerData) File "/usr/local/chimera/share/VolumeViewer/__init__.py", line 138, in save_session_cb session.save_volume_state(self, file) File "/usr/local/chimera/share/VolumeViewer/session.py", line 22, in save_volume_state t = objecttree.instance_tree_to_basic_tree(s) File "/usr/local/chimera/share/SessionUtil/objecttree.py", line 69, in instance_tree_to_basic_tree d[k] = it2bt(getattr(itree, attr)) File "/usr/local/chimera/share/SessionUtil/objecttree.py", line 37, in it2bt return instance_tree_to_basic_tree(it, c, a) File "/usr/local/chimera/share/SessionUtil/objecttree.py", line 72, in instance_tree_to_basic_tree raise ValueError, "Can't convert type " + str(t) ValueError: Can't convert type <type 'bool'> -- The session file is written, but it doesn't contain the files I have read into chimera. Cheers, Juha Huiskonen

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Re: [Chimera-users] chimera and hydrophobic potentials
by Thomas Goddard 12 Apr '04

12 Apr '04

Hi Miguel, If GRID computes the hydrophobic potential on a surface, it seems like a bad strategy to save it in a volume format. If you interpolate onto a slightly different surface, you will get values interpolated with zeros in the volume because the hydrophobicity wasn't computed at most grid vertices. It seems it would be better to render the hydrophobicity values with exactly the GRID surface. Can GRID output the triangulated surface with hydrophobicity values? I looked at the MSMS library. It does not look like it provides a triangulated version of the solvent accessible service needed by Chimera. It can give you the surface area contributed by each atom to the solvent accessible surface. Tom > Date: Sun, 11 Apr 2004 22:39:40 +0100 > From: Miguel Ortiz <mol(a)ysbl.york.ac.uk> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] chimera and hydrophobic potentials > > Dear Tom, > > I've tested your cns2delphi script and, as expected, it works wonderful- > ly. The problem with colouring the surface using these maps actually > comes from the fact that for the hydrophobic probe, grid only calculates > the potential on what it's called the "solvent accessible surface" and > not on the whole volume (as delphi does for electrostatics and grid for > other probes). Being this the case, the best solution would be to > render in chimera this surface (at present, msms renders the "solvent > excluded surface" defined as you said in your email) > > I will try to find out how msms renders its surfaces, because the only > difference between "solvent accessible " and "solvent excluded" is that > the first is the "surface" defined by the center of the probe, while > the second (msms one) is the contact surface between the surface of the > probe and that of the protein (as defined by the Van der Waals radii of > its atoms). And it seems to me that it shouldn't be difficult to convert > from one to the other. Or perhaps I'm wrong and it's more tricky... > > Thank you again for all your help. It has been not only useful but > also instructive. > > Best regards, > > Miguel

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Re: [Chimera-users] chimera and hydrophobic potentials
by Thomas Goddard 09 Apr '04

09 Apr '04

Hi Miguel, I wrote a conversion program cns2delphi.py that takes the k2f output and produces a delphi file and tried it on the data you sent. The delphi file is read properly by Chimera DelphiViewer and can be used to color an MSMS surface. A problem with the data you sent is that the hydrophobicity map is zero over the entire MSMS surface. There are blobs of hydrophobicity a few angstroms away from the surface but they don't touch the surface. I observed this by showing the map with the Chimera volume viewer (just use File/Open...). You can change the probe radius for generating the MSMS surface by going to Favorites/Model Panel, selecting the MSMS surface, clicking the Attributes button, changing the probe radius setting, and pressing Enter. (You need to set the surface color to a solid color before changing the radius or an error message is generated.) Unfortunately that does not push the molecular surface out uniformly -- only the surface in the cavities is pushed further from the molecule. Apparently the probe radius is the radius of a ball rolled over the molecule with standard atom radii. The MSMS surface is the surface of the region that cannot be touched by the ball. So a bigger ball does not change the surface location at protrusions. Maybe a better approach is to specify larger atom radii. Below is the cns2delphi.py Python program. It requires the Numeric Python module which is not a standard part of Python. The Python that comes with Chimera includes Numeric. You can convert k2f output to delphi format as follows. % /usr/local/chimera/bin/python2.3 cns2delphi.py 1ltlA.k2f 1ltlA.phi This creates the 1ltlA.phi file. To use the Chimera DelphiViewer extension, start Chimera, open 1ltlA.pdb, make a molecular surface with Actions/Surface/Show, start Extensions/Delphi/DelphiViewer, enter Potential File 1ltlA.phi, click the Browse button next to MSMS Surface in the Molecular surface pane so the surface is listed, then press Apply in the Molecular surface pane. This will color the surface. You can also just use File/Open... on 1ltlA.phi to see an isosurface of the hydrophobicity map. You can drag the vertical bar on the histogram shown in the volume viewer dialog to change the isosurface threshold level. Tom ----- cns2delphi.py follows. Preserve indentation since it is important in Python. #!/usr/bin/env python # ---------------------------------------------------------------------------- # Convert CNS volume to Delphi format. # # ---------------------------------------------------------------------------- # Returns matrix, xyz_origin, and xyz_step # def read_cns_file(path): f = open(path, 'r') f.readline() # First line is blank ntitle_line = f.readline() # integer number of comment lines try: ntitle = int(ntitle_line.split()[0]) except ValueError: raise SyntaxError, ('Invalid CNS comment line count on line 2: %s' % ntitle_line[:80]) for t in range(ntitle): f.readline() extent_line = f.readline() extent = split_fields(extent_line, 8, 9) try: na, amin, amax, nb, bmin, bmax, nc, cmin, cmax = map(int, extent) except ValueError: raise SyntaxError, 'Invalid CNS grid size line: %s' % extent_line[:80] cell_line = f.readline() cell = split_fields(cell_line, 12, 6) try: cell_params = map(float, cell) except ValueError: raise SyntaxError, ('Invalid CNS cell parameters line: %s' % cell_line[:80]) cell_size = cell_params[0:3] cell_angles = cell_params[3:6] axis_order_line = f.readline() # Must be ZYX asize, bsize, csize = (amax - amin + 1, bmax - bmin + 1, cmax - cmin + 1) if asize <= 0 or bsize <= 0 or csize <=0: raise SyntaxError, ('Bad CNS grid size (%d,%d,%d)' % (asize, bsize, csize)) import Numeric data = Numeric.zeros((csize, bsize, asize), Numeric.Float32) for c in range(csize): read_floats(f, 1) # c section number values = read_floats(f, asize * bsize) array = Numeric.array(values, Numeric.Float32) plane = Numeric.reshape(array, (bsize, asize)) data[c,:,:] = plane f.readline() # footer - int value must be -9999 f.readline() # density average and standard dev f.close() xyz_step = (cell_size[0]/na, cell_size[1]/nb, cell_size[2]/nc) xyz_origin = map(lambda gmin, step: gmin * step, (amin, bmin, cmin), xyz_step) return data, xyz_origin, xyz_step # ----------------------------------------------------------------------------- # Read ascii float values on as many lines as needed to get count values. # def read_floats(f, count): values = [0.0] * count c = 0 while c < count: line = f.readline() if line == '': raise FileFormatError('File is shorter than expected') fields = split_fields(line, 12, 6) if c + len(fields) > count: fields = fields[:count-c] for v in map(float, fields): values[c] = v c = c + 1 return values # ----------------------------------------------------------------------------- # def split_fields(line, field_size, max_fields): fields = [] for k in range(0, len(line), field_size): f = line[k:k+field_size].strip() if f: fields.append(f) else: break return fields[:max_fields] # ---------------------------------------------------------------------------- # def write_delphi_file(path, matrix, xyz_center, scale): zsize, ysize, xsize = matrix.shape if xsize != ysize or xsize != zsize: raise ValueError, "Matrix size (%d,%d,%d) has to be the same in all 3 dimensions" % (zsize, ysize, xsize) size = xsize uplbl = delphi_record('Converted from ' + path) morelabels = delphi_record('%70s' % '') import Numeric data_flat = Numeric.ravel(matrix) data = delphi_record(floats_as_string(data_flat)) botlbl = delphi_record('') params = delphi_record(floats_as_string((scale,) + tuple(xyz_center)) + integer_as_string(size)) f = open(path, 'wb') f.write(uplbl + morelabels + data + botlbl + params) f.close() # ---------------------------------------------------------------------------- # def delphi_record(data): size_str = integer_as_string(len(data)) r = size_str + data + size_str return r # ---------------------------------------------------------------------------- # def integer_as_string(i): import Numeric return Numeric.array((i,), Numeric.Int32).tostring() # ---------------------------------------------------------------------------- # def floats_as_string(f): import Numeric return Numeric.array(f, Numeric.Float32).tostring() # ---------------------------------------------------------------------------- # def cns_to_delphi_file(cns_path, delphi_path): data, xyz_origin, xyz_step = read_cns_file(cns_path) if xyz_step[0] != xyz_step[1] or xyz_step[0] != xyz_step[2]: raise Value_Error, 'Step sizes (%.2g, %.2g, %.2g) are not the same along all axes' % xyz_step scale = 1.0 / xyz_step[0] size = list(data.shape) size.reverse() xyz_center = map(lambda o, st, sz: o + st * ((sz-1)/2), xyz_origin, xyz_step, size) write_delphi_file(delphi_path, data, xyz_center, scale) # ---------------------------------------------------------------------------- # if __name__ == '__main__': import sys if len(sys.argv) != 3: sys.stderr.write('Syntax: cns2delphi <cnsfile> <delphifile>\n') sys.exit(1) cns_path = sys.argv[1] delphi_path = sys.argv[2] cns_to_delphi_file(cns_path, delphi_path)

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Re: [Chimera-users] chimera and hydrophobic potentials
by Thomas Goddard 08 Apr '04

08 Apr '04

Hi Miguel, Send me some example k2a output and I'll send you a little Python program that will convert it into a Delphi file readable by Chimera DelphiViewer. Tom > Date: Thu, 8 Apr 2004 19:33:31 +0100 > From: Miguel Ortiz =?iso-8859-15?Q?Lombard=EDa?= <mol(a)ysbl.york.ac.uk> > Subject: Re: [Chimera-users] chimera and hydrophobic potentials > > Hi Tom, > > Thank you very much for your comments. > Part of the problem is that I don't trust the "delphi" maps that > GRID produces. Actually, I've been able to open some of them with > chimera. Other programs ablo to open such maps (like vmd) can't > open any of them. > > Yes, I've used k2a, and it works: it produces an ascii map that > looks sensible. My problem here is that my programming skills are > very reduced! I could work it out on a "model" program, but not > from scratch. Have you something like that? > > Thank you again, your answer has been very useful. > > Best regards, > > Miguel > > -- > Miguel Ortiz Lombardía > email: mol(a)ysbl.york.ac.uk > http://www.ysbl.york.ac.uk/~mol > ----------------------------------------------------------------------- > Our business in life is not to succeed, but > to continue to fail in good spirits. R.L. Stevenson >

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chimera and hydrophobic potentials
by Miguel Ortiz Lombardía 08 Apr '04

08 Apr '04

Hi, I would like to display the hydrophobic potential of a protein onto its MSMS surface. One program that calculates such potentials is GRID (from Molecular Discovery: http://www.moldiscovery.com/ ) GRID can produce the map in different formats. One of them is like delphi (grasp mode) map. This has the drawback that the map has to be 65x65x65 grid points and the grid points separation has to be an integer starting with 1 Ansgtroem. Hence, it's not appropriate for medium-big proteins. The GRID format hasn't those limitations. I can __sometimes__ read in chimera (throught the DelphiViewer) the delphi maps produced by GRID. Sometimes they are unreadable (and this seems to me more a problem with GRID than with chimera: something wrong in the header) But even when they are readable I'm not sure they are covering the region they are supposed to be covering. Does anyone know if chimera can read any other of the GRID map formats: GRID (this would be the optimal) Chem-X Frodo Insight Molcad Quanta Sybyl Otherwise: does anybody how to the kind of representation I'm looking for in any other way? Thank you for any advice! Miguel -- Miguel Ortiz Lombardía email: mol(a)ysbl.york.ac.uk http://www.ysbl.york.ac.uk/~mol ----------------------------------------------------------------------- Our business in life is not to succeed, but to continue to fail in good spirits. R.L. Stevenson

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compiling minrms on mac os10.2.8
by Chris Adams 02 Apr '04

02 Apr '04

Hi: I am also trying to get minrms on my OS10.2.8 machine. I followed the commands you recommended to Howard to get the "make" command to work. However, my ls output was not at all like what you said would happen in the message. I get this: ls -1 /usr/bin/*make /usr/bin/automake and am unable to compile the minrms program. I am not very unix savvy but am learning, perhaps you can help? thank you, Chris Adams UW-Biochemistry Madison, WI 53704

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correction re sessions
by Elaine Meng 31 Mar '04

31 Mar '04

Hello, in my previous message about saving parts of PDB files, I included some text from older replies to users, and this part about sessions is no longer true: >The command "save" (or File... Save Session As... ) doesn't save coordinates, >only how they are positioned/colored/displayed, etc. In fact, restarting >a saved session will use the original input file(s) for coordinates. Actually in the last few versions, the session files do include coordinates and do not look for the original input files. Sorry about that, Elaine

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writing out part of a PDB
by Elaine Meng 31 Mar '04

31 Mar '04

Hi Shuanghong, Question (1), surface problem: I don't think the problem where nothing happens when you type the command "surface" has been reported. Sometimes there is a delay while the surface is being calculated, but it shouldn't be terribly long. Problems have been reported in some cases, but they generally cause some sort of error message. To register a problem more formally, you could send mail to chimera-bugs(a)cgl.ucsf.edu and be sure to include what version of Chimera and what kind of computer you are using, and what structure(s) cause the problem. Question (2), writing out part of a PDB file: If you are on a **non-Windows** system, you can use the command "pdbrun" to save just the atoms that are displayed. You could display only the atoms you want by first selecting what you want to measure the distance to. Then, use Select...Zone... to select all the atoms in the region you want to write out. Then the command "show sel" will undisplay the rest of the stuff. (Or, instead of selecting you could do it all in one command, for example show :212.a za<4.5 for all atoms within 4.5 A of any atom in residue 212 of chain A. Specifying zones in the command line is described in the manual page on atom specification, which is listed in the Basic Functions index.) Next, use pdbrun (see man page using the command "help pdbrun"), for example: pdbrun nouser cat > myzone.pdb Pdbrun literally sends the information for only the displayed atoms in their displayed positions to another command, in this case "cat" to send the information to the file myzone.pdb. If you want the coordinates to be the same as in the original file, first use the command "reset." The command "save" (or File... Save Session As... ) doesn't save coordinates, only how they are positioned/colored/displayed, etc. In fact, restarting a saved session will use the original input file(s) for coordinates. The command "write" (same as the function "write PDB" in the Model Panel) saves coordinates into a file. However, these will save the entire coordinates whether displayed or not. If you are on **Windows** the only way I can think of is to actually delete the atoms/bonds you don't want to write out ("delete" command or Actions... Atoms/Bonds... delete). For example, when only what you want to write out is displayed, delete @/!display actually deletes the other stuff. Subsequently, a file created with "write" would only contain the atoms/bonds that had not been deleted. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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crashing when calculating larger surfaces
by Elaine Meng 31 Mar '04

31 Mar '04

>From eperozo(a)virginia.edu Wed Mar 31 15:15:53 2004 >Sorry to bother you, but I'm having terrible problems with the generation of >surfaces. The program crashes as soon as I request a surface to be built (a >tetramer with ~250 residues/monomer). Interestingly, I don't seem to have >problems with a smaller protein (120 residues). When it crashes it gives me >exit code - 1073741819. Tried two versions of chimera in two different >computers. Same result. >Is this a known bug? >Thanks in advance. >Eduardo Hi Eduardo, It is a known problem that the surface routine is a memory hog. If you are on a unix-type machine it might help to type "unlimit" in the shell before starting Chimera. Otherwise, it might just be trying to use more memory than your machines have. We have been using code developed elsewhere, MSMS, for these surfaces. Due to memory/robustness problems, we are generating some code in-house which will eventually replace MSMS. However, this is still in progress, and has not been incorporated into any Chimera release. You could try deleting extra monomers before using surface or instead show the low-resolution surface generated by the Multiscale Models tool (although it builds multimers with matrix info, even if there is no matrix info, it will still show the low-res surface for the structure you have open). Tools...Multiscale... Multiscale Models, click the "Make models" button. Then if you select All chains (button near the top) you can change the Resolution value and then click Resurface to see different levels of detail. There is a man page for this tool in the Tools section of the User's Guide if you want more info. If you want to register the problem more formally, please send a message to chimera-bugs(a)cgl.ucsf.edu including version, platform, and an example or few of which structures (e.g. their PDB IDs) cause the problem. Best, Elaine

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Re: [Chimera-users] Rotating molecules
by Elaine Meng 30 Mar '04

30 Mar '04

Hi Eduardo, yes, the command "move" does translations by a specified amount and the command "turn" rotates by a specified amount. Type help move in the command line to see the man page for move, and help turn for the man page for turn. You might also want to take a look at the commands "rock" and "roll" Hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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Rotating molecules
by Eduardo Perozo 30 Mar '04

30 Mar '04

Hello, Is there a way to rotate/translate a molecule by a specific amount? Clearly I can do "freehand" rotations with the mouse but I will like to define rotations and translation numerically. Thanks! Eduardo

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Re: [Chimera-users] export pdb file
by Elaine Meng 29 Mar '04

29 Mar '04

Hi Shuanghong, there are two ways to export a PDB file. One is by choosing the "write PDB" function from the Model Panel. The other is by using the "write" command. Each way has an option to save the transformed coordinates or the coordinates relative to the untransformed coordinates of a particular model (take a look at the User's Guide for detailed descriptions). Hope this helps! Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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Re: [Chimera-users] v1.1917 OpenGL misconfiguration detected.
by Greg Couch 29 Mar '04

29 Mar '04

Got it. The /usr/X11R6/lib/ligGL.so.1 file should have been removed as part of the NVidia driver installation. We just confirmed that with the Red Hat 9 and the NVIDIA-Linux-x86-1.0-5336-pkg1.run driver distribution. You had version 53.28, so maybe it was a bug in that driver? We had previous installed NVidia version 43.63 using the same mechanism, so it's probably not a problem with the driver, but something went wrong during the installation. You should uninstall and install that driver again (or just upgrade to the 53.36). Good luck, Greg On Mon, 29 Mar 2004, Pattanayek, Sabuj wrote: > Here is the output > > -rwxr-xr-x 1 root root 367092 Jan 3 12:17 /usr/lib/libGL.so.1 > -rwxr-xr-x 1 root root 264888 Feb 12 13:22 /usr/X11R6/lib/libGL.so.1 > > I am using RH9. > > Quoting Greg Couch <gregc(a)cgl.ucsf.edu>: > > > Chimera checks /usr/lib/libGL.so.1 and /usr/X11R6/lib/libGL.so.1 to see > > if they point to the same file or not. If they do not, then that indicates > > that there was an OpenGL driver installation error -- sometimes resulting > > in chimera not using the hardware accelerated OpenGL driver. > > > > Could you send the output from: > > > > ls -Ll /usr/lib/libGL.so.1 /usr/X11R6/lib/libGL.so.1 > > > > I'd like to confirm that they are different. And which version of Linux > > are your running -- Red Hat 8.0? Mandrake? Suse? Debian? We'd like to > > try to recreate the problem here. > > > > Greg Couch > > UCSF Computer Graphics Lab > > gregc(a)cgl.ucsf.edu > > > > On Mon, 29 Mar 2004, Pattanayek, Sabuj wrote: > > > > > Finally got around to installing the latest development linux version. At > > > startup I'm getting the following messages: > > > > > > OpenGL misconfiguration detected. > > > Please reinstall graphics driver. > > > > > > v1.1872 & v1.1892 still work on the machine with no problems. > > > > > > The video card on the machine is nvidia quadro 750 xgl running this driver > > from > > > nvidia's ftp site: > > > > > > NVIDIA-Linux-x86-1.0-5328-pkg1.run > > > > > > I know this is not the latest version of the driver, would upgrading it > > make a > > > difference? > > >

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v1.1917 OpenGL misconfiguration detected.
by Pattanayek, Sabuj 29 Mar '04

29 Mar '04

Hi, Finally got around to installing the latest development linux version. At startup I'm getting the following messages: OpenGL misconfiguration detected. Please reinstall graphics driver. v1.1872 & v1.1892 still work on the machine with no problems. The video card on the machine is nvidia quadro 750 xgl running this driver from nvidia's ftp site: NVIDIA-Linux-x86-1.0-5328-pkg1.run I know this is not the latest version of the driver, would upgrading it make a difference? Thanks, ----------------------------------------------------------------- Sabuj Pattanayek Martin Egli Lab Vanderbilt University Dept. Biochemistry http://linegli.mc.vanderbilt.edu

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export pdb file
by Shuanghong Huo 29 Mar '04

29 Mar '04

Hi, I remember that Midus can export pdb file, but I cannot find this function in Chimera. Thanks, Shuanghong

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question
by Wendy Ochoa 28 Mar '04

28 Mar '04

Could you please tell me how can I define the secondary structure of the protein i am displaying with chimera. I know the secondary structure of my pdb, so I would like to draw a picture of the protein showing the B sheets and alpha helix in different colors. Thansk a lot!!!

2 1

32 bit / 64 bit Linux mixup
by Thomas Goddard 12 Mar '04

12 Mar '04

The 32 bit Linux Chimera 1917 was accidentally replaced with the 64 bit Linux version yesterday (Thursday 11 AM PST, March 11). The 32 bit version has been restored Friday 7 PM PST, March 12. Tom

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Re: [Chimera-users] chimera-1.1917-linux.exe: Exec format error. Wrong Architecture.
by Pattanayek, Sabuj 12 Mar '04

12 Mar '04

[root@eglimp]# uname -iorsp Linux 2.4.22-openmosix2smp athlon i386 GNU/Linux it seems the link to chimera-1.1917-linux.exe on the download page is actually the link to the x86_64 version: [root@eglimp]# head chimera-1.1917-linux.exe ELF> @@@@"@@@@@�@@@@d�d�PP��``P`@@ P�d � � �||Q�/lib64/ld-linux-x86-64.so.2GNU etc.. and [root@eglimp]# head chimera-1.1872-linux.exe ELF44 (#�#��x▒�@ /lib/ld-linux.so.2GNUCVN>LU@SB<5QF/4)1K$.TG!J▒= Can you please put the correct link to the x86_32 linux version on the download page? Thanks, Sabuj Pattanayek Quoting Greg Couch <gregc(a)cgl.ucsf.edu>: > The linux distribution is only for the Intel/AMD x86 architecture. Are > you trying in install on something else? For example, and Alpha or > PowerPC? > > - Greg > > On Fri, 12 Mar 2004, Pattanayek, Sabuj wrote: > > > I'm getting this error when I try to run the installation > > > > -rwx------ 1 root root 26226504 Mar 12 12:02 > chimera-1.1917-linux.exe > > [root@eglimp]# chimera-1.1917-linux.exe > > chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. > > [root@eglimp]# ./chimera-1.1917-linux.exe > > ./chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. > > [root@eglimp]# md5sum chimera-1.1917-linux.exe > > 67e955ce87d000916039d94c7d6d0a56 chimera-1.1917-linux.exe > > [root@eglimp]# uname -rs > > Linux 2.4.22-openmosix2smp > > > > web page: > > > > linux chimera-1.1917-linux.exe > > Size: 26226504 bytes > > MD5: 67e955ce87d000916039d94c7d6d0a56 >

2 1

save session stripping TER statements from PDB's
by Pattanayek, Sabuj 12 Mar '04

12 Mar '04

In version 1.1892 (and older possibly), file > save session seems to be stripping TER statements from PDB files. The TER statement is helpful for specifically telling Chimera and other PDB viewers not to connect consecutive residues in a PDB (for example ATP/water molecules at the end of a PDB that are not part of the main protein chain). Re-inserting TER's manually into the .py file can become cumbersome especially when one PDB insertion in the .py is 27000+ columns long. Would it be possible to fix this in future versions? Thanks in advance, Sabuj Pattanayek

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[Chimera-users] chimera-1.1917-linux.exe: Exec format error. Wrong Architecture.
by Pattanayek, Sabuj 12 Mar '04

12 Mar '04

I'm getting this error when I try to run the installation -rwx------ 1 root root 26226504 Mar 12 12:02 chimera-1.1917-linux.exe [root@eglimp]# chimera-1.1917-linux.exe chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. [root@eglimp]# ./chimera-1.1917-linux.exe ./chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. [root@eglimp]# md5sum chimera-1.1917-linux.exe 67e955ce87d000916039d94c7d6d0a56 chimera-1.1917-linux.exe [root@eglimp]# uname -rs Linux 2.4.22-openmosix2smp web page: linux chimera-1.1917-linux.exe Size: 26226504 bytes MD5: 67e955ce87d000916039d94c7d6d0a56 Thanks in advance Sabuj Pattanayek

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mac version of 1.1917 snapshot
by Eric Pettersen 10 Mar '04

10 Mar '04

Hi again, If you downloaded the Mac version of 1.1917 before about 5pm PST today, you should download it again because we updated it to fix a bug. The non-Mac versions are fine. The Mac version was not displaying atoms in stick, ball-and-stick, or sphere modes (wireframe mode was okay). Sorry for the possible inconvenience! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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new snapshot release (1.1917)
by Eric Pettersen 09 Mar '04

09 Mar '04

Hi, We've just put a new snapshot release of Chimera up for download on the web site (http://www.cgl.ucsf.edu/chimera) Here are the highlights of the changes between this snapshot (1.1917) and the previous one (1.1892): tools: Match -> Align can create sequence alignments for multiple matched structures (not just pairs) Multalign Viewer can show/edit sequence annotations for relevant formats (RSF, Stockholm) SimpleSession -- saves label font/size and secondary structure assignments -- compiles to .pyc file: 50% less memory use, 15% less time to restore added Export Surfaces as VRML (in Utilities category) -- save surfaces made by Multiscale Models and Volume Viewer as VRML files added Browser Configuration (also in Utilities) -- configure browsers to send certain file types to Chimera (see also new Web Data preferences) FindHBond and PBReader allow line width to be set Movie has preliminary support for reading GROMOS trajectories newly available commands: bondcolor -- color bonds independent of flanking atoms bonddisplay -- set how bond display depends on flanking atom display bondrepr -- set bond representation to be wire or stick (independent of atoms) hbonds -- command equivalent of FindHBond tool rlabel -- whether residue name/number is included in the first atom label per residue Model Panel new 'render attrs...' button allows coloring by model/residue/atom attributes (e.g. B-factor) The 'render attrs...' interface is in preliminary form and will be changing. It also isn't documented yet but is pretty easy to use. Just pick an attribute of interest and a histogram of values will be displayed. By default there will be three color bars on the histogram that you can grab and move around with the mouse, or add or remove with control-click. You can use the 'Color' color well to set the color of the last bar you picked. The 'No value' color well is used in the rare case of the attribute being missing (or set to None) in the atom/residue/model. Click Apply or OK to make the coloring happen. Several parts of the interface are grayed out since they haven't been implemented yet. In the future you will be able to select by attribute value, and change atom radii or ribbon widths based on attribute values. If you are using the last production release (1.1872) instead of the previous snapshot, then you will also be getting these features when you go to 1.1917: general: additional file formats for saved images (PS, EPS) different lighting scheme in graphics window (over-the-shoulder instead of headlight) tools: added Shininess Control (in Viewing Parameters) -- adjust shininess, brightness, and the color used for shiny highlights Collaboratory section in Preferences allows designation of port number and IP address (for firewalls/NAT) Movie -- allows definition of scripts to be run at each time step -- looping can be turned off Multalign Viewer allows structure selection by arbitrary % residue conservation Volume Viewer options added to subdivide and smooth isosurfaces commands: copy command now offers supersampling and PS/EPS formats new ribbackbone command controls whether ribbon and backbone atoms are shown simultaneously Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Use of Chimera for Trends Plant Sci March 2004...
by John F. Allen 24 Feb '04

24 Feb '04

....for article and issue cover illustration. Final proofs attached. Acknowledged. Great program. Will send reprint(s) and final pdf on request. Many thanks John F. Allen Professor of Plant Cell Biology Plant Biochemistry Center for Chemistry and Chemical Engineering Lund University Box 124 SE-221 00 Lund Sweden Tel: +46 46 222 7788 (Office); +46 46 222 4073 (Laboratory) Fax: +46 46 222 4009 (Direct); +46 46 222 4116 (Departmental) E-mail: john.allen(a)plantbio.lu.se Plant Cell Biology: http://plantcell.lu.se Publications: http://plantcell.lu.se:591/john/

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CHIMERA help - coloring density maps
by Padmaja Natarajan 02 Feb '04

02 Feb '04

Hi, I have just started using CHIMERA to look at volume files in the CCP4 format for virus particles. I would like to color the density as a color ramp continuously changing between ANY two specified colors depending on the radial distance from the center of the virus particle (as shown in the attached figure). How do I achieve this with CHIMERA? thank you very much for your help in advance. -Padma

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Chimera dead after NVidia driver install...
by Patrick Ladam 12 Jan '04

12 Jan '04

Hi all, I had chimera 1.1872 working OK on my MDK 9.2 Linux box until I installed the NVidia driver for my GeFOrce2 card. What happens now is that chimera launches but stops during start-up with an error box indicating this message: "Togl: Couldn't get visual" This sounds like an OpenGL problem to me but I am far from being a specialist on this. Does anyone have a clue how I can debug/fix this ? Bye -- ----------------------------------------------------------------- | Patrick LADAM | | | Laboratoire CSSB | THE BIG BANG THEORY: | | UFR SMBH | | | 74 rue Marcel Cachin | In the begining there was | | 93017 Bobigny CEDEX | nothing at all. | | e-mail: | | | ladam(a)smbh.smbh.univ-paris13.fr | Then, it exploded... | | Tel: 01 48 38 77 26 / 76 85 | | | Fax: 01 48 38 77 77 | | -----------------------------------------------------------------

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hi
by amutha ramaswamy 08 Jan '04

08 Jan '04

Dear Sir 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. Looking forward for your kind reply Sincerely Amutha Dr Amutha Ramaswamy Postdoctoral Fellow, Department of Biomedical Informatics 3184 Graves Hall, 333 West 10th Avenue The Ohio state University, Columbus, OHIO 43210 Phone: 614-688-3236 (Office); 614-291-0071(Residence) Fax: 614-292-7659 (Office) --------------------------------- Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes

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Re: save selected atoms in a pdb file?
by Elaine Meng 08 Jan '04

08 Jan '04

Hi Sabuj, You can make surfaces that surround a set of atoms without making a separate PDB file. For example, if you have those atoms selected already, just use the command: surfcat mygroup sel where "mygroup" could be whatever you choose to name this set of atoms and "sel" means what is currently selected. Then, the command surface mygroup will show surface surrounding that group. There are several ways you could select the atoms of interest, and it sounds like you already figured out that part; the following detailed example is just one possibility: open pdb:2gbp sel :glc z<4.5 ~sel :glc ~sel solvent surfcat nearby sel ~sel surf nearby Here I opened a glucose-binding protein structure, selected all residues with any atom within 4.5 A of the ligand glucose (glc), then subtracted glucose itself and waters from the selection. Then I made the selected atoms a surface category with "surfcat," unselected them, and showed the corresponding surface. If you really want to save the selection to a file, it can be done on unix systems. Chimera can send information on what atoms are displayed to the system, and then the system command "cat" can send the information to a file. In Chimera, if the atoms of interest are selected: show sel pdbrun nouser cat > ~homedir/myfile.pdb (where "homedir" is your username) saves the displayed atoms to a PDB file named myfile.pdb in your home directory. It is necessary to use show (which undisplays everything else) since pdbrun includes all atoms that are displayed. The coordinates are transformed, so will be different from the original coordinates if you have moved the view around. If you want the untransformed coords, use the "reset" command before the "pdbrun" command. This process doesn't work on Windows as there is no cat command. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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save selected atoms in a pdb file?
by Pattanayek, Sabuj 08 Jan '04

08 Jan '04

Hi, Is it possible to save only the currently selected set of atoms/bonds or the atoms/bonds currently shown in the display into a pdb file? This is would be useful when doing surfaces for a particular location (e.g. atoms surrounding a central cavity), since the command "surface selected" seems to leave gaps in inaccessible areas (behind the atoms surrounding the cavity). Thanks, Sabuj Pattanayek

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[Chimera-users] shininess/brightness/specular color of surfnet surfaces
by Pattanayek, Sabuj 05 Jan '04

05 Jan '04

Hi, Is it possible to alter the shininess/brightness/specular color of Surfnet surfaces? Also is it possible to save the surfaces so they don't have to be recreated every time? Thanks, ----------------------------------------------------------------- Sabuj Pattanayek Martin Egli Lab Vanderbilt University Dept. Biochemistry http://linegli.mc.vanderbilt.edu

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Old version for Sparky
by laurent volpon 05 Jan '04

05 Jan '04

Hello, I would like to download an old version of Chimera (1.1442) because I have to use it with the same Python version (2.1) as Sparky. I tried at http://www.cgl.ucsf.edu/chimera/distrib/oldreleases.html but I had this: "Error: The URL you used is malformed". Please can you help me to find this version, or is there a way to use the version I have (1.1872) with the version 2.1 of Python (instead of 2.2). Thank you by advance for your answer. Sincerely Dr Laurent VOLPON ______________________________ Dr Laurent Volpon 3575 Avenue du Parc, Suite 5315 P.O. Box #85 Montréal, Qc, H2X 4A3 tel.: (514) 847-9494 ______________________________ --------------------------------- Lèche-vitrine ou lèche-écran ? Yahoo! Magasinage.

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vdw viewer
by Terry Downing 23 Dec '03

23 Dec '03

Hey CGL, I would like to be able to visualize several different vdw parameter sets on the same molecule. Is there a way to visualize just the vdw surface? Can I change the parameter files easily? As always, thanks in advance for your help. Sincerely, Terry Downing -- P. Therese Downing Chemistry and Chemical Biology Graduate Program Kuntz and James Labs, UCSF Voice: (415)476-3986 Fax: (415)502-1411

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ribbon+atoms
by Eric Pettersen 22 Dec '03

22 Dec '03

Hi, the 1892 snapshot release we just put out allows control over whether backbone atoms can be displayed with ribbons (on a per-model basis). There is a "ribbackbone" command, an entry in the New Molecules preference category, and a control in the attributes panel (reached via the "attributes..." button in the model panel). Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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interactive volume segmentation
by Juha Huiskonen 18 Dec '03

18 Dec '03

Hello, currently it is possible to select only box-shaped subregions in Volume Viewer. I would be especially interested in segmenting electron density maps or their isosurfaces to different subregions with any shape interactively. Is anyone planning to add a feature like this? Regards, Juha Huiskonen

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Re: [Chimera-users] Chimera export to VRML?
by Thomas Goddard 16 Dec '03

16 Dec '03

Hi Morgan, I've written an extension to export Chimera multi-scale and volume surfaces as VRML. I wasn't able to export the molecular (MSMS) surfaces because the code does not provide access to the surface coloring. I've submitted a request to enhance the molecular surface code to make surface colors readable. I'm not sure if the VRML surface exporting will make it into the coming snapshot release. If it doesn't I will provide it to you by email. I'll let you know when we have the snapshot ready, probably later this week. Tom

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Re: [Chimera-users] Chimera export to VRML?
by Thomas Goddard 16 Dec '03

16 Dec '03

Hi Morgan, We hope to have a snapshot Chimera release later this week. I'll try to get VRML output of multi-scale and msms surfaces in that release. Snapshot releases aren't as well tested as production releases, but are intended for trying out new features like this. Tom PS: Your email does not go to chimera-users unless you explicitly CC it to that list. We like to post to that list so others can benefit from it. I've included your email below and CC'ed this to chimera-users. Let me know if you want to keep your email private. > From: Morgan Ryan <mryan1(a)nc.rr.com> > Subject: Re: [Chimera-users] Chimera export to VRML? > Date: Tue, 16 Dec 2003 14:35:27 -0500 > > Thanks, Thomas. (Am I broadcasting to the list? I'm not sure if I'm > talking to a list or just you and Eric Petterson...) > > > For a large structure like a > > ribosome the VRML file ...might have a million triangles, and the file > > will > > at least be 30 megabytes. > > The 3D programs I use have fairly refined mesh management tools for > reducing complexity selectively, although being able to choose the mesh > density directly through MSMS would be pleasing. > > > You can choose the resolution of the multi-scale surfaces. We don't > > currently have VRML output for the multi-scale surfaces but that > > could be added fairly easily. I could look into that. > > The advantage of VRML output (or 3dmf, or dxf, or some other > interchange format) is that you could open the model in Maya, Studio > Max, Strata, Cinema 4D, any of the 3D animation programs, and make > startling movies wiith Hollywood special effects--light sabers! > Atomic-resolution recreations of enzyme reaction mechanisms! (The > latter is what I'm working on...) > > It would be a wonderful extension of Chimera if VRML output were added. > Morgan

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Chimera export to VRML?
by Morgan Ryan 16 Dec '03

16 Dec '03

VRML seems to be a native internal format for (the magnificent) Chimera. Is it possible to export VRML models from Chimera? Or do you worldly folks know of a mechanism for converting msms output into vrml files? Thanks! Morgan Ryan, enthusiastic amateur ____________________ Morgan Ryan Development editor W H Freeman 209 Adams Way Chapel Hill NC 27516 phone: 919 942 4890 fax: 651 846 5265 mryan(a)whfreeman.com

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help
by amutha ramaswamy 16 Dec '03

16 Dec '03

Dear sir I am using the Chimera molecular visualising software. I am not able to color the PDB structure according to the B-factors. could you plase let me know how do i color accroding to the bfactor. i would greatly apprecuate your help in this regard sincerely amutha Dr Amutha Ramaswamy Postdoctoral Fellow, Department of Biomedical Informatics 3184 Graves Hall, 333 West 10th Avenue The Ohio state University, Columbus, OHIO 43210 Phone: 614-688-3236 (Office); 614-291-0071(Residence) Fax: 614-292-7659 (Office) --------------------------------- Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing

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Re: Gaussians
by Thomas Goddard 10 Dec '03

10 Dec '03

Hi Lars, I'm not sure what you mean by visualizing some Gaussians. If you mean you want to make a volume which contains some specified Gaussians then I can give you a separate Python program that will do that. I already wrote it for another user. It is included at the end of this email. It outputs a netcdf format volume file. Tom % ./spots.py Make a volume array that is the sum of specified Gaussians. The first line of the input file has the grid cell size. Each subsequent line has 5 fields giving x, y, z, width, height. A volume grid is made that includes each Gaussian out to 3 widths. The resulting volume is written in netcdf format. Syntax: spots.py <infile> <outfile> % cat spotfile .5 15.49100 7.05000 17.16500 0.38 1.00 14.94600 7.55000 15.88800 0.35 1.00 16.01100 7.60400 14.81400 0.34 1.00 ... % ./spots.py spotfile gspottest.nc The spots.py code follows. Note that it contains a path to your Chimera installation because it needs Chimera modules to write the netcdf volume. #!/usr/bin/env python # ----------------------------------------------------------------------------- # Make a volume array that is the sum of specified Gaussians. # The resulting volume is written in netcdf format. # # Syntax: spots.py <infile> <outfile> # # The input file has a grid cell size on the first line followed by one # line per gaussian with 5 fields specifying x, y, z, width, height. # import os.path import sys # Need Chimera path to use VolumeData and Numeric modules CHIMERA_PATH = '/usr/local/chimera' sys.path.insert(0, os.path.join(CHIMERA_PATH, 'lib')) sys.path.insert(0, os.path.join(CHIMERA_PATH, 'share')) import Numeric # ----------------------------------------------------------------------------- # def make_spot_grid(path): step_size, spot_parameters = read_spots(path) range = 3 # in spot widths xyz_min, xyz_max = bounding_box(spot_parameters, range) xyz_origin = xyz_min xyz_step = (step_size, step_size, step_size) xyz_size = map(lambda a,b: a - b, xyz_max, xyz_min) import math grid_size = map(lambda s, step, math=math: 1 + int(math.ceil(s/step)), xyz_size, xyz_step) a = spot_array(spot_parameters, range, xyz_origin, step_size, grid_size) from VolumeData import Array_Grid_Data g = Array_Grid_Data(a, xyz_origin, xyz_step) return g # ----------------------------------------------------------------------------- # def read_spots(path): f = open(path, 'r') lines = f.readlines() f.close() step_size = float(lines[0]) spot_params = [] for line in lines[1:]: params = map(float, line.split()) spot_params.append(params) return step_size, spot_params # ----------------------------------------------------------------------------- # def bounding_box(spot_parameters, range): xmin = ymin = zmin = None xmax = ymax = zmax = None for x, y, z, w, h in spot_parameters: pad = range * w if xmin == None or x - pad < xmin: xmin = x - pad if ymin == None or y - pad < ymin: ymin = y - pad if zmin == None or z - pad < zmin: zmin = z - pad if xmax == None or x + pad > xmax: xmax = x + pad if ymax == None or y + pad > ymax: ymax = y + pad if zmax == None or z + pad > zmax: zmax = z + pad return (xmin, ymin, zmin), (xmax, ymax, zmax) # ----------------------------------------------------------------------------- # def spot_array(spot_parameters, range, xyz_origin, step_size, grid_size): shape = list(grid_size) shape.reverse() # array indices are z, y, x. array = Numeric.zeros(shape, Numeric.Float) for x, y, z, width, height in spot_parameters: add_spot((x,y,z), width, height, range, xyz_origin, step_size, array) return array # ----------------------------------------------------------------------------- # def add_spot(xyz, width, height, srange, xyz_origin, step_size, array): ijk = map(lambda a,b,s=step_size: (a - b)/s, xyz, xyz_origin) w = width / step_size w2 = w * w r = srange * width / step_size import math imin, jmin, kmin = map(lambda l, r=r, math=math: int(math.floor(l-r)), ijk) imax, jmax, kmax = map(lambda l, r=r, math=math: int(math.ceil(l+r)), ijk) for k in range(kmin, kmax+1): for j in range(jmin, jmax+1): for i in range(imin, imax+1): di, dj, dk = i-ijk[0], j-ijk[1], k-ijk[2] s2 = di*di + dj*dj + dk*dk e = height * math.exp(-s2/(2*w2)) array[k,j,i] += e # ----------------------------------------------------------------------------- # def bfactor_backbone_spots(path, molecule = None): if molecule == None: import chimera molecule = chimera.openModels.list()[0] out = open(path, 'w') out.write('.5\n') # step size import math for a in molecule.atoms: if a.name in ('C', 'N', 'CA') and hasattr(a, 'bfactor'): x, y, z = a.coord().xyz.data() w = math.sqrt(a.bfactor / (8 * math.pi**2)) h = 1 out.write('%8.5f %8.5f %8.5f %6.2f %6.2f\n' % (x,y,z,w,h)) out.close() # ----------------------------------------------------------------------------- # def syntax(): msg = ('Make a volume array that is the sum of specified Gaussians.\n' + 'The first line of the input file has the grid cell size.\n' + 'Each subsequent line has 5 fields giving x, y, z, width, height.\n' + 'A volume grid is made that includes each Gaussian out to 3 widths.\n' + 'The resulting volume is written in netcdf format.\n' + 'Syntax: spots.py <infile> <outfile>\n') sys.stderr.write(msg) sys.exit(1) # ----------------------------------------------------------------------------- # def run_command(): if len(sys.argv) != 3: syntax() inpath = sys.argv[1] outpath = sys.argv[2] grid = make_spot_grid(inpath) from VolumeData.netcdf.netcdf_grid import write_grid_as_netcdf write_grid_as_netcdf(grid, outpath) # ----------------------------------------------------------------------------- # if __name__ == '__main__': run_command()

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B-Factor
by Luis Cuello 08 Dec '03

08 Dec '03

Hello, My name is Luis Cuello and I am a graduate student at the University of Virginia..I started using chimera recently but I have not been able to colored my files by B-factors values, Is there any way to do that with chimera software??? If you could help me in this matter I would appreciated..Sincerely Luis Cuello University of Virginia Molecular Physiology 1(434)9245473 e-mail:lgc4r@virginia.edu

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Re: [Chimera-users] delphi potenital map viewing
by Thomas Goddard 05 Dec '03

05 Dec '03

Hi Klaas, The Delphi Viewer is the only tool that can color a molecular surface according to the potential value. Can you email me the Python traceback you get when the "_cubes error: ..." occurs? This shows exactly where in the code the error happened. You find it by looking at Favorites/Reply Log. Having the traceback alone might be enough for me to figure out and correct the problem. If you could put the phi file on the web so I could download it I would almost certainly be able to figure out the problem. The Delphi Viewer is supposed to be able handle maps of any size. It will be much slower than volume viewer, but it should not generate an error with a large map. Tom > Date: Fri, 05 Dec 2003 21:10:20 +0100 > From: Klaas Decanniere <Klaas.Decanniere(a)pandora.be> > Reply-To: Klaas.Decanniere(a)pandora.be > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] delphi potenital map viewing > > Thomas Goddard wrote: > > >Hi Klaas, > > > > The size of the Delphi potential map Chimera can display is only > >limited by the size of your computer memory. > > > > If you open a large map it does not get shown immediately if the map > >is larger than 1 Mvoxels (~100^3). > > > > > > When I tried using the "delphi viewer" option, I get _cubes error: grid > index out of range > Using the volume viewer I can indeed load everything. > Is there a way to tie the volume viewer thing to a molecular surface? > With a colour gradient showing different levels of potential? (As in the > Molecular surface option in the Delphiviewer) > Or maybe I can save the subsampled map somehow and then read it into the > delphiviewer thing? > > Thanks again for your help. > > Klaas > > P.S.: I like the program more each day. > P.P.S.: If you ever have a day with nothing to do: the automatic > fetching of pdb files doesn't work for me as I'm behind a proxy server.

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delphi potenital map viewing
by Klaas Decanniere 04 Dec '03

04 Dec '03

Hello, Thinking that more is better I ended up with Delphi potential maps on a rather large grid which I would like to visualize with chimera (gsize=213) Chimera seems to think the grid is to large. Is there an easy way to have chimera accept bigger grids (speed is not really an issue)? Alternatively, what is the largest grid that chimera can accept? Thanks for your help. Klaas Decanniere

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ribbon+atoms
by Elaine Meng 25 Nov '03

25 Nov '03

Dear Soren, Thanks for the compliments - we're trying! You're right that in recent versions of Chimera , showing ribbon turns off the backbone atoms. There is an easy workaround: open two copies of the same molecule, use one copy to show ribbon and the other copy to show atoms. The reason for the behavior is when the ribbon is drawn as a smooth curve, it does not exactly pass through the backbone atoms. Often one wants to show just the ribbon and certain side chains, and the current behavior is to extend the side chain to meet the ribbon (even when the backbone atoms are not on the ribbon) so that they are not floating in space. However, we agree that sometimes one will want to display both the ribbon and the backbone atoms, and in the future there will a preference to switch between: (a) show ribbon, not backbone atoms, and extend the side chains to meet the ribbon (b) show ribbon and whatever backbone atoms are displayed by the user, do not extend side chains to meet the ribbon Until this switchable preference becomes available, we hope that the suggested workaround will let you do what you want. Sincerely, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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ribbon+atoms
by Soren M. Kristensen 25 Nov '03

25 Nov '03

Dear Chimera developers You have createdt an absolutely brilliant program. I have a small question/suggestion about displaying atoms and ribbons simultaneously. When displaying a number of backbone atoms and then putting on a ribbon, then some of the atoms dissapear in release 1700 and onwards. Is there a way to avoid this behaviour? It basically means that I am stuck with the pre-1700 version, but maybe there is some parameter I can tweak to make it work in the new versions? I would be grateful for your help. I reproted this as a bug some 6 months ago, but was told that it was supposed to be like this. I measure experimental values for selected backbone atoms and display them as colorcoded spheres on top of a ribbon to indicate what is measured different places in the structure. If you have suggestions to acieve this behaviour in another way I would be grateful. Thank you in anticipation, Søren -- Søren M. Kristensen, Ph.D. Phone: (+45) 3532 0301 University of Copenhagen FAX: (+45) 3535 0609 Department of Chemistry E-mail: smk(a)kl5.ki.ku.dk H. C. Ørsted Institutet http://kl5.ki.ku.dk/~smk Universitetsparken 5 Room: C508 DK-2100 København Ø Denmark

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some CADD tools released
by gentamicin5 19 Nov '03

19 Nov '03

Dear all, I have written some CADD tools, and the details are described below. All of these programs are released under GNU/GPL. You can download them from: http://home.pchome.com.tw/team/gentamicin/mol/mol.htm ------------------------------------------------------------------- CADD tools (linux & irix) pscan_2.2.0 PSCAN is a small but a practical tool for finding any potential binding site of a protein. It can picture the size and appearance of a binding site, and point out the possible pharmacophore.Thus it is helpful for drug design. While running DOCK, QCPE_MS is necessary for autoMS and even the next step sphgen. QCPE_MS, however, is a commercial package. Now, PSCAN and SPHBOX can do the same job. After removing all dots outside of the target binding site by SPDBV (or others), and choosing several positions you are interesting, run SPHBOX to generate sph and box files. pmol2q_2.1.1_rc2 PMOL2Q is a specific file format converter for protein pdb file to mol2 file with adding hydrogens and partial charges. From v2.1.1, PMOL2Q can also output pdbq and pdbqs format. (The pdbqs format is added solvation data according with ADDSOL in AutoDock) It can recognize each amino acid and reconstruct the coordination precisely. The bond length of 109 pm for C-H, 101 pm for N-H, 96 pm for O-H and 134 pm for S-H are used for adding hydrogens.You can choose to add global hydrogens or only polar hydrogens. KOLL and AMBER95 partial charges are available in PMOL2Q. PMOL2Q can also check probabel error of protein coordination, including incomplete atom_missing residues and atom bumps. Hydrogens will not be added on incomplete residues if they exist. You need to fix it by other program before converting file format. (ex. SPDBV can fix the incomplete residues by mutate function) dbfilter_2.2.1 DBFILTER can check the mol2 format database, and pick out any problematic structure which results in "segmentation fault" of DOCK during flexible docking. (for example, salt or structure which contains multi-molecular built in....) And DBFILTER will output a new database which you want. There are also 12 kinds of filters for spotlighting drug-like properties. Including: Common_atoms_only, Molecular_weight, LogP, H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens, Rings, Big_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-. ----------------------------------------------------------------- 每天都 Yahoo!奇摩海的顏色、風的氣息、愛你的溫度，盡在信紙底圖 http://tw.promo.yahoo.com/mail_premium/stationery.html

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Fwd: MidasPlus version 2.1 (1997/02/04)
by Robin Parsons 17 Nov '03

17 Nov '03

Begin forwarded message: > From: Devleena Mazumder <devleena(a)chem.ucsb.edu> > Date: Fri Nov 14, 2003 6:04:37 PM US/Pacific > To: Robin Parsons <rparsons(a)cgl.ucsf.edu> > Subject: Re: MidasPlus version 2.1 (1997/02/04) > > Dear Robin, > Thanks for your email. > I have installed Chimera. Its easier to use than Midas. Unfortunately, > I > dont see the label3d option in it that was available with Midas. So, I > am > unable to get labels in neon. > Thanks > Devleena > > On Thu, 6 Nov 2003, Robin Parsons wrote: > > :>To: Devleena, > :>University of California, Santa Barbara, > :> > :>Thank you for your interest in our MidasPlus molecular modeling > :>software. You should know, however, that MidasPlus 2.1 is the final > :>version of MidasPlus and will not be developed further. You may wish > :>to explore our next generation of molecular modeling software, > Chimera. > :> You can look over Chimera's capabilities on our web site at: > :> > :>www.cgl.ucsf.edu/chimera/ > :> > :>In addition, Chimera is offered at no cost to educational and > :>non-profit institutions. > :> > :>Please contact me if you have any further questions. > :> > :>Robin Parsons > :>UCSF Computer Graphics Lab > :>Resource for Biocomputing, Visualization and Informatics > :>600 16th St., Room N-472B, Box 2240 > :>San Francisco, CA 94143-2240 > :>Commercial Carrier Zip Code: 94107 > :>tel. 415-476-1540 > :>fax 415-502-1755 > :>rparsons(a)cgl.ucsf.edu > :> > :> > > > > _______________________________________________________________ > DEVLEENA MAZUMDER-SHIVAKUMAR > PhD Candidate, Dept of Chemistry & Biochemistry > UNIVERSITY OF CALIFORNIA SANTA BARBARA > http://www.chem.ucsb.edu/~devleena/ > > **Although the past gives us lessons, it does not > give the whole answer to what must be done now.** > > Robin Parsons UCSF Computer Graphics Lab Resource for Biocomputing, Visualization and Informatics Assistant to Thomas Ferrin, PhD 600 16th St., Room N-472B, Box 2240 San Francisco, CA 94143-2240 Commercial Carrier Zip Code: 94158 tel. 415-476-1540 fax 415-502-1755 rparsons(a)cgl.ucsf.edu

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quick question
by vreyes 30 Oct '03

30 Oct '03

To Whom It May Concern: Our system is SUN Solaris 64bit Sparc III. Should I select #4 from the list below when downloading Chimera? 1.) SGI IRIX Platforms 2.) i386 Linux Platforms 3.) Mac OS X using X windows 4.) Tru64 UNIX 5.0/5.1 Platforms 5.) Microsoft Windows Platforms Please let us hear from you ASAP. Thanks very much for your help. V. Reyes San Diego Supercomputer Center Structural Bioinformatics group

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Delphi controller
by Marco Sette 21 Oct '03

21 Oct '03

Dear all, I'm trying to use the Delphi controller but I have problems to interface Delphi to Chimera.I created a link to Delphi under the Chimera directory but it does not seems the correct way. Is there some place to look to solve this problem ? I use Linux RedHat 9.0 Thanks, Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Delphi under Chimera
by Marco Sette 20 Oct '03

20 Oct '03

Dear all, I'm trying to use the Delphi controller but I have problems to interface Delphi to Chimera.I created a link to Delphi under the Chimera directory but it does not seems the correct way. Is there some place to look to solve this problem ? I use Linux RedHat 9.0 Thankks to all. Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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by solomon 15 Oct '03

15 Oct '03

Hi, I'm a new chimera user. Now I have some difficult to use chimera. How can I save the amino acid that I select as a new .pdb file. For example, I select the amino acids that is around the ligand within 10 A,and I want to save these residues as an another .pdb file. How can I do? Best regards, xiaogaokeng

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how to edit pdb file
by solomon 15 Oct '03

15 Oct '03

dear sir, I'm a new chimera user. Now I have some difficult to use chimera. How can I save the amino acid that I select as a new .pdb file. For example, I select the amino acids that is around the ligand within 10 A,and I want to save these residues as an another .pdb file. How can I do? Best regards, xiaogaokeng

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Re: bug? (HETATMs)
by Eric Pettersen 06 Oct '03

06 Oct '03

On Saturday, October 4, 2003, at 10:21 AM, solomon wrote: > when i open a pdb format file like below: > HETATM ................................. > HETATM ................................. > HETATM ................................. > ... > ... > ... > HETATM ................................. > > then I find that all the HETATM type atoms are bonding each other. All > the HETATM need a ter card to split them. As for HETATM type, I think > maybe there is some wrong with chimera. > best regards > gaokeng xiao Dear Gaokeng, As far as know, Chimera will connect HETATM segments of all standard PDB files (i.e. those distributed by the RCSB) correctly. That being said, Chimera has to do a lot of guessing when it comes to connecting non-standard PDB files (which I'm pretty sure is the kind of file you're talking about here). One thing to keep in mind with HETATMs is that they don't necessarily imply a chain break. Also, they are supposed to have CONECT records detailing their connectivity. So for instance, part of PDB entry 1f1j looks like this: ATOM 3688 OG SER B 602 58.714 25.290 29.976 1.00 66.81 O TER 3689 SER B 602 HETATM 3690 C ACE C 701 29.751 29.860 -0.650 1.00 52.20 C HETATM 3691 O ACE C 701 28.552 30.100 -0.812 1.00 55.72 O HETATM 3692 CH3 ACE C 701 30.801 30.183 -1.675 1.00 52.54 C ATOM 3693 N ASP C 702 30.252 29.308 0.427 1.00 51.48 N The ACE residue in the HETATM records is connected to residue 702 (as detailed in the CONECT records for the file). So in summary, you can have sequences like these where the HETATM residues are connected: ATOM ATOM HETATM HETATM HETATM ATOM ATOM -or- HETATM HETATM HETATM ATOM ATOM Now the really big problem is that the SCOP web site returns "PDB" files with just these kinds of sequences but with _no_ CONECT records! So, Chimera guesses as best it can in this situation. The rule of thumb that it uses is that HETATMs are connected unless they occur somewhere after a TER card with no intervening ATOM record. Explicit CONECT records can add connectivity. So for your file of all HETATMs where nothing should be connected, there is a silver lining: in order to get nothing connected you just have to add a _single_ TER card at the beginning of the file, like this: TER HETATM ................................. HETATM ................................. HETATM ................................. --Eric

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graphics accelorator choice of chip
by David Griffiths 02 Oct '03

02 Oct '03

Since Fire GL2 is now discontinued does anybody have experience of latest graphics acceloratots for use on chimera It has been suggested to me that the following should be OK but does anybody have experience of using them ? NVidia Geforce FX 5600/5900 ATI 9700/9500. david griffiths d.g.griffiths(a)herts.ac.uk

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Re: [Chimera-users] how to color ribbons?
by Elaine Meng 20 Aug '03

20 Aug '03

Hi Mario, I'll include two different ways you could do this in Chimera 1.1700: ---------------- with menu ---------------- Actions... Atoms/Bonds... hide Actions... Ribbon... show Actions... Ribbon... edged Actions... Color... white Select... Structure... secondary structure... helix Actions... Color... red Select... Structure... secondary structure... sheet Actions... Color... cyan Select... Clear selection ---------------- with commands ---------------- ~display ribbon ribrepr edged ribcolor white ribcolor red :/isHelix ribcolor cyan :/isSheet ---------------- In both approaches, first the atoms are undisplayed, then the ribbon is turned on. The step setting the ribbon type to "edged" is optional; you could use whichever ribbon type you want. Then, I make everything white before making helices red and strands cyan. The reason I don't use the turn descriptor is that it only applies to explicit PDB TURN records, whereas in most cases, the PDB only contains HELIX and SHEET records. You could just put the commands in a plain text file, for example named "sscolor.com," and then use the command "source sscolor.com" to execute all the commands in the file. (The file must be in the working directory; otherwise you will have to include the whole path in the source command.) I hope this helps! Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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how to color ribbons?
by Mario Albrecht 20 Aug '03

20 Aug '03

Hi, I'm new to Chimera but I'm missing a simple script in the menu for the normal display of ribbons. Helices in ribbons should be colored in red, strands in cyan, and the rest in white. May you provide such a script? Thank you much, Mario Albrecht

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background manipulation
by Jacob Schmidt 18 Aug '03

18 Aug '03

Greetings: Can you tell me how to completely get rid of the black background on which structures appear? As you probably know printer ink is not cheap. Thanks - Jakob Schmidt, Dept . Biochem and Cell Biol. SUNY Stony Brook

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saving partial coordinates
by Elaine Meng 21 Jul '03

21 Jul '03

Hi Mark, In the current release of Chimera: if you are on a non-Windows system, you can use the command "pdbrun" to save just the atoms that are displayed. You can see the manual page for this command by typing "help pdbrun" in the Chimera Command Line (by default, Favorites... Command Line). example: pdbrun nouser cat > myzone.pdb Pdbrun literally sends the information for only the displayed atoms in their displayed positions to another command, in this case "cat" to send the information to the file myzone.pdb. If you want the coordinates to be the same as in the original file, first use the command "reset." All the atoms should be in view (i.e. if you are zoomed in and the atoms around the periphery cannot be seen in the Chimera window, they won't be in your output file either). The command "save" (or File... Save Session As... ) doesn't save coordinates, only how they are positioned/colored/displayed, etc. In fact, restarting a saved session will use the original input file(s) for coordinates. The command "write" (same as the function "write PDB" in the Model Panel) saves coordinates into a file. However, these will save the entire coordinates whether displayed or not. If you are on Windows, I am not aware of a solution in the current release. In our working version and thus the next release (late summer or early fall, I believe) there is a delete action. This would allow you to select the atoms/bonds outside a zone, for example, and then actually delete them. (Actions... Atoms/Bonds... delete). Subsequently, a file created with "write" would only contain the atoms/bonds that had not been deleted. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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I Need Help!
by Mark Cunningham 20 Jul '03

20 Jul '03

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Re: ribbons, chimera, and collagen
by Eric Pettersen 18 Jul '03

18 Jul '03

Hi Randy, You can force Chimera to treat collagen as helical without too much difficulty. First, select a chain or chains (either Select...Chain, or pick an atom or atoms in the graphics window and use up-arrow several times until the chain(s) are selected). Then use the selection inspector (Tools...Inspectors...Selection Inspector, or click the button showing the selection in the lower-right part of the Chimera window). Change what is being inspected to 'Residue' and then set 'in helix' to true. The problem is that the ribbons don't look very good (they're too "twisty") because it's not an alpha helix. Maybe Conrad can suggest something. I don't have any suggestions myself (I tried making them "strands" and that was pretty twisty also). --Eric > I'm trying to make a ribbon plot of collagen using chimera, but it > doesn't > recognize collagen's secondary structure. > Can I just tell it to make a ribbon with the backbone atoms (or peptide > bonds), and not worry about what kind of secondary structure it really > is? > If so, how? > Have a nice day, > Randy

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Delphi and Chimera
by Marco Sette 09 Jul '03

09 Jul '03

Dear all, I have seen Chimera is able to create potential map using Delphi but, in your site, it is stated that this is valid only for unix systems. I have Delphi installed into windows and linux systems: it will be possible in the (near) future to run DelphiController onto these systems ? Thanks a lot for your attention, Best Regards, Marco -- Dr.Marco Sette, Ph.D. Deaprtment of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Re: [Chimera-users] Chimera - Dock grid
by Thomas Goddard 20 Jun '03

20 Jun '03

Hi Joel, The voldata.tar.gz file had a bug. I forgot to do byte swapping on the grid values. So it works on SGI and Mac or on Linux and Windows, but not both. I fixed this problem. The new code is at: http://www.cgl.ucsf.edu/home/goddard/voldata.tar.gz Tom

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Chimera - Dock grid
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi there, I'm quite impressed with chimera and its dock functionality. My query is about dock grid. I can't find any documentation about this ie what the values and their ranges represent. Also I can't seem to turn them off once they are on. And not to be too ungrateful different colours would be handy as well...how can I change those? While I'm at it is there a delete molecule button? Thanks for your help in advance joel -- ________________________________________ Joel Tyndall, PhD Research Officer http://www.imb.uq.edu.au Institute for Molecular Bioscience incorporating Centre for Drug Design and Development Centre for Cellular and Molecular Biology The University of Queensland Brisbane Australia 4072 Tel: +61 7 3346 2988 Fax: +61 7 3346 2101 email: J.Tyndall(a)imb.uq.edu.au

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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writing Mol2 format
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi David, Writing out Mol2 format can in principle be done, but there are a few caveats. If the original format is Mol2, the original information could be retained and written back out. I don't know how simple/hard this would be to implement (feel free to chime in, other members of the team). When the original format is not Mol2, there is less information in the molecule data than is needed to write the file. Chimera uses a fairly rich set of atom types, but there is still not a one-to-one relationship with all Mol2 types. One would need to create a mapping between the types. Also, I believe Chimera currently knows connectivity but not bond orders, and does not retain any point charge information. The online Chimera Programmer's Guide actually includes an example of code required to write out a mol2 file. I had forgotten about this when visiting your office earlier. It discusses a mapping between atom types (if you use this, you should examine this mapping and make sure it works the way you think it should). The example code writes out all bonds as single. Check it out: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html click the "Examples" link and then "Chimera's Object Model" This example is "writeMol2.py" If you have a molecule open in Chimera, you can view the type assignments using Actions... Label... IDATM type (version 1.1700). A listing/explanation of Chimera types can be seen at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html Best, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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Writing to mol2
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Hi, I'm one of your "neighbors" working in the Shoichet lab for the summer. I think it'd be neat if you could output in mol2 format rather than just pdb format, especially if the input is in mol2. Is this in the works? Has it already been done? Is it easy to do? David Minh

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Chimera & dock grids
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Dear Dr. Tyndall, Thanks for your interest - DOCKgrid is indeed undocumented, partly because we have a much more advanced extension for viewing 3D data sets, Volume Viewer. This would let you have multiple contour surfaces or transparent solids in colors of your choosing, with interactively adjustable thresholds. The current hitch is that the DOCK grid formats have not yet been added to the Volume Viewer extension. We are actively looking into this and hope to incorporate it soon (we will let you know when this happens). I believe the values are directly those stored in the grid files, which (for dock 4 at least) are described in http://dock.compbio.ucsf.edu/dock4/html/Manual.1c.html#pgfId=850 The VDW repulsion, VDW attraction, and electrostatic grid values are described in equation 9 (all three are in the *.nrg grid). These are not in energy units until multiplied by ligand atom parameters. I believe the color choices in DOCKGrid are red and red. Display with Volume Viewer should be a vast improvement. To close molecules and also these contour surfaces, one way is to open the Model Panel (Tools... Inspectors... Model Panel in version 1.1700). In the Model Panel, choose the model(s) you want to close on the left side, then click "close" on the right side (not the Model Panel Close button). Unfortunately the contour surfaces created by DOCKgrid are each VRML files without an informative title, so it may be hard to tell which is which. If you only have one, of course, it will be obvious. I hope this helps! Best regards, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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Re: Chimera graphics card requirements
by chimera-users＠cgl.ucsf.edu 10 Jun '03

10 Jun '03

Hi Jim, I think Chimera will start without an OpenGL stencil buffer. But the outline highlighting of selected atoms/bonds/... will not work. Fill mode highlighting settable with Favorites/Preferences/General/ Selection highlight method will work. With a Quadro4 700 XGL on Linux you should definitely have a stencil buffer available. Below is the output of "glxinfo -t" on my Linux system with Quadro4 500 graphics. It shows half the visuals have 8 bit stencil buffer. It shows I am using the Nvidia 4191 driver OpenGL version string: 1.4.0 NVIDIA 41.91 Check the OpenGL version string on your machine to make sure you are using the Nvidia driver and not Mesa (software opengl). Tom $ glxinfo -t name of display: :0.0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: NVIDIA Corporation server glx version string: 1.3 server glx extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer client glx vendor string: NVIDIA Corporation client glx version string: 1.3 client glx extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_SGI_video_sync, GLX_SGIX_swap_group, GLX_SGIX_swap_barrier, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_NV_float_buffer GLX extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_ARB_get_proc_address OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro4 500 GoGL/AGP/SSE2 OpenGL version string: 1.4.0 NVIDIA 41.91 OpenGL extensions: GL_ARB_imaging, GL_ARB_multitexture, GL_ARB_point_parameters, GL_ARB_texture_compression, GL_ARB_texture_cube_map, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat, GL_ARB_transpose_matrix, GL_ARB_vertex_program, GL_ARB_window_pos, GL_S3_s3tc, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint, GL_EXT_compiled_vertex_array, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels, GL_EXT_paletted_texture, GL_EXT_point_parameters, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shared_texture_palette, GL_EXT_stencil_wrap, GL_EXT_texture_compression_s3tc, GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, GL_EXT_texture_object, GL_EXT_vertex_array, GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, GL_NV_blend_square, GL_NV_fence, GL_NV_fog_distance, GL_NV_light_max_exponent, GL_NV_packed_depth_stencil, GL_NV_pixel_data_range, GL_NV_point_sprite, GL_NV_register_combiners, GL_NV_texgen_reflection, GL_NV_texture_env_combine4, GL_NV_texture_rectangle, GL_NV_vertex_array_range, GL_NV_vertex_array_range2, GL_NV_vertex_program, GL_NV_vertex_program1_1, GL_NVX_ycrcb, GL_SGIS_generate_mipmap, GL_SGIS_multitexture, GL_SGIS_texture_lod glu version: 1.3 glu extensions: GLU_EXT_nurbs_tessellator, GLU_EXT_object_space_tess Vis Vis Visual Trans buff lev render DB ste r g b a aux dep ste accum buffers MS MS ID Depth Type parent size el type reo sz sz sz sz buf th ncl r g b a num bufs ---------------------------------------------------------------------------------------------------- 0x21 24 TrueColor 0 32 0 rgba 1 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x22 24 DirectColor 0 32 0 rgba 1 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x23 24 TrueColor 0 32 0 rgba 1 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x24 24 TrueColor 0 32 0 rgba 0 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x25 24 TrueColor 0 32 0 rgba 0 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x26 24 TrueColor 0 32 0 rgba 1 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x27 24 TrueColor 0 32 0 rgba 1 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x28 24 TrueColor 0 32 0 rgba 0 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x29 24 TrueColor 0 32 0 rgba 0 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x2a 24 DirectColor 0 32 0 rgba 1 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x2b 24 DirectColor 0 32 0 rgba 0 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x2c 24 DirectColor 0 32 0 rgba 0 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x2d 24 DirectColor 0 32 0 rgba 1 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x2e 24 DirectColor 0 32 0 rgba 1 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x2f 24 DirectColor 0 32 0 rgba 0 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x30 24 DirectColor 0 32 0 rgba 0 0 8 8 8 8 0 0 0 16 16 16 16 0 0 > From: Jim Procter <procter(a)zbh.uni-hamburg.de> > Reply-To: procter(a)zbh.uni-hamburg.de > Organization: Zentrum Bioinformatik Hamburg > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Chimera graphics card requirements > Date: Tue, 10 Jun 2003 10:53:20 +0200 > > Hi. I'm sorry to bother you again - particularly with some trivial hardware > question, but I've been wondering about the minimum specification of OpenGL > graphics driver needed for Chimera. > > We have Quadro4 700 XGL/AGP/SSE2 drivers for our linux-installations, on what > I would expect to be fairly high-end PCs. There doesn't seem to be any way to > force these drivers to generate a stencil buffer - is this what other people > have found ? > > Thanks. > Jim

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Re: Chimera at NCMI
by chimera-users＠cgl.ucsf.edu 09 May '03

09 May '03

Hi Steve, I'll ask the other Chimera developers about making independent mode rotation use the center of the whole model when it is undisplayed. Unfortunately that is a change in the C++ that would not be available for a while. I'll try making a rotation/translation undo button next week. I think it can be done all in Python and I could just email you the code. Tom > Date: Fri, 9 May 2003 20:48:49 -0500 (CDT) > From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> > Reply-To: sludtke(a)bcm.tmc.edu > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Yeah, a rotation/translation undo would be great! The miscentering > problem isn't an issue for what I'm doing right now (at least not much of > one, but a more generic way of setting the center would be nice. Perhaps > using the origin you set for the volume data as a center for rotation. The > manual translations seem to be independent of this value... > > cheers... > > -- > ---------------------------------------------------------------------------- > Steven Ludtke, PhD | Baylor College of Medicine > sludtke(a)bcm.tmc.edu | Co-Director > stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging > V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. > instant messenger: sludtke42 | * Those who do ARE * > http://ncmi.bcm.tmc.edu/~stevel | The converse also holds

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independent rotation mode
by chimera-users＠cgl.ucsf.edu 09 May '03

09 May '03

Date: Fri, 9 May 2003 13:57:27 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi again. I just ran across a bug I thought I'd report. The session file is rather large, so I won't attach it initially. Let me know if you have problems reproducing it. Anyway, I have loaded several volume data sets which represent different versions of the same structure. Then: 1) set 'independent' rotation mode 2) set one model so it is active, but not shown (in the model panel) 3) rotate the models 4) set the model in 2 to be shown again Even though it was active, the model in 2 was not rotated. I have a complex scenario of models where I need to do this operation frequently, so right now all my rotations keep getting messed up unless I make sure all the models are active AND shown before rotating anything. Cheers... PS - This happens with both the current 1700 version and the previous one. -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds Date: Fri, 9 May 2003 15:04:20 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Not THAT big a rush. Whenever you have a chance :^) Anyway, I was trying to avoid having to explain the whole situation, but here goes. I have a PDB model, a density map based on the PDB model and 3 different EM maps of the same molecule (each a little different). All are aligned and centered. What I want to do is have the EM map(s) with overlaid PDB structure on the left side of the screen and the x-ray map with overlaid structure on the right half of the screen. Then I use 'independent mode' to rotate everything about its own center so I can see how the EM map and x-ray map compare. As long as everything is active and displayed, it works beautifully (except the PDB model center seems very slightly off, so you see a very small amount of the centering artifact you described). Anyway, on the 'EM' side, I have 3 models overlaid. Generally I want to turn their display on and off as I rotate each one around and look at them. However, even though all 3 remain active, when I turn off the display of a model (ONLY in independent mode), it no longer gets rotated properly. Hope that helps clarify... cheers. -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds From: Tom Goddard The problem is that indepedent rotation mode only rotates about the the center of the displayed part of the model. If nothing is displayed there is no center to rotate about. Date: Fri, 9 May 2003 20:02:39 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> I understand. I sort of figured it was something like this. Well, I'll give you my perspective as a 'user' from the EM community. As funny as it seems, I would actually want the opposite of the behavior you stated. That is, the molecules would always rotate about their 'true' center even if part wasn't displayed. The best solution from my perspective would either A) have a different 'independent' mode where things always rotated about their true centers or B) Make it so models that aren't displayed at all use their true center. This doesn't seem quirky to me. If the model is active, you assume some sort of rotation will occur. Presumably if part of the molecule is visible, the whole thing still gets rotated, just about a different center. So, it's odd for it not to get rotated at all. >From a user perspective, a problem I keep running into is that I accidentally do a rotation when not all of the molecules are active. This produces a relative rotation that is virtually impossible to undo through the GUI. Translations aren't a problem. They're pretty easy to 'undo' almost perfectly. But rotations are really tricky. When that happens I end up having to revert to my last saved session. So, having the model not rotate at all just because it isn't visible is doubly annoying... Anyway, just my perspective... -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds Hi Steve, I agree it is odd for the undisplayed model not to be rotated at all. It seems reasonable that when the model is undisplayed it should use the center of the whole model if you are using independent rotation mode. There is the additional problem that the centers of the models don't coincide. When you display an isosurface, it uses the center of the bounding box that just contains the surface. It does not use the actual bounds of the whole density map. I see that Chimera has support for fixing the center of rotation for each model. This could be used to get exactly the rotation behaviour you want. But we need a user interface to let you say which models you want to group together with a common center. I could write something like this in Python. This would address both the undisplayed models not rotating, and the not quite right centers of rotation. I realize that accidentally unaligning two models in Chimera is a disaster -- it usually means starting over. I think we need a rotation and translation undo to address this. Tom

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Re: Chimera and O brix format
by chimera-users＠cgl.ucsf.edu 06 May '03

06 May '03

Hi Ed, I wrote the SPIDER volume file reader for Chimera. You can get it from http://www.cgl.ucsf.edu/home/goddard/spidervol.tar.gz and unpack it % cd /usr/local/chimera/share % tar zxf spidervol.tar.gz It includes a new VolumeData/fileformats.py that adds the SPIDER file reader to the list of supported file formats, and a VolumeData/spider directory that contains the Python code to read the data. I don't think this should be announced on the SPIDER newsgroup until we make our next Chimera release that includes it. I'd like to figure out how the spacing between grid points in physical units is handled by SPIDER. I see a "scale" parameter in the SPIDER file header, but the documentation says SPIDER does not use this, and in the file you sent me it was set to zero. Chimera likes to know the correct scale in physical units (eg angstroms or nanometers) so when a second model is opened they are drawn to the same scale. There are entry fields to hand set the scale in the Volume Viewer dialog, but it is nicer to be able to extract this from the file header. Tom

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Re: Chimera and O brix format
by chimera-users＠cgl.ucsf.edu 05 May '03

05 May '03

Hi Ed, I extended the current Chimera DSN6 file reader to handle the BRIX files. The changed files are in chimera/share/VolumeData, specifically fileformats.py and the dsn6/*.py files. Here is a tar file you can extract in chimera/share to update these files. http://www.cgl.ucsf.edu/home/goddard/voldata.tar.gz % cd /usr/local/chimera/share % tar zxf voldata.tar.gz Let me know if you have trouble with it. I have only tested it on the file you gave me. I used BRIX format documentation from the web though and expect it should work with all files. It will be included in the next Chimera release. Tom

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Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 24 Apr '03

24 Apr '03

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

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Re: [chimera-dev] Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 24 Apr '03

24 Apr '03

Hi Geoff, Eric Pettersen tells me Chimera is hanging when you display diamond.pdb in ball and stick or sphere mode because it is searching for rings. There are too many rings to find. Eric will look at fixing the ring finding code. The reason it needs to know the rings for some display modes is so it can identify atom types (classed by connectivity) so it can assign correct atom radii. You can work around the problem by issuing a Chimera command to set the vdw radii before using ball and stick or sphere display. Use Favorites/Command Line and type a command like vdwdefine * * 1.0 This example sets all atom radii to 1 angstrom (for sphere display). See the User's Guide under Commands for details on setting the radii of specific atoms if you want different atoms shown with different sizes. Any application, Aqua or not, can have an icon in the Dock -- it just has to be packaged with the Mac App directory layout and have an icon file. But Force Quit apparently only lists Aqua applications. The Aqua version of Chimera is shown in the Force Quit list. Tom

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Re: [chimera-dev] Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 24 Apr '03

24 Apr '03

Hi Geoff, Chimera freezes up for me after I open diamond.pdb and then try to show it as ball and stick or sphere. It doesn't freeze up with wire display style. When it freezes I use: % ps -xwww | grep python2.2 3676 ?? R 0:44.37 /Users/goddard/Applications/Chimera-X11-1700.app/Contents/Resources/bin/python2.2 /Users/goddard/Applications/Chimera-X11-1700.app/Contents/Resources/share/__main__.pyp % kill 3676 The Chimera executable is python2.2 and this just kills Chimera, not the X server. It doesn't appear in the Force Quit dialog because it is not a native Aqua windows application. Are you using Chimera build 1700 (March 27, 2003)? The Chimera Help/Version Info menu entry will tell you which version you have. I'll look into why Chimera 1700 is freezing on diamond.pdb. Tom

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Re: [chimera-dev] Mailing list, etc.?
by chimera-users＠cgl.ucsf.edu 08 Apr '03

08 Apr '03

> Now to a comment. After some tinkering, I finally managed to output a > new PDB file that contained models from several other PDB files. This, > however, wasn't exactly an easy of intuitive thing to do. My first > thought had been to use the 'Write PDB' command in the Model Panel. > However, that button automatically greys itself out when more than one > model is selected. I finally stumbled upon the command line command > 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to > go through a rather backdoor method. Any chance that things like > 'Write PDB' will be enabled when more than one model is selected? I could enable 'write PDB' with multiple models selected. I guess my question is why do you want multiple PDB models in a single file? What will you do with that file? Knowing how you want to use the file will help me decide if simply enabling the button is the way to go or if some other interface is more appropriate. If I enabled it, the models would be separated by END records. > And what about a method of adding more atoms, other than just > hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd > love to see Chimera become a more fully featured molecular modeler, and > to that end, I'm quite happy to give all kinds of input.) I'm currently working on smarter hydrogen addition (avoiding steric conflicts and maintaining hydrogen-bonding interactions). I should be done with that in time for our next release. I intend to work on some limited structure-building features after that. So a preliminary version might be available two releases from now. Even I'm not aware of backdoor ways to add non-hydrogen atoms! I guess the swapaa command _sort_ of does this, but it's not at all generic. Are you writing Python code to do this? Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [chimera-dev] Mailing list, etc.?
by chimera-users＠cgl.ucsf.edu 07 Apr '03

07 Apr '03

On Monday, April 7, 2003, at 10:06 AM, Thomas Goddard wrote: > Now to a comment. After some tinkering, I finally managed to output a > new PDB file that contained models from several other PDB files. This, > however, wasn't exactly an easy of intuitive thing to do. My first > thought had been to use the 'Write PDB' command in the Model Panel. > However, that button automatically greys itself out when more than one > model is selected. I finally stumbled upon the command line command > 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to > go through a rather backdoor method. Any chance that things like > 'Write PDB' will be enabled when more than one model is selected? > And what about a method of adding more atoms, other than just > hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd > love to see Chimera become a more fully featured molecular modeler, and > to that end, I'm quite happy to give all kinds of input.)

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