- Chimera-users - RBVI Mailing Lists

Gallery PDB source
by David Piper 24 Jun '05

24 Jun '05

Chimera Folks, I was looking at the gallery images and noticed that one is of the FlAsH molecule. Are the PDB coordinate available somewhere for this molecule? Or ReAsH? Thanks, David

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Electron density
by C. Parry 22 Jun '05

22 Jun '05

Could anyone help with loading and displaying CNS or XPLOR electron density maps in Chimera. I have tried many times and also the dialog boxes in the user guide do not exactly correspond to the version (12/2004) of Chimera I have. Thanks. ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com

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mutation tool?
by ROBERT LAVIERI 17 Jun '05

17 Jun '05

I am exploring/using the program and I was wondering if there was any sort of point mutation tool? Such that one could graphically see say a mutation like ser23trp? Thanks, Robert R Lavieri

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how to open bug-report dialog in v1.2105
by Sabuj Pattanayek 13 Jun '05

13 Jun '05

Hi, In v1.2105 (irix) the report a bug command under the help menu is not available (as stated in the current development documentation I assume for v1.2129). How do I open the bug report submission dialog from the command line or from the menus even if a crash or error has not occurred? Thanks, Sabuj Pattanayek

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Stereo monitors
by Thomas Goddard 06 Jun '05

06 Jun '05

Steve Ludtke reports what his lab is using for hardware stereo. Tom ------- Start of forwarded message ------- Date: Mon, 6 Jun 2005 12:59:39 -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> Subject: Re: Chimera Suggestion We have the Sharp 15" one. As I said, it works ok as long as you stay in the sweet spot, but gives me a nasty headache (which the glasses do not). We haven't tried any of the high-refresh LCD's yet. We still use CRT's for that at the moment. We're about to try a homebrew polarized glasses solution. We do actually have a (800x600) high refresh projector for use with the shutter glasses which works well. - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Asst. Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | instant messenger: sludtke42 | Those who Do, Are http://ncmi.bcm.tmc.edu/~stevel | The converse also applies On Mon, 6 Jun 2005, Thomas Goddard wrote: > Hi Steve, > > Our stereo monitor that requires no glasses was a 20" flat panel > type display from Opticality (formerly X3D). I just found out we have > returned it because it worked so poorly. I'd be curious what > make/model you have. Also have you tried any normal flat panels with > fast refresh rates and LCD glasses? > > Tom > ------- End of forwarded message -------

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Red / blue stereo
by Thomas Goddard 06 Jun '05

06 Jun '05

Steve Ludtke would like red / blue stereo. Tom ------- Start of forwarded message ------- Date: Sat, 4 Jun 2005 02:13:29 -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> Subject: Chimera Suggestion We've had a minor resurgance of stereo work in the lab recently. We have a couple of SGI's still with the standard shutter-glasses, and a single PC with a CRT and an active stereo capable projector. We tried the Sharp autostereographic monitor, but it works only so-so, and gives me a headache almost instantly. It would be really useful to have simple stereo set up for occasional use on all of the desktop machines in the lab (which have normal LCD panels now). Anyway, I was just wondering if you guys thought about implementing analglyph (red/blue glasses) stereo ? I've done this manually for snapshots using the 'left eye' and 'right eye' mode in chimera to get the separation right, and it works surprisingly well as long as you don't mind sacrificing color. It would be very useful to have this available for interactive use. Any chance ? (it's also very useful for posters, since many people can't do the eye-crossing thing). Just a suggestion :^) - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Asst. Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | instant messenger: sludtke42 | Those who Do, Are http://ncmi.bcm.tmc.edu/~stevel | The converse also applies ------- End of forwarded message -------

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Selection question in --nogui mode
by Miguel Ortiz Lombardia 26 May '05

26 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello. I'm trying to execute this: $chimera --nogui cmd:findselhbonds where the file findselhbonds contains: open 01.pdb select :59-62 hbonds selRestrict any saveFile tmp.bonds In the graphic mode those instructions work as expected, however in the - --nogui mode I get this error: Opening 01.pdb... warning: Ignored bad PDB record found on line 1 warning: Ignored bad PDB record found on line 2 Computed secondary structure assignments (see reply log) Model 0 (01.pdb) appears to be a protein with no secondary structure assignments. Computing assignments for it using the ksdssp algorithm (Kabsch and Sander Define Secondary Structure of Proteins) with an energy cutoff of - -0.5, minimum helix length of 5, and minimum strand length of 4. If these parameters don't produce good results for this structure, you can rerun the algorithm with different settings using the 'compute SS' button in the model panel (under 'infrequent' actions) or via the 'ksdssp' command in the Midas emulator. The model panel will also allow you to save new default parameters. 1 model opened Opened 01.pdb containing 1 model, 632 atoms, and 62 residues Error while processing cmd:forchimera: NameError: global name 'selMode' is not defined (see reply log for Python traceback info) Traceback (most recent call last): File "/usr/local/linux_prg/Chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 287, in init prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1043, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 17, in func File "CHIMERA/share/Midas/midas_text.py", line 88, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand File "CHIMERA/share/Midas/midas_text.py", line 1039, in doSelect File "CHIMERA/share/Midas/__init__.py", line 620, in chimeraSelect File "CHIMERA/share/chimera/tkgui.py", line 1604, in selectionOperation NameError: global name 'selMode' is not defined Any clues? Thank you very much! Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: miguel.ortiz(a)cnio.es - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées >>> And the boring bits follow... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.6 (GNU/Linux) iD8DBQFCleiGF6oOrDvhbQIRAi6cAJ415IJkwKrdjmhOofNbff34aEM3OQCeMdHj GNtxhKnI0DVyUDenbeAHOmw= =VDTj -----END PGP SIGNATURE----- **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Dipole
by Miguel Ortiz Lombardia 18 May '05

18 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, Maybe a silly question, but I couldn't find anything in the docs. Given one structure pdb and an electrostatic potential calculated by delphi, can Chimera display the resulting dipole as a vector? Thank you very much! Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: miguel.ortiz(a)cnio.es - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées >>> And the boring bits follow... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.6 (GNU/Linux) iD8DBQFCi3u+F6oOrDvhbQIRAsvpAJ40rweZtnhVlp3HPYt8sVDODfzEjgCfdAyq efdpkP4wOqyWcrCTT23aJCM= =rxYo -----END PGP SIGNATURE----- **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Re: [Chimera-users] New 64-bit Linux version of Chimera
by Thomas Goddard 17 May '05

17 May '05

The 64-bit Linux Chimera 1.2123 installer was broken. A packaged file did not have execute permission. The fixed version is on the download page now with the same version number and date. If you got the broken version (by downloading in the past 8 hours), please try again. Sorry for the gaff. Tom

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Draw user specified object
by Reza Khayat 17 May '05

17 May '05

Hi, I was wondering if there is a way to draw a user specified object. For example, draw a cylinder (bond) from vertex x to vertex y. Thank you. Reza rkhayat(a)scripps.edu

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New 64-bit Linux version of Chimera
by Thomas Goddard 17 May '05

17 May '05

A new 64-bit Linux Chimera snapshot (version 1.2123) is available on the Chimera download page. http://www.cgl.ucsf.edu/chimera/download.html Unless you are viewing large data sets (> 1 Gb), we suggest you use 32-bit versions of Chimera on 64-bit Linux systems. 32-bit versions will likely run faster and use less memory. The 32-bit versions are more likely to be compatible with your Linux distribution. We are not yet making regular distributions for 64-bit linux so our 32-bit version will usually be newer. Tom

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Re: [Chimera-users] Exporting VRML of MSMS surfaces
by Thomas Goddard 16 May '05

16 May '05

The VRMLoutput/__init__.py I posted in my previous two emails worked for the newly added MSMS surface output, but was broken for volume contour surfaces. Here is the corrected code. Tom ---- VRMLoutput/__init__.py follows: # ----------------------------------------------------------------------------- # Output displayed _surface models as VRML. # # ----------------------------------------------------------------------------- # def surfaces_as_vrml(surface_models): surf_vrml = ['#VRML V2.0 utf8\n', 'Transform {', ' children ['] import _surface import chimera for m in surface_models: if m.display: if isinstance(m, _surface.Surface_Model): glist = filter(lambda g: g.display, m.surface_groups()) for g in glist: vrml = surface_group_as_vrml(g) surf_vrml.append(vrml) elif isinstance(m, chimera.MSMSModel): vrml = msms_surface_as_vrml(m) surf_vrml.append(vrml) surf_vrml.extend([' ]', '}']) vrml = '\n'.join(surf_vrml) return vrml # ----------------------------------------------------------------------------- # def surface_group_as_vrml(g): vertex_rgba = g.vertex_colors() solid_rgba = g.color() m = g.model() mat = m.material shine = mat.shininess / 128.0 srgb = mat.specular if g.display_style() == g.Solid: v, vi = g.geometry() n = g.normals() ts = g.two_sided_lighting() vrml = surface_vrml(v, vi, n, vertex_rgba, solid_rgba, ts, shine, srgb) else: v, vi = g.edges() # Mesh lighting not supported in VRML97. vrml = mesh_vrml(v, vi, vertex_rgba, solid_rgba) return vrml # ----------------------------------------------------------------------------- # def msms_surface_as_vrml(m): vertex_rgba, solid_rgba, mat, shine, srgb = msms_colors(m) # TODO: Use m.drawMode (Filled, Mesh, Dot) to control vrml style vfloat, vint, tri = m.triangleData() v = vfloat[:,:3] n = vfloat[:,3:6] vi = tri[:,:3] ts = True vrml = surface_vrml(v, vi, n, vertex_rgba, solid_rgba, ts, shine, srgb) return vrml # ----------------------------------------------------------------------------- # def msms_colors(m): if m.colorMode == m.Custom: vertex_rgba = colors_to_rgba(m.customColors) elif m.colorMode == m.ByAtom: vfloat, vint, tri = m.triangleData() alist = m.atomMap() vatoms = map(lambda i: alist[i-1], vint[:,1]) vertex_rgba = colors_to_rgba(map(atom_color, vatoms)) else: vertex_rgba = None mol = m.molecule if mol: c = mol.surfaceColor if c == None: c = mol.color solid_rgba = c.rgba() mat = c.material else: solid_rgba = (1,1,1,1) import chimera mat = chimera.MaterialColor(0,0,0).material shine = mat.shininess / 128.0 srgb = mat.specular return vertex_rgba, solid_rgba, mat, shine, srgb # ----------------------------------------------------------------------------- # def colors_to_rgba(color_list): rgba = map(lambda c: c.rgba(), color_list) import Numeric rgba_f32 = Numeric.array(rgba, Numeric.Float32) return rgba_f32 # ----------------------------------------------------------------------------- # def atom_color(atom): c = atom.surfaceColor if c == None: c = atom.color if c == None: c = atom.molecule.surfaceColor if c == None: c = atom.molecule.color return c # ----------------------------------------------------------------------------- # def surface_vrml(vertices, vertex_indices, vertex_normals, vertex_rgba, solid_rgba, two_sided_lighting, shininess, specular_rgb): vrml_template = \ '''Shape { appearance Appearance { material Material { diffuseColor %s transparency %.3f shininess %.3f specularColor %s } } geometry IndexedFaceSet { coord Coordinate { point [ %s ] } normal Normal { vector [ %s ] } coordIndex [ %s ] %s solid %s } } ''' pts = tuple_string(vertices, '%.6g %.6g %.6g') ns = tuple_string(vertex_normals, '%.6g %.6g %.6g') m = polygon_size(vertex_indices) vi_format = ' '.join(['%d'] * m + ['-1']) ci = tuple_string(vertex_indices, vi_format) if vertex_rgba: clrs = tuple_string(vertex_rgba[:,:3], '%.3f %.3f %.3f') cspec = 'color Color {\n color [\n%s]\n }\n' % clrs else: cspec = '' srgb, trans = material_colors(vertex_rgba, solid_rgba) specular = '%.3f %.3f %.3f' % specular_rgb if two_sided_lighting: solid = 'FALSE' else: solid = 'TRUE' vrml = vrml_template % (srgb, trans, shininess, specular, pts, ns, ci, cspec, solid) return vrml # ----------------------------------------------------------------------------- # VRML does not handle normals for lines. # def mesh_vrml(vertices, vertex_indices, vertex_rgba, solid_rgba): vrml_template = \ '''Shape { appearance Appearance { material Material { emissiveColor %s transparency %.3f } } geometry IndexedLineSet { coord Coordinate { point [ %s ] } coordIndex [ %s ] %s } } ''' pts = tuple_string(vertices, '%.6g %.6g %.6g') m = polygon_size(vertex_indices) vi_format = ' '.join(['%d'] * m + ['-1']) ci = tuple_string(vertex_indices, vi_format) if vertex_rgba: clrs = tuple_string(vertex_rgba[:,:3], '%.3f %.3f %.3f') cspec = 'color Color {\n color [\n%s]\n }\n' % clrs else: cspec = '' srgb, trans = material_colors(vertex_rgba, solid_rgba) vrml = vrml_template % (srgb, trans, pts, ci, cspec) return vrml # ----------------------------------------------------------------------------- # def material_colors(vertex_rgba, solid_rgba): if vertex_rgba: srgb = '0 0 0' trans = 1 - max(vertex_rgba[:,3]) else: srgb = '%.3f %.3f %.3f' % solid_rgba[:3] trans = 1 - solid_rgba[3] return srgb, trans # ----------------------------------------------------------------------------- # def polygon_size(vertex_indices): if vertex_indices: return len(vertex_indices[0]) return 0 # ----------------------------------------------------------------------------- # def tuple_string(tuples, format): tuple_strings = [] for t in tuples: tuple_strings.append(format % tuple(t)) tstring = '\n'.join(tuple_strings) return tstring # ----------------------------------------------------------------------------- # def surface_models(): import chimera import _surface mlist = chimera.openModels.list(modelTypes = [_surface.Surface_Model, chimera.MSMSModel]) return mlist # ----------------------------------------------------------------------------- # def write_surfaces_dialog(): import os.path dir = os.path.dirname(__file__) help_path = os.path.join(dir, 'helpdir', 'vrml_output.html') help_url = 'file://' + help_path filters = (('VRML', ('*.wrl', '*.vrml'), '.vrml'),) import OpenSave od = OpenSave.SaveModeless(title = 'Save Surfaces as VRML', filters = filters, defaultFilter = 0, command = write_surfaces_cb, multiple = 0, help = help_url) od.enter() # ----------------------------------------------------------------------------- # def write_surfaces_cb(okayed, dialog): if okayed: paths = dialog.getPaths() if len(paths) == 1: write_surfaces_as_vrml(paths[0]) # ----------------------------------------------------------------------------- # def write_surfaces_as_vrml(path): mlist = surface_models() vrml = surfaces_as_vrml(mlist) f = open(path, 'w') f.write(vrml) f.close()

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matching scale for different sessions
by jinghua＠ucsd.edu 16 May '05

16 May '05

to our friendly developer, Is there a way to specify the physical size for a view, so that different sized molecule or map is shown at the same physical scale from different sessions. By the way, is there a command to specify the pixel size of the window? the shrink to fit or grow to fit doesn't work well. many 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://cryoem.ucsd.edu/~jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><

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by Klinkhardt＠em.uni-frankfurt.de 13 May '05

13 May '05

Hello, I have a question concerning the surface resolution of multiscale models. My intention was to create a surface from pdb data, export it as vrml and reimport it in maya for further animation, shading etc. It works quite well (I had to convert the vrml file in ascii with Deep Explorer first) but the problem is, that I do not get a fine surface with all its convexities and sites for binding. This is important for my work because I would like to animate receptor binding and subsequent signaling in maya. I am looking for a fine surface like these MSMS main surface from pdb data. I do not need many copies of single pdb surfaces but I guess I will only get a #real# surface using the multiscale models tool?? I tried to change the surface resolution (the best result was with resolution: 3, threshold atom density 0.00, smoothing factor 0.5 and smoothing interations 2/3) but I was not able to create a really fine surface. Is there any possibility to get a finer surface (like MSMS main surface) for VRML export? If not, do you have an idea if there are other tools to do that? It would be rally great if you could give me a short reply. Thanks a lot in advance (and sorry for my english...). Best regards Ute

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Scale bar in Chimera
by Haixiao Gao 09 May '05

09 May '05

Hi, I have a problem with the "scale bar" option in Chimera. I was trying to show the scale bar together with a EM density map in spider/brix format. Howerver, it seems that when I changed zoom in/out position, the size change of the "scale bar" is not proportional to the size change of the density map? My chimera version is win32, bata version from 12/15/2004. Thanks for the help! -Haixiao

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Re: [Chimera-users] os x tiger
by Thomas Goddard 05 May '05

05 May '05

We've put code in the Chimera 1.2121 snapshot (released May 5, 2005) to work around a bug in the Apple OpenGL driver that caused Chimera to crash when displaying molecule ribbons. You need to use Chimera 1.2121 or later on Mac OS 10.4. Tom

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beta version of Sequence.py
by Bryan W. Lepore 05 May '05

05 May '05

i'm trying out the secondary structure matching stuff that Eric wrote, and i'm wondering if there is a updated Sequence.py package (that has the StructureSequence functions)? b/c the new MatchMaker/__init__.py trys to import StructureSequence, but its not in chimera/Sequence.py. -bryan

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os x tiger
by Grant Geske 04 May '05

04 May '05

has anyone tried running chimera on the new mac os tiger?? i did and it did not work. does anyone have any suggestions?? grant ________________________________ Grant Geske Blackwell Group University of Wisconsin-Chemistry 1101 University Ave Madison, WI 53706 PH: 608-262-9043 email: chemg(a)mac.com

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circular permuation
by Bryan W. Lepore 04 May '05

04 May '05

i want to test my understanding about the "circular permuation" during matching: is this for proteins that result from gene duplication? -bryan

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Fwd: [Chimera-users] writing alignment
by Elaine Meng 04 May '05

04 May '05

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: Wed May 4, 2005 1:56:54 PM US/Pacific > To: "Bryan W. Lepore" <lepore(a)brandeis.edu> > Subject: Re: [Chimera-users] writing alignment > > > On Wednesday, May 4, 2005, at 01:41 PM, Bryan W. Lepore wrote: >> however i'd like to ask if mmaker is in fact not written to handle >> specific stretches of a model - e.g you can do #1:.a at the least? >> e.g., not something like #1:.a1-10,a15-20... to prune out areas to >> ignore. >> >> -bryan >> > > Hi Brian, > You can specify which chains (like in that example you included > in a previous mail) to construct an alignment with, but not > subparts of those chains. > > However, remember that the structure matching will only use > residues that are actually aligned in the initial sequence alignment. > So, it doesn't matter if the sequences have other parts > that are essentially unalignable. > Elaine >

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mmaker
by Bryan W. Lepore 03 May '05

03 May '05

i'm confused about the command "mmaker". `chimera --nogui mmaker` causes a "no such file or directory" error, so i tried `chimera --nogui --mmaker` which isnt' right either. also tried just `mmaker` even though its not in bin/ lib/. so do i make a heredoc script? i suspect i am missing a fundamental point (that i didn't find with `google: mmaker site:www.cgl.ucsf.edu/chimera`) i've tried both the latest official release and the lastest snapshot. -bryan

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by Ihms, Elihu C 02 May '05

02 May '05

I noted that Apple still has X11 availible for download, just that it's not publicized. http://a1408.g.akamai.net/7/1408/1388/20030317/akamai.info.apple.com/X11/us… Keep up the good work on Chimera! -- Elihu Ihms [ ihms(a)tamu.edu ]

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Chimera Surface Area/Volume
by Elaine Meng 27 Apr '05

27 Apr '05

Hi Dieter, Just a few add-ons to Tom's reply: Another approach to getting the surface area of the receptor buried by the ligand is to run Surface Area/Volume (a) on the complex of ligand and receptor (must delete water and anything else first). Then use Attribute Calculator to sum the surface areas of the receptor atoms only. (b) after deleting ligand, run it again on the receptor. The total is all from the receptor, so it is not necessary to use Attribute Calculator. Subtract the value from (a) from this value. Tom gave a link to the development documentation, which is slightly ahead of the Chimera version you have. It is almost the same, except that the Tools menu has been reorganized. Probably in the version you have, both Attribute Calculator and Surface Area/Volume are in the Utilities submenu of the Tools menu. To get the documentation that goes with your version, use the Help buttons on those dialogs or open the User's Guide from the Help menu. If you have the latest snapshot (1.2105, March) there is an "Attributes" tutorial (Help... Tutorials). Part 2 has one example of using Surface Area/Volume and Attribute Calculator. Finally, if anything is confusing or hard to find in the documentation, please feel free to complain to me! 8-) 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

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buried surface area
by Thomas Goddard 27 Apr '05

27 Apr '05

Hi Dieter, The surface area / volume tool (menu entry Tools -> Utilities -> Surface Area / Volume) could give buried surface areas if you ran it for the unbound receptor, unbound ligand, and then the complex, and then calculated { Area(receptor) + Area(ligand) - Area(receptor+ligand) } / 2 When you use this tool it reports the total area to the Reply Log (menu entry Favorites / Reply Log) and atoms are assigned an attribute saying how much area they contribute. It is a bit of a pain to run it 3 times and do the math yourself. The surface area is calculated by a web server as described in the Chimera User's Guide http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.ht… so you will need an internet connection to use it. The Chimera User's Guide is only available in HTML as far as I know. It is written in HTML. Tom > From: "Dieter Blaas" <dieter.blaas(a)meduniwien.ac.at> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Date: Wed, 27 Apr 2005 21:38:46 +0200 > Subject: buried surface area > > Hi Tom, > two quick questions: 1/ can Chimera calculate/display > the surface area buried by e.g. a ligand when bound on > a receptor? 2/ is there a documentation other than htlm > (e.g. pdf file)? > Thanx, Dieter >

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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

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

16 Sep '04

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

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

15 Sep '04

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

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chimera in fink
by Ersatz Sophist 15 Sep '04

15 Sep '04

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

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