- Chimera-users - RBVI Mailing Lists

turning off PipesAndPlanks or Axes
by Boaz Shaanan 21 Mar '08

21 Mar '08

Hi, How do I turn off PipesAndPlanks once they're depicted ? The same holds for Axes. (build 2492). Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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source headers, release
by Randy Heiland 20 Mar '08

20 Mar '08

Before I attempt to rebuild a plugin, can someone tell me if the 1.2349 headers that you currently provide: http://www.cgl.ucsf.edu/ chimera/sourcecode.html will play nice with the current, 1.2470, release? thanks, Randy

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problem with 17/03 build linux 64
by Jean-Didier Maréchal 19 Mar '08

19 Mar '08

Hi guys, thanks a lot for the different answers. I wanted to test Elaine's suggestion and I install the last linux 64 build. When running chimera I have: Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 304, in init from chimera import tkgui File "CHIMERA/share/chimera/tkgui.py", line 80, in <module> File "CHIMERA/share/chimera/printer.py", line 444, in <module> AttributeError: 'module' object has no attribute 'No' Some problem in my installation ? All the best JD El mié, 19-03-2008 a las 12:00 -0700, chimera-users-request(a)cgl.ucsf.edu escribió: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Principal axis of inertia (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Mar 2008 11:47:51 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Principal axis of inertia > To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <DDE1C65B-AD42-48C1-9414-91625662D812(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed > > Just wondering why you weighted by atomic number rather than mass > (a.element.mass)? > > --Eric > > On Mar 19, 2008, at 11:42 AM, Tom Goddard wrote: > > > Hi JD, > > > > Attached is a script that computes the inertia axes of molecules. > > Open a molecule, then open the script. It will print the axes in > > the reply log and show an inertia ellipsoid. It is weighting the > > atoms by their atomic number, not by the average isotopic mass. > > Tested in Chimera 1.2498. Should work in older Chimera versions. > > > > Tom > > > > Jean-Didier Mar?chal wrote: > >> Hi everyone, > >> > >> I was wondering if there is a method available to calculate the > >> principal axis of inertia of a protein (or a part of a protein) in > >> chimera? > >> > >> If not what would be the easiest way to move forward? > >> > >> All the best, > >> > >> JD > >> > >> > > > > > > # > > ---------------------------------------------------------------------- > > ------- > > # Compute inertia tensor principle axes for molecule. > > # > > def inertia_ellipsoid(m): > > > > atoms = m.atoms > > n = len(atoms) > > from _multiscale import get_atom_coordinates > > xyz = get_atom_coordinates(atoms) > > anum = [a.element.number for a in atoms] > > from numpy import array, dot, outer, argsort, linalg > > wxyz = array(anum).reshape((n,1)) * xyz > > mass = sum(anum) > > > > c = wxyz.sum(axis = 0) / mass # Center of mass > > v33 = dot(xyz.transpose(), wxyz) / mass - outer(c,c) > > eval, evect = linalg.eigh(v33) > > > > # Sort by eigenvalue size. > > order = argsort(eval) > > seval = eval[order] > > sevect = evect[:,order] > > > > return sevect, seval, c > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def ellipsoid_surface(center, axes, lengths, color = (.7,.7,.7,1)): > > > > from Icosahedron import icosahedron_triangulation > > varray, tarray = icosahedron_triangulation(subdivision_levels = 3, > > sphere_factor = 1.0) > > from numpy import dot, multiply > > es = dot(varray, axes) > > ee = multiply(es, lengths) > > ev = dot(ee, axes.transpose()) > > ev += center > > > > import _surface > > sm = _surface.SurfaceModel() > > sm.addPiece(ev, tarray, color) > > return sm > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def show_ellipsoid(axes, d2, center, model): > > > > from math import sqrt > > d = [sqrt(e) for e in d2] > > sm = ellipsoid_surface(center, axes, d) > > sm.name = 'inertia ellipsoid for %s' % m.name > > from chimera import openModels as om > > om.add([sm], sameAs = model) > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def print_axes(axes, d2, m): > > > > from math import sqrt > > paxes = ['\tv%d = %6.3f %6.3f %6.3f d%d = %6.3f' % > > (a+1, axes[a][0], axes[a][1], axes[a][2], a+1, sqrt(d2[a])) > > for a in range(3)] > > from chimera.replyobj import info > > info('Inertia axes for %s\n%s\n' % (m.name, '\n'.join(paxes))) > > from Accelerators.standard_accelerators import show_reply_log > > show_reply_log() > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > from chimera import openModels as om, Molecule > > mlist = om.list(modelTypes = [Molecule]) > > for m in mlist: > > axes, d2, center = inertia_ellipsoid(m) > > print_axes(axes, d2, m) > > show_ellipsoid(axes, d2, center, m) > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 59, Issue 18 > *********************************************

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Un-tile
by Jim Nettles 19 Mar '08

19 Mar '08

Thanks that is a useful function I hadn't explored. However, how to you un-tile to go back to a previously aligned system? Thanks, Jim > > Message: 4 > Date: Wed, 19 Mar 2008 16:53:11 +0530 > From: "Bharat Yadav" <bharatbioinformaticshau(a)gmail.com> > Subject: [Chimera-users] Requesting to solve my poblem > To: chimera-users(a)cgl.ucsf.edu > Message-ID: > <e162fe4e0803190423k5651193amf41e192251b613c3(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hello Sir / Madam > > Good Evening > > My name is Bharat Yadav and I am perusing Master's Degree in > Bioinformatics from Chaudhary Charan Singh Haryana Agriculrual > University - Hisar (India). I am working here on Molecular Modeling. > With a long time I am using UCSF Chimera. It is the one of wonderful > Molecular visiualization software haivng some very peculear features. > Respected Sir / Madam, In my present work I am facing a bit problem. > Hoping form you to help regarding this. My problem is as follows. I > have generated five models of protein. when I open all these modles > these were overlapping each other. I want to view all these five > models in a single panel non overlapping. I mean I want to view these > 3D models in panel as follows > ----------------------------------------- > | | | > | | | > | Model 1 | Model 2 | > | | | > ----------------------------------------- > | | | > | | | > | Model 3 | Model 4 | > | | | > ----------------------------------------- > | | | > | | | > | Model 5 | Model 6 | > | | | > ----------------------------------------- > > Hope that you now easily understand what actually I want. Please Help > me regarding this and mail me its solution or steps or commands for > this task. Please free to ask any question. > > Thanks in anticipation > > Warm regards from Bharat Yadav > > > ------------------------------ > > Message: 5 > Date: Wed, 19 Mar 2008 10:11:52 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Requesting to solve my poblem > To: "Bharat Yadav" <bharatbioinformaticshau(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <37BB555C-E967-43BB-B6EA-5CD8A75853FD(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Bharat, > > Thanks for your kind words! I think you just need to use "tile" in > the Model Panel. Open Model Panel (Favorites... Model Panel). In > there, choose all 5 models on the left side. Then, on the right, > change the menu from "frequently used" to "infrequently used" - now > there should be a "tile" button on the right - try using that. > > I hope this helps, > 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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Data of Slice display
by Jason 19 Mar '08

19 Mar '08

Hi all I am using slice display to plot the profile of density map. That is the function that I want to exam the profile of virus density map without spherical average. Where can I get the data of each dot of profile, so I can plot profile at Excel for further use. Thank you for your help Kind regards Jason Chen -- Open WebMail Project (http://openwebmail.org)

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Average slab thickness
by Tom Goddard 19 Mar '08

19 Mar '08

Hi Jeff, The Chimera mask command code can be adapted to calculate the average thickness of a slab defined by two surfaces. I've attached the adapted Python code. You select the surfaces then open the script and it reports the mean thickness, standard deviation of thickness, min/max thickness and number of thickness samples used. The script contains a projection axis which should be perpendicular to the slab and a grid step which defines the grid spacing. The thickness is measured on a grid perpendicular to the axis and only grid points where the projection axis intersects the surfaces at least twice are used. You have to edit the script (at the bottom) to set the projection axis and grid step to appropriate values. Those values could be automatically set using the Python code of the inertia ellipsoid script I gave you earlier. Tested in Chimera version 1.2498 on a spherical surface. Tom Jeff wrote: > hi Tom, > > I'd like to compute the 'average distance' between two surfaces to > calculate the width of a cellular compartment (have attached an image, > the two surfaces delineating the compartment are colored blue). > > one way that has been suggested to me is to calculate the volume > between the two surfaces, and then just divide by a mean path length > along one of the surfaces. I know that chimera has a volume > calculation tool for an isosurface, and was wondering if I could use > the surfaces you see to do a volume calculation (and, if so, how I > would go about capping those surfaces to create a closed surface). If > able to calculate the volume that way, I could just use the path > length of a contour (which I have) that generated one of the two > surfaces to derive the "average width". > # ----------------------------------------------------------------------------- # Script to calculate average thickness of a slab defined by surfaces. # Adapted from mask command code for Jeff Triffo, March 18, 2008. # # Adapted version of masked_volume() from depthmask.py. # # Only uses first two surface layers along projection axis. # def average_thickness(projection_axis = (0,0,1), grid_step = 1.0, surfaces = None): # Use selected surfaces if none are passed in. if surfaces is None: from Surface import selected_surface_pieces plist = selected_surface_pieces() from Mask.depthmask import surface_geometry surfaces = surface_geometry(plist, tf = None, pad = None) # Determine transform from vertex coordinates to depth array indices from Mask.depthmask import orthonormal_frame fx,fy,fz = orthonormal_frame(projection_axis) from numpy import array, float32, intc, zeros tf = array(((fx[0], fx[1], fx[2], 0), (fy[0], fy[1], fy[2], 0), (fz[0], fz[1], fz[2], 0)), float32) / grid_step # Transform vertices to depth array coordinates. zsurf = [] tcount = 0 for vertices, triangles in surfaces: varray = vertices.copy() from Mask.depthmask import apply_transform apply_transform(tf, varray) zsurf.append((varray, triangles)) tcount += len(triangles) if tcount == 0: return 0,0,0,0,0 from Mask.depthmask import bounding_box vmin, vmax = bounding_box(zsurf) voffset = -(vmin - 0.5) tf[:,3] += voffset from _contour import shift_vertices for varray, triangles in zsurf: shift_vertices(varray, voffset) from math import ceil, floor dxsize = int(ceil(vmax[0] - vmin[0] + 1)) dysize = int(ceil(vmax[1] - vmin[1] + 1)) # Create depth arrays depth = zeros((dysize,dxsize), float32) tnum = zeros((dysize,dxsize), intc) depth2 = zeros((dysize,dxsize), float32) tnum2 = zeros((dysize,dxsize), intc) # Copy volume to masked volume at masked depth intervals. max_depth = 1e37 depth.fill(max_depth) tnum.fill(-1) from Mask.depthmask import surfaces_z_depth any = surfaces_z_depth(zsurf, depth, tnum, None, None) if not any: return 0,0,0,0,0 depth2.fill(max_depth) tnum2.fill(-1) surfaces_z_depth(zsurf, depth2, tnum2, depth, tnum) # Find thicknesses at grid points that intercept surfaces twice. dlist = [] for i in range(dysize): for j in range(dxsize): if tnum[i,j] != -1 and tnum2[i,j] != -1: d = (depth2[i,j] - depth[i,j]) * grid_step dlist.append(d) if len(dlist) == 0: return 0,0,0,0,0 from numpy import mean, std return mean(dlist), std(dlist), min(dlist), max(dlist), len(dlist) # ----------------------------------------------------------------------------- # projection_axis = (0,0,1) grid_step = 1.0 m, sd, mn, mx, n = average_thickness(projection_axis, grid_step) print ('Slab thickness along axis %s sampled at grid spacing %.3g' % (str(projection_axis), grid_step)) print 'Mean %.5g, sdev %.5g, min %.5g, max %.5g, samples %d' % (m,sd,mn,mx,n) from Accelerators.standard_accelerators import show_reply_log show_reply_log()

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Requesting to solve my poblem
by Bharat Yadav 19 Mar '08

19 Mar '08

Hello Sir / Madam Good Evening My name is Bharat Yadav and I am perusing Master's Degree in Bioinformatics from Chaudhary Charan Singh Haryana Agriculrual University - Hisar (India). I am working here on Molecular Modeling. With a long time I am using UCSF Chimera. It is the one of wonderful Molecular visiualization software haivng some very peculear features. Respected Sir / Madam, In my present work I am facing a bit problem. Hoping form you to help regarding this. My problem is as follows. I have generated five models of protein. when I open all these modles these were overlapping each other. I want to view all these five models in a single panel non overlapping. I mean I want to view these 3D models in panel as follows ----------------------------------------- | | | | | | | Model 1 | Model 2 | | | | ----------------------------------------- | | | | | | | Model 3 | Model 4 | | | | ----------------------------------------- | | | | | | | Model 5 | Model 6 | | | | ----------------------------------------- Hope that you now easily understand what actually I want. Please Help me regarding this and mail me its solution or steps or commands for this task. Please free to ask any question. Thanks in anticipation Warm regards from Bharat Yadav

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interface residues
by Francesco Malatesta 17 Mar '08

17 Mar '08

Hello, could anyone help me out with this problem. I would like to exclusively colour interface residues in a dimeric protein represented as spheres or surface. Is this possible? Thank you very much Francesco Malatesta

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preferences - povray - keep input files doesn't
by Klaas Decanniere 17 Mar '08

17 Mar '08

For at least some versions of Chimera, the "keep pov-ray input files" option in the Favorites - Preferences- Pov-ray tab does not work ( .pov files are deleted after rendering during animation) This is true e.g for build 2491 2008/02/11 (Platform: linux2 windowing system x11). Is there a way to force this option? I would like to do some post processing on the .pov files before rendering. An option to generate an animation series .pov files without doing the actual rendering would be even better - how can I do that? Thanks for the help and kind regards, Klaas Decanniere

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segmentation fault - surface rendering
by Michael DiMattia 13 Mar '08

13 Mar '08

Hello, I am trying to surface render a few different proteins within the same Chimera session and I keep encountering a segmentation faullt. I imagine this is due to a memory limit being reached, although I do not know if it is a Chimera parameter that can be increased/overriden. Instead of having the different macromolecules in the same pdb, I have actually split it up into many pdbs and opened them one at a time, surface rendering one at a time. This worked for awhile but it seems I can't even get that far now. Any advice or tips on what I can do? I realize surface rendering is very computationally intensive but I would love to get this to work! Thanks Mike DiMattia

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[chimera-users]torsional angle
by 吴超 11 Mar '08

11 Mar '08

Hi, folks! I have a problem about the measurement of torsional angle. In the chimera users' guide about the command angle, as follows, it says that if I select the atoms simultaneously, the order information will get lost. How can I keep the order information since I need it to calculate the angle I want exactly? For example, in the following command I originally want to calculate the n-ca-c-n(182) dihedral, angle :181.a@n,ca,c:182.a@n but in fact what chimera gave me was may be c-ca-n-n(182). I want to calculate a lot of diheral information so I can not click one by one in the gui mode, I wonder is there any way that I can get what I want . Thanks! Usage: *angle* *atom1 atom2 atom3* [ *atom4* ] *Angle* reports the bond angle for three specified<http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/midas/atom_spec.html…>atoms or the dihedral angle for four specified<http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/midas/atom_spec.html…>atoms. The order of specification is important, but atoms need not be connected. The angle value in degrees is reported in the status line<http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/chimerawindow.html#s…>and *Reply Log*<http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/reply.html>. The atoms can be specified collectively using the word *selected*, *sel*, or *picked* if the current selection<http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/selection.html>contains only the three or four atoms of interest; the order in which the atoms were selected<http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/selection.html>(most likely picked<http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/selection.html#picks…>) is used. When order information is lacking (for example, the atoms were selected simultaneously), the angle actually measured may not be the one intended. There are no automatic updates if the angle changes. A new command must be issued to measure the changed angle. -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206 Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao(a)gmail.com

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pdb format and charges
by Terry Lang 06 Mar '08

06 Mar '08

Hey Everyone, I would like to use Chimera to write charges for a pdb file in the b-factor column. I feel like this is possible but couldn't quite figure out how to do it. Sincerely, Terry -- P. Therese Lang Post Doc Alber Lab, UC Berkeley

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one question about slicing
by Martin 06 Mar '08

06 Mar '08

Hi, I write in this mail to ask your great help on the slicing of MRC files. I want to slice a map in MRC format in half and save it as a new MRC file which only contains the remaining half map. However, it seems that the "Per-Model Clipping" function of Chimera can only work on the visualization mode, without connection to the "Save map as" function to attain a new map file. I am wodering if there is any other method to realize my intention. Thank you very much! Sincerely yours, Jian

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Unit cell coordinates, Python / Chimera
by Tom Goddard 05 Mar '08

05 Mar '08

Hi Rachel, Attached is Python code that prints the unit cell axes of open PDB models to the reply log. You open the PDB models, then open this script, and the results appear in the reply log (menu Favorites / Reply Log), for example: 1a0m.pdb unit cell axes a axis = 44.400 0.000 0.000 b axis = 0.000 44.400 0.000 c axis = 0.000 0.000 23.500 I figured out the needed Chimera calls by looking at the Chimera Python code for the Unit Cell tool located in your Chimera distribution in chimera/share/UnitCell/__init__.py and I homed in on the show_outline_cb() function to quickly figure out the attached code. On the Mac this code is in Chimera.app/Contents/Resources/share/UnitCell/__init__.py and to look inside the Chimera.app folder click on its icon with the ctrl key held and select "Show Package Contents". Tom > *From: *Rachel Karchin > *Date: *March 4, 2008 5:42:36 PM PST > > Me again. Is there a way to get the coordinates of the unit cell > vertices or the plane equation from Chimera running through a python > script? > > Tx!! > > -- rk # Get currently opened PDB models from chimera import openModels, Molecule mlist = openModels.list(modelTypes = [Molecule]) # Print crystal unit cell axes for each molecule. from PDBmatrices.crystal import crystal_parameters, unit_cell_axes for m in mlist: a, b, c, alpha, beta, gamma, space_group, zvalue = \ crystal_parameters(m.pdbHeaders) a_axis, b_axis, c_axis = unit_cell_axes(a, b, c, alpha, beta, gamma) print m.name, 'unit cell axes:' print ' a axis = %8.3f %8.3f %8.3f' % tuple(a_axis) print ' b axis = %8.3f %8.3f %8.3f' % tuple(b_axis) print ' c axis = %8.3f %8.3f %8.3f' % tuple(c_axis)

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Step through trajectory from command line?
by Kristina Furse 05 Mar '08

05 Mar '08

Hi- Can you advance a trajectory by one frame from the command line, or do you have to use the controls in the MD Movie panel? Thanks, Kristina -- Kristina Furse Postdoctoral Research Associate 262 Stepan Chemistry Hall Notre Dame, IN 46556 (574)631-3904

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Graphics cards for Mac
by Tom Goddard 04 Mar '08

04 Mar '08

Here's a comparison of Chimera graphics benchmarks for the current standard PowerMac graphics versus the top-of-the-line graphics: Radeon HD 2600 - no additional cost Quadro FX 5600 - $2850 additional cost Surfaces and meshes: 1.8x faster Volume solid style: size 443**3 vs 325**3. Quadro system was limited 32-bit main memory address space. Molecule: Neglible difference for 34000 atom model in wire, stick, ball and stick, ribbon, sphere styles. The Quadro card has 1.5 Gbytes of memory and will probably have significantly higher performance on solid style volume rendering if the Chimera volume display code is optimized. Probably adding more main memory will not help because the limitation is the 32-bit address space (a limit of Mac OS graphical applications). The Quadro card did not correctly display volume data in solid style with 3d textures (solid rendering 2d texture option turned off) -- displayed a chessboard pattern. Did not test 3d textures on Radeon card. Tom

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scens/movies rendered with povray
by Klaas Decanniere 03 Mar '08

03 Mar '08

Hello, The option to make movies using povray works nice and easy, so I want to push the boundaries a bit :-) - the standard texture included in the .pov files has a very simple finish - is there an easy way to include a spiced-up version? - when not using a "wait" command, several movements (roll, move, scale) are combined. When using the wait command, movements become separated with a small "hesitation" before the second movement starts. Is there a way to minimize this hesitation? Thanks, Klaas P.S.: if you know why powerpoint would play a movie fine 3 or 4 times in a row and then fail after that (nothing else changes, except maybe time), please let me know.

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saving positions
by William Jeffrey Triffo 03 Mar '08

03 Mar '08

hello, if I have used 'savepos' to save several orientations in a chimera session, is there a way to list these positions if I have forgotten what I named some of them? thanks, -Jeff

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Re: [Chimera-users] longer bonds in image
by Elaine Meng 03 Mar '08

03 Mar '08

Hi Bala, This is an expected behavior of Chimera: the ribbon is a smoothed path that does not go exactly through the atom positions. When ribbon is shown, the default is to simply draw the longer or shorter bonds where the ribbon is farther from or closer to the displayed atoms (ribose/base or amino acid side chain) than are the backbone atoms that the ribbon represents. However, there are ways to change the behavior: (A) use the command "ribbackbone" to allow display of both backbone atoms and ribbon. This will not make any bonds look longer or shorter, but it is usually ugly because the ribbon is not in the same place as the backbone atoms. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html (B) with Ribbon Style Editor, "Residue Class" section, you can set which atoms control the ribbon path and which are hidden automatically (by default, without using "ribbackbone") when ribbon is shown: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ ribbonstyle.html I hope this helps, 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 P.S. you can send attachments such as images to chimera-users, but the message will not appear until the moderator has a chance to approve it... just be patient and it will be sent! On Mar 2, 2008, at 9:00 PM, bala wrote: > -----Original Message----- > From: bala > Sent: Fri 2/29/2008 12:13 PM > To: chimera-users(a)cgl.ucsf.edu > Subject: longer bonds in image > > Hi all, > > Thank you for the suggestions for my previous query. > > When the ribbons are displayed for the backbone of a RNA molecule. > Some of the bonds look longer than usual. Herewith i have attached > the image of a RNA molecule in which residues colored in cyan have > some bonds longer in appearance. Kindly help me to get this of this. > > Thanks, > Bala

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surface "holes"
by Fabian Gmail 29 Feb '08

29 Feb '08

Hi all, I enjoy very much using chimera, I have a question regarding surfaces. When I am working on a multi chain protein complex, and I want to present only one chain as surface and the others as ribbon or sticks, oftenly the surface present "holes" on the contact points with the ribbon. I understand they represent contact points between the chains, but I don't like how the surface looks like. Is there a way to avoid this? (I do that but uploading another copy of the chain). Thanks a lot, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

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longer bonds in image
by bala 28 Feb '08

28 Feb '08

Hi all, Thank you for the suggestions for my previous query. When the ribbons are displayed for the backbone of a RNA molecule. Some of the bonds look longer than usual. Herewith i have attached the image of a RNA molecule in which residues colored in cyan have some bonds longer in appearance. Kindly help me to get this of this. Thanks, Bala

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Re: [Chimera-users] command line mode
by snoze pa 28 Feb '08

28 Feb '08

Hi Eric, Is there some API with examples of chimera available. I am trying to add hydrogen in previous script. I tried cmdAddH and simpleAddhydrogens but it is not working. I am trying to put hydrogen and then charge to each ligand in the database. May be later I will call mmtk minimization from chimera itself to minimize each ligand. thanks in advance s

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calculating interphosphate distance
by bala 28 Feb '08

28 Feb '08

Dear chimera users, i) Greetings. I have a trajectory of 1000 conformations of a RNA molecule. I want to see the distribution of interphosphate distance. say i want to see the P-P distance of the residue 3 paired with a residue 38 in the opposite strand. Is it possible in anyways. ii) Suppose when i source a file from command line option : source dist, chimera nicely takes the distance commands in the file and displays the distances in the GUI. Is it possible to send the output to a file rather than seeing in GUI. Thanks, Bala

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distance in log
by 吴超 28 Feb '08

28 Feb '08

Hope it helps... And thanks Elaine and Eric again! :) ---------- Forwarded message ---------- From: 吴超 <lynnwuchao(a)gmail.com> Date: 2008/2/23 Subject: [Chimera-users] distance To: Eric Pettersen <pett(a)cgl.ucsf.edu> Cc: Elaine Meng <meng(a)cgl.ucsf.edu>, Chimera BB <chimera-users(a)cgl.ucsf.edu> Thanks very much, Elaine and Eric! Both of methods worked very well... On Sat, Feb 23, 2008 at 4:00 AM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > In particular, if you have a script (name "dist.com" for instance) > that sets up your distance measurements, something like: > > dist :12@c :17@c > dist :14@c :19@c > > Then you could run chimera like this: > > chimera --nostatus --nogui pdb:1gcn dist.com printDist.py > > to produce: > > #0:12.A@C <-> #0:17.A@C 8.74043923381 > #0:14.A@C <-> #0:19.A@C 8.19707020831 > > on standard output. You could redirect the output into a file named > "dist.out" with: > > chimera --nostatus --nogui pdb:1gcn dist.com printDist.py > dist.out > > --Eric > > On Feb 22, 2008, at 11:40 AM, Elaine Meng wrote: > > > Hi! > > Eric has kindly provided a python script (attached at the bottom) > > that will write all the current distance measurements to the Reply > > Log. Just open the python file with Chimera and it will happen. > > > > Alternatively, depending on your situation, you could use > > "findclash," as discussed in these chimera-users messages a few > > months ago: > > > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ > > 002061.html > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ > > 002069.html > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ > > 002070.html > > > > I hope this helps, > > 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 Feb 21, 2008, at 5:24 PM, 吴超 wrote: > > > >> Thanks, Elaine! > >> The problem is that I want to automatically calculate a number of > >> distances in non-gui interface, and sent the date to a file, just > >> like the logfile. > >> So is there a chance that I can achieve it using chimera? > >> > >> On Fri, Feb 22, 2008 at 1:00 AM, Elaine Meng <meng(a)cgl.ucsf.edu> > >> wrote: > >> > >> The distances are listed in a separate dialog - choose "Tools... > >> Structure Analysis... Distances" from the menu to open that dialog. > >> You can adjust the number of decimal places in the measurement, and > >> there is a "Save" button if you want to save distances or other > >> measurements to a text file. > > > > <printDist.py> > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206 Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao(a)gmail.com -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206 Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao(a)gmail.com

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Re: [Chimera-users] minimize command
by snoze pa 27 Feb '08

27 Feb '08

Elaine, I guess i can use either 'minimize' or "addh and addcharge" otherwise it will run the antechamber twice. *minimize is working fine but i can not save the result in mol2 format using COMMAND option. I try wrtiemol2 but it is not accepting it as a command. save is also not saving in mol2 format. *Any help, thanks in advance. s * * On Wed, Feb 27, 2008 at 5:48 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Conrad, > From looking at the documentation, sounds like you can't use the > minimize command with any nondefault settings of Dock Prep, addh, and > add charge. Is that correct? > > It would be nice if it could tell that you already added hydrogens > and charges to your liking and skip those steps. However, since this > is all done via Dock Prep, that may or may not be possible. > 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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