- Chimera-users - RBVI Mailing Lists

Chimera
by Robert Hilton 27 Mar '08

27 Mar '08

When using Chimera, I want to be able to use XY translation. In the help menu, I found that if I hold down the middle mouse button, I can control XY translation. However, I have a mac, and so have no middle mouse button. How can I control XY translation using a mac? Thanks, Rob Hilton hiltonlds(a)gmail.com

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copy cmd in nogui script
by Nick Horelik 26 Mar '08

26 Mar '08

Hi, This (http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-March/001396.html) answered most of my questions, but I have one more followup question. Is there any way for me to accept the POV-Ray Liscence in nogui mode? I don't have the capability to use the gui at this time. Thanks, Nick -- Tufts University 508.527.9625

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Re: [Chimera-users] using chimera on 3D EM map
by Tom Goddard 26 Mar '08

26 Mar '08

Hi Weimin, Thanks for explaining these problems. We intend to solve all of them (though it will take some time) and perhaps some already have solutions. 1) Volume eraser ball can't be made small enough. The ball can have any floating point radius value > 0. So you should be able to make it as small as you like. I've tried and had no trouble making it tiny. A radius value of 0 is not valid and the ball radius will be left at whatever it was prior to attempting to set it to zero. 2) There is no "undo" in volume eraser. Yes. This is a serious problem we plan on fixing. 3) No way to add density (as opposed to subtracting with volume eraser). I guess you mean you would like to use a 3d ball to mark the density you wish to keep instead of the density you want to erase. It might be easy to make a tool like this where you can paint the volume using a ball (like volume eraser). You could paint using one or more colors and then separate the different colored pieces into separate maps. The underlying code to do this is already in Chimera (color zone tool, and split map by color zone). It requires a way to place a marker that matches the painting ball -- basically just a "Color" button on the volume eraser dialog. Might be able to add this soon. I recently added plane by plane loop drawing for hand tracing surfaces that can be used with the new "mask" command to segment out the enclosed region (in current daily builds). But from what you say that is less useful in your high resolution case. 4) Statistical comparison of two maps. Chimera can report the correlation coefficient between two maps and it can optimize the position of one map within another. This tools was called "Fit Map in Map" in the current Chimera production release (version 1.2470) and is called "Fit in Map" (which also handles fitting models) in current Chimera daily builds. There is also a new option in "Fit in Map" that will update the correlation coefficient in real time as you move one map within the second map. Also there is a new "Fit in Map" option that will compute a simulated map from a PDB at a given resolution (like EMAN pdb2mrc) and will fit the simulated map and report its correlation in the experimental map. Are there other measures besides correlation coefficient that you want? From your example, maybe you want rotations in degrees between two different fits? Tom Weimin Wu wrote: > Dear Prof.: > > I am one postdoctoral in Prof. Wenjiang's group. We have employed > Chimera in our research and really appreciate it. However when our 3D > map goes beyond 5A (see Feb. 28, 2008 Nature paper) which enabled us > to see the boundaries among alpha helices and beta sheets, we meet > some problems in the segmentation which we do think you could help us > out. > > One problem is that the viewer eraser ball is too big even the radius > is set to zero. It prevented us from completely clearing the > neighboring signals. There is no undo option when using the eraser > function. Therefore we have to keep saving the intermediate maps. > > Another problem is that there is no 3D volume editor which can let us > add density in 3D EM map. Sometimes this is the most important for the > segmentation, because it is hard to tell which density should be > included if we go slice by slice, but it is much easier to tell > directly in 3D map with the stereo function. > > Another problem is that there is no statistical tool for analyzing the > slight difference between two 3D EM maps. Therefore it makes hard to > determine the fit quality of one map into the other, for example, when > fitting one subunit into the other, there is some conformation > difference between them, but we need quantitative values to evaluate > the difference and make a story. Something like in two PDBs, we can > fit one domain and check the difference of the other domain. > > If I don't explain the problems clearly, please let me know. Many thanks, > > weimin wu

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Re: [Chimera-users] [chimera-dev] fit map in map -- also fit a/pix at the same time ?
by Tom Goddard 26 Mar '08

26 Mar '08

Hi Stefan, Chimera cannot optimize the volume grid spacing when fitting a molecule model. I agree that would be useful. I'll add it to our requested features list. http://www.cgl.ucsf.edu/chimera/plans.html You can do this scale optimization by hand using the volume dialog Coordinates panel to change the voxel size (press the return key after you change the number), then press the Fit button on the Fit in Map dialog. With small scale changes the fit should converge each time and you can quickly try several different scales. The newer Chimera releases (Jan 31, 2008, 1.2492) available on the daily builds page can make a simulated map for your molecule at the desired resolution and report correlation coefficients which is probably better than average map values for this scale optimization. Tom

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Chimera_v1.2470
by Brittney L. Gurda 26 Mar '08

26 Mar '08

Hello, I have a general question about opening files in the new version. Upon opening my EM maps (in .pif format), my structure is in a solid box which makes viewing difficult. Has anyone encountered this problem before? The older version that I had (not sure which one) never had this issue. Currently I am converting the .pif to a .map file and that seems to work just fine, but I am still curious about where the box is coming from and how I can get rid of it...artificial unit cell perhaps? Thanks, Brittney L. Gurda

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pdb to density map function
by Jeff Triffo 25 Mar '08

25 Mar '08

hi, I think I recall seeing information about a pdb -> density map function (like an MRC density map). is this currently implemented/contained within Chimera? I can use an outside program to do this, but if it is already in Chimera I would prefer to do that. thanks, -Jeff

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Displaying volumes with negative densities
by Tom Goddard 24 Mar '08

24 Mar '08

Hi Julio, If you are creating volume contour surfaces where the objects of interest have more negative data values then you should turn off the "cap high values at box faces" option in the volume dialog surface and mesh options panel. Since you view these inverted density maps often you probably want to save that setting using volume dialog menu entry "Features / Save default dialog settings" so Chimera will use it in future sessions. Tom Dr .Julio Ortiz wrote: > Dear Thomas, > > I noticed that when displaying volumes as isosurfaces we can not > visualize negative densities. The volumes turns a solid cube bellow > cero. I can imagine that with volumes coming from some programs of > SPA like in EMAN, this is not a matter, because they use > protein=white. But we are always using protein=black. > > I wanted to ask you if there is a simple way to correct that, because > I love to use chimera for fast check of my volumes and it will be not > fun to change the contrast each time. > > Just for your info: the last version that works for me was: > chimera-1.2422-win32 > > Greetings, > Julio

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Principal axis of inertia
by Jean-Didier Maréchal 21 Mar '08

21 Mar '08

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 -- Dr. Jean-Didier Maréchal Professor Lector Computational Bioorganic and Bioinorganic Chemistry @Transmet Office C7/018 Edifici C.n. Campus de Bellaterra Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra, Catalunya, Spain Tel: (+34).935814936 Fax: (+34).935812920 e-mail: jeandidier.marechal(a)uab.es www: http://asklipio.qf.uab.es/cmc

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BILD object question
by William Jeffrey Triffo 21 Mar '08

21 Mar '08

hello, I have been writing simple .bild files for BILD objects (arrows, spheres) that I then load into Chimera. what would the commands be in a python script to generate a BILD model within the current session, so that I don't have to keep hand-writing and re-loading the .bild file (the contents of the .bild file are often outputted coordinates from such a script, that I then copy into a text file and load)? thanks, -Jeff

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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

2 1

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)

1 0

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

2 3

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

4 5

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.

4 3

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

2 1

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

1 0

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

2 1

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

1 0

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

3 2

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

2 1

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

1 0

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 > > > > >

2 1

POV-Ray Export
by Greg Williams 27 Feb '08

27 Feb '08

I would like to render my files externally in POV-Ray, but I get error messages. As a test, I set the leucine zipper in wire mode and exported the file. I opened POV-Ray, turned on antialiasing and rendered at 640x480. I immediately get the following: Possible Parse Error: Could not find file 'transforms.inc' File zipper.pov line 6 Parse Warning: Check that the file is in a directory specifed with a +L switch or 'Library_Path=' .INI item. Standard include files are in the include directory or folder. Please read your documentation carefully. File zipper.pov line 6 I cut the line ³#include ³transforms.inc² and rendered again, and I get a new set of parsing errors, which include a couple errant bracket symbols that I managed to fix, at which point I get: Parse Error: Expected 'object or directive', undeclared identifier 'Axis_Rotate_Trans' found instead File zipper.pov line 1322 So I cut the ending lines of the file: Axis_Rotate_Trans(<0.000000, 0.000000, 1.000000>, 0.000000) translate <0.000000, 0.000000, 0.000000> } } Now the render works. I guess I should be happy with that, but I¹m wondering what it was I cut from the file. Any help here? Thanks, Greg

2 1

command line mode
by snoze pa 26 Feb '08

26 Feb '08

Dear Chimera Users, How can I use chimera in --nogui mode to screen 1000 compunds from ZINC database and save them in to mol2 format. Is there any script so that I can convert preselected 1000 compound from ZINC database and convert them t o mol2 format so that I can use them in DOCK program. thanks in advance

3 5

Making an omnimax POVray movie
by Kristina Furse 26 Feb '08

26 Feb '08

Hi- We're interested in using Chimera to prepare POVray files for a movie to be shown on a hemispherical dome. The first part of the movie will be a 360 degree rotation of a DNA/drug complex showing water occupancy around the drug, and the second half will come from an AMBER MD trajectory. We've figured out the content and rendering. The two remaining issues are that the camera must be changed from "perspective" to "omnimax" (fisheye), and the extensive rendering time that will be required for the large system at very high resolution (4096x4096). Here is our plan: 1. Use a command-line script to rotate the system and export the scene to x3d files. 2. Use per-frame scripting in MD movie to export each trajectory frame to x3d files. 3. Use x3d2pov to translate into *.pov files. 4. Change the camera from perspective to omnimax in each .pov file. 5. Render the individual images in parallel on our cluster using povray (different version than the one that ships with Chimera). 6. Compress to jpeg. 7. Assemble movie as .mov (format compatible with projection system in the dome). Does anyone have a better idea? I'm assuming that I can't change the camera to omnimax from within Chimera? Thanks for any suggestions! Kristina -- Kristina Furse Postdoctoral Research Associate 262 Stepan Chemistry Hall Notre Dame, IN 46556 (574)631-3904

2 2

[chimera-users] --nogui
by 吴超 25 Feb '08

25 Feb '08

Hi, folks! I came across with a problem when using chimera --nogui file.cmd > data.log the file.cmd is as follows: open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C2 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C3 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C4 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C5 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C6 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@S overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C7 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C12 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CF overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CH overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CI overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C11 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@O11 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@N8 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C9 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@O9 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@N10 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CA overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@OB overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CC overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CD overlap -1 hbond 0 ignoreIntraRes true log true If i use the graphic version and read the cmd file, it worked quite well and I can find all I need in the reply log. But when it came to the nogui version, the data file only contains the result of the first two lines of the cmd file. That is open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true Results are: Opening 1C1C.pdb... 1 model opened Opened 1C1C.pdb containing 1 model, 7997 atoms, and 1096 residues Allowed overlap: -1 H-bond overlap reduction: 0 Ignore overlap between atoms separated by 4 bonds or less Ignore intra-residue overlaps 5 overlaps atom1 atom2 overlap distance #0:999.het@C1 #0:100.A@CD1 -0.352 4.112 #0:999.het@C1 #0:100.A@CD2 -0.643 4.403 #0:999.het@C1 #0:188.A@CD2 -0.723 4.363 #0:999.het@C1 #0:188.A@CB -0.883 4.643 #0:999.het@C1 #0:188.A@CG -0.989 4.479 Error in the shell is as follows: $ /usr/local/chimera/bin/chimera --nogui /home/lynn/cmd/1C1C.cmd > /home/lynn/project/data/distance/1C1C.dist Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in ? value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 358, in init replyobj.reportException( File "CHIMERA/share/chimera/replyobj.py", line 610, in reportException File "CHIMERA/share/chimera/replyobj.py", line 438, in nogui_message ValueError: I/O operation on closed file $ Could anyone give me hand? I am really frustrated! Thanks in advance... -- 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

2 1

NOT ABLE TO VIEW SURFACE USING PHYRE MODEL DATA
by nyyount＠cox.net 25 Feb '08

25 Feb '08

Hi, I have not been able to view my Phyre pdb files using Chimera�s surface view. I get the error code -1073741785 and am immediately shut out of the program. I am not a computer person � yet. Are there any quick fixes that I can add to my Phyre generated PDB files to be able to view them in �surface� view? I�m very pleased with Chimera and have used it for all of the molecular graphics for our next publication. I would like to be able to view my Phyre models using the same software. Thank you! Nannette Y. Yount, Ph.D. Harbor-UCLA

3 2

save manipulated electron density maps in spider
by Jan-Christian Schuette 25 Feb '08

25 Feb '08

Dear Chimera Developers, I quite often have to manipulate electron density maps in the spider format. When using chimeras volume eraser function, it doesn't allow me to save the new map back to spider or another easy-to-convert file format (such as brix or ccp4). I would be great if you could add such a feature in the next version of the software. Best regards, Jan-Christian Schuette

3 2

Re: [Chimera-users] distance
by Elaine Meng 22 Feb '08

22 Feb '08

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.

3 2

Driving matchAtoms from the IDLE
by Jean-Didier Maréchal 22 Feb '08

22 Feb '08

Hi Guys, I'd like to superpose two inorganic complexes using two differently "ordered" atom sets. My compound has quite similar substructures but I am sure at all what is the best "ordered" selection of atom pairs to align. Therefore, I'd like to make a "extensive" search (with an heuristic approach to define...) passing by the idle. I am unfortunately missing something before getting to this point! Lets say that I just want to align the nitrogen atoms of the my two structures. I have: import chimera import numpy from chimera import match from chimera import runCommand runCommand("select #1@N=") an1=chimera.selection.currentAtoms() runCommand("select #0@N=) an2=chimera.selection.currentAtoms() chimera.match.matchAtoms(an1,an2) And then it's when I am already stuck! the resulting prompt does not provide mistake an gives: chimera.match.matchAtoms(an1,an2) (<_chimera.Xform object at 0x9463ef8>, 0.034256915079603358) But how this results can be send to the graphical window? I guess I have to use the Xform object, but I can not clearly understand how to do this. Thanks for any help! JD On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > 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: distance (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Feb 2008 09:00:37 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] distance > To: "??" <lynnwuchao(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed > > Hi! > > 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. > > 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 20, 2008, at 11:38 PM, ?? wrote: > > > Hi, folks, > > I select two atoms and measured their distance using the command > > distance and can see the exact distance value in the graphic > > interface, but when I go the log file i can not find it. > > Can anybody give me a hand and tell me why can I find it? Thanks.. > > _______________________________________________ > > 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 58, Issue 24 > *********************************************

2 1

placing a helium atom at a given position.
by Jean-Didier Maréchal 22 Feb '08

22 Feb '08

Hi again, that follows an e-mail exchange with Eric a while ago. I am trying to place a given atom (for the moment, helium is fine) to given x,y,z coordinates. You told me that the new BuildStructure module could do that, unfortunately after having imported the module import BuildStructure when I do BuildStructure.placeHelium(res,model=0,position=13.2909,75.4474,25.4248) I have SyntaxError: non-keyword arg after keyword arg I tried different argumentations of this but I can't have it working, if you can tell me how to do this, that would be perfect. All the best, JD some time ago Eric On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > 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: distance (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Feb 2008 09:00:37 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] distance > To: "??" <lynnwuchao(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed > > Hi! > > 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. > > 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 20, 2008, at 11:38 PM, ?? wrote: > > > Hi, folks, > > I select two atoms and measured their distance using the command > > distance and can see the exact distance value in the graphic > > interface, but when I go the log file i can not find it. > > Can anybody give me a hand and tell me why can I find it? Thanks.. > > _______________________________________________ > > 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 58, Issue 24 > *********************************************

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managing bond order
by Victor Kenyon 21 Feb '08

21 Feb '08

hi all, typically when i import a paired back active site of a protein, chimera wants to connect atoms that should not be connected. is there a way to select bonds that violate a certain bond length so i can remove them? or a possible work around? thanks for your help. victor Victor A. Kenyon kenyon(a)chemistry.ucsc.edu 831.252.7667.

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distance
by 吴超 21 Feb '08

21 Feb '08

Hi, folks, I select two atoms and measured their distance using the command distance and can see the exact distance value in the graphic interface, but when I go the log file i can not find it. Can anybody give me a hand and tell me why can I find it? Thanks..

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modifying presets
by glenn millhauser 20 Feb '08

20 Feb '08

Hi Folks, Is there a way to edit the Presets to include additional protein features? Specifically, I work with quite a few disulfide rich proteins and it would be great to select the Preset Interactive 1 and have it automatically draw Cys side chains with disulfide links. Many thanks, glenn Glenn L. Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 566 3337 cell 831 459 2935 fax http://chemistry.ucsc.edu/~glennm http://www.chemistry.ucsc.edu/faculty/millhauser.html

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Re: [Chimera-users] [chimera-dev] change hand ?
by Tom Goddard 20 Feb '08

20 Feb '08

Hi Stefan, You can flip the hand of the map by making the grid spacing negative along one axis. Chimera wasn't intended to do this so I'm not sure everything will work correctly. To make this change use the volume dialog Coordinates panel and change voxel size from (for example) 0.37 to 0.37 0.37 -0.37. The three numbers are grid plane spacing along the x, y, z axes. If they are all the same Chimera just shows one number. In Chimera 1.2470 the volume surface will become dark. To remedy this use the volume dialog Surface and Mesh options panel and turn off "two-sided surface lighting". A current Chimera daily build will not have that problem. Chimera won't correctly save the flipped map. So this is not an ideal way to proceed. I don't know of software that will write out the flipped map though it must exist. Tom Stefan Backstrom wrote: > Hi. > > Is it possible to flip the hand of a cryo-EM map in chimera ? > > Best wishes, > > Stefan Bäckström > Medical Biochemistry and Biophysics > Umeå University > Sweden > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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volume rendering depth issue with multiple volumes (segmented layers)
by William Jeffrey Triffo 19 Feb '08

19 Feb '08

hello, I remember past posts mentioning depth issues when rendering multiple volumes. I have several layers (6) that I have segmented out individually. Last night, they appeared to render 'in order' (the layers are parallel, and up to 6 thus overlap if rotated into the correct view). this morning, though, I notice that 'volume 2' is rendering 'on top' of everything else. is there a way I can trick this to work, or is there something I may be missing / clicked wrong? thanks, -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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menssage error
by DRT/BA - Elias Silva dos Santos 19 Feb '08

19 Feb '08

Hi!! I am preparing a molecule for docking that he has two centers of iron sulphur [ 4FE-4S]+2 and one molecule of FAD. When trying to place loads I am recebeno error messages (DOCK Prep). As I must proceed to decide the problem Elias

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Mac OSX install issue: SOLVED
by Greg Williams 19 Feb '08

19 Feb '08

Thanks for the help. An upgrade from X11 1.1.1 to 1.1.3 solved the problem. GW

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