April 2004 - Chimera-users - RBVI Mailing Lists

Coloring by bfactor
by Thomas Goddard 23 Apr '04

23 Apr '04

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

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

23 Apr '04

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

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install question
by Randy Heiland 23 Apr '04

23 Apr '04

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

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

23 Apr '04

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

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

22 Apr '04

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

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

12 Apr '04

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

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

09 Apr '04

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

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

08 Apr '04

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

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

08 Apr '04

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

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

02 Apr '04

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

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Chimera-users April 2004