May 2005 - Chimera-users - RBVI Mailing Lists

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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