- 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 > *********************************************

2 1

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.

2 1

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..

2 1

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

2 4

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 >

2 2

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

2 4

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

2 1

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

1 0

Raytracing
by Bernard Heymann 19 Feb '08

19 Feb '08

Hi I'm trying to use povray directly from Chimera and everything works. However, the isosurface of my density comes out practically black, even though the clipping plane is rendered fine. I played a bit with lighting, but that does not seem to make a difference. Could you give me some guidance? I can send an output picture if needed. Bernard Heymann Rm 1515, 50 South Dr, NIH, Bethesda, 20892-8025 Tel 301-451-8241, Fax 301-480-7629

3 2

Mac OSX install issue
by Greg Williams 19 Feb '08

19 Feb '08

I am running OSX 10.4.10 on an iMac with a 2.16 GHz Intel Core 2 Duo, 1 GB 66h MHz DDR2 SDRAM. I have installed X11 1.1.1 XFree86 4.4.0. I have downloaded the current production release of Chimera for Mac X11. The application doesn't open, either on a double click from the desk top or from the dock. I have also tried the Snapshot release dated 2-11-8, with the same result. The application will not open. I have also tried the Mac OSX (Aqua) version of 6-21-7. This version does open, and it works well, in limited doses. However, it is very unstable and closes spontaneously after a few minutes of work. Any ideas what may be incompatible between the X11 versions and my Mac? Thanks, Greg Williams

3 2

surface color and coloring particular residues
by Michael DiMattia 19 Feb '08

19 Feb '08

hello, Is there a way to both color a surface-rendered protein by radius AND simultaneously color certain residues of the same chain with a distinct color? I have figured out how to do each one of these tasks, but can't seem to get both colorings to remain at the same time on the same protein. If I color by radius using "surface color" and then decide to highlight a particular residue, the particular residue is indeed colored, but at the expense of losing the color by radius to whatever color the protein was before that. thanks. mike

2 1

Viewing mode
by James Fethiere 19 Feb '08

19 Feb '08

Hi, I'm trying to save an image of an EM map with atomic models fitting in and can't get pov-ray to write-out the displayed image. Using the side view panel, I cut out part of the surface and models to get the view I want. When I save the image without pov-ray, I get what is displayed but when I try using the pov-ray option, I get the full map and models without the clipping I imposed using the side view mode. What would be the right procedure? Thanks James

2 1

color by radius and other color simultaneously
by Michael DiMattia 18 Feb '08

18 Feb '08

hello, Is there a way to both color a surface-rendered protein by radius AND simultaneously color certain residues of the same chain with a distinct color? I have figured out how to do each one of these tasks, but can't seem to get both colorings to remain at the same time on the same protein. If I color by radius using "surface color" and then decide to highlight a particular residue, the particular residue is indeed colored, but at the expense of losing the color by radius to whatever color the protein was before that. thanks. mike

1 0

selection of different part of the protein through the sequence prompt
by Jean Didier Pie Marechal 16 Feb '08

16 Feb '08

Hi guys, I'd like to select two precise beta strands of my prot and I thought it would be easier to do so from the sequence editor. Unfortunately, I can't find a way to select different parts of the same protein in the sequence editor; I alwys select the full length between first and last selected residues whatever combo I use (shift, ctrl and so on). Is it possible to do this in the sequence editor? Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Febrer 13, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 58, Issue 15 > 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. Split into models (Sadler, Evan) > 2. Re: Split into models (Elaine Meng) > 3. Opaque volume planes (Tom Goddard) > 4. Re: Opaque volume planes (William Jeffrey Triffo) > 5. Re: Opaque volume planes (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 12 Feb 2008 17:51:30 -0600 > From: "Sadler, Evan" <ESADLER(a)dom.wustl.edu> > Subject: [Chimera-users] Split into models > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <C3D78D22.18B15%esadler(a)dom.wustl.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Recent email address change caused the first try to bounce, so I > resent it. > > I've loaded a file (2rjp.pdb) with 4 chains and want to split it > into 4 > models so I can align them. But "split" returns: > > unrecognized command: "split" > > What am I doing wrong? > > Evan > > -- > J. Evan Sadler, M.D., Ph.D. > Howard Hughes Medical Institute > Washington University > 660 S. Euclid Ave., Box 8022 > St. Louis, MO 63110 > Tel: 314-362-9067 > FAX: 314-454-3012 > email: esadler(a)im.wustl.edu > > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 Feb 2008 16:09:22 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Split into models > To: "Sadler, Evan" <ESADLER(a)dom.wustl.edu> > Cc: chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <84C5F9DD-BED6-4476-B29C-F39C322D4BEB(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Evan, > You must be using a version of Chimera older than the "split" > command. If you use the documentation that came with your download > > (opened from the Help menu) it should be fairly synchronized with > your software and you won't get confused by features you don't > have! > However, in this case, just get a newer version. > > The pages at our web site under http://www.cgl.ucsf.edu/chimera/ > docs/UsersGuide/ > > are "development documentation," which I am constantly changing as > Chimera changes. It will generally have newer things than your > downloaded software. > > The pages under http://www.cgl.ucsf.edu/chimera/current/docs/ > UsersGuide/ > > are documentation for the most recent production release (currently > > Nov 2007) and I see it also lists "split". So to use that feature > you can get that production release: > http://www.cgl.ucsf.edu/chimera/download.html#production > > There are also much newer "daily builds" although they are > essentially untested and exist mainly to provide access to the very > > latest developments. > http://www.cgl.ucsf.edu/chimera/download.html#production > > I just tried your structure in the production release and last > night's daily build; "split" worked in both, so you should be all set! > 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 12, 2008, at 3:51 PM, Sadler, Evan wrote: > > > Recent email address change caused the first try to bounce, so I > > resent it. > > > > I've loaded a file (2rjp.pdb) with 4 chains and want to split it > > into 4 > > models so I can align them. But "split" returns: > > > > unrecognized command: "split" > > > > What am I doing wrong? > > > > Evan > > > > -- > > J. Evan Sadler, M.D., Ph.D. > > Howard Hughes Medical Institute > > Washington University > > 660 S. Euclid Ave., Box 8022 > > St. Louis, MO 63110 > > Tel: 314-362-9067 > > FAX: 314-454-3012 > > email: esadler(a)im.wustl.edu > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > Message: 3 > Date: Tue, 12 Feb 2008 17:41:06 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: [Chimera-users] Opaque volume planes > To: William Jeffrey Triffo <triffo(a)rice.edu>, "'Chimera BB'" > <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B24AB2.3060501(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Jeff, > > The trouble obtaining opaque volume planes is not related to > volume > plane display being built into the volume dialog. It is related to > a > change I made in how transparency is handled in solid mode back in > Aug 2007. > > Today I changed transparency in "solid" style volume rendering so > it > is easier to obtain completely opaque data planes. In tonight's > builds > (if they succeed, may not since we are switching to Python 2.5 > today) > you can obtain completely opaque volume planes by using the > "Brightness > and Transparency" panel of the volume dialog to set transparency to > 0. > This transparency value represents the fraction (0-1) of the depth > of > the volume required to produce opacity to the degree indicated by > the > height of the yellow curve on the histogram. In other words it > modulates the overall transparency. But until today it was > arbitrarily > deciding not to modulate the transparency if this depth was less > than > one grid spacing. This meaning of the transparency factor was > introduced in August 2007, and prior to that the transparency > factor > just scaled the opacity given by the yellow curve. > > Tom > > Jeff wrote: > > hi Tom, > > > > in the older (plug-in) volume planes tool, I was able to generate > > images that were opaque planes. I don't seem to be able to do > this > > anymore, even with transparency = 0. is there a way for me to do > this > > in the current Chimera? > > > > ------------------------------ > > Message: 4 > Date: Tue, 12 Feb 2008 17:47:37 -0800 > From: William Jeffrey Triffo <triffo(a)rice.edu> > Subject: Re: [Chimera-users] Opaque volume planes > To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B24C39.10306(a)rice.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > thanks, > > do you know when tonight's builds will go through, I will test it > at > that point to see if the functionality made it in > > -Jeff > > > Tom Goddard wrote: > > Hi Jeff, > > > > The trouble obtaining opaque volume planes is not related to > volume > > plane display being built into the volume dialog. It is related > to a > > change I made in how transparency is handled in solid mode back > in Aug > > 2007. > > > > Today I changed transparency in "solid" style volume rendering > so it > > is easier to obtain completely opaque data planes. In tonight's > > builds (if they succeed, may not since we are switching to Python > 2.5 > > today) you can obtain completely opaque volume planes by using > the > > "Brightness and Transparency" panel of the volume dialog to set > > transparency to 0. This transparency value represents the > fraction > > (0-1) of the depth of the volume required to produce opacity to > the > > degree indicated by the height of the yellow curve on the > histogram. > > In other words it modulates the overall transparency. But until > today > > it was arbitrarily deciding not to modulate the transparency if > this > > depth was less than one grid spacing. This meaning of the > > transparency factor was introduced in August 2007, and prior to > that > > the transparency factor just scaled the opacity given by the > yellow > > curve. > > > > Tom > > > > Jeff wrote: > >> hi Tom, > >> > >> in the older (plug-in) volume planes tool, I was able to > generate > >> images that were opaque planes. I don't seem to be able to do > this > >> anymore, even with transparency = 0. is there a way for me to do > this > >> in the current Chimera? > > > > > > -- > ------------------------------------------------------------- > 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 > > > > ------------------------------ > > Message: 5 > Date: Tue, 12 Feb 2008 18:10:01 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Opaque volume planes > To: William Jeffrey Triffo <triffo(a)rice.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B25179.5050005(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The Chimera nightly builds usually run around 9 pm pacific standard > time > (california). The nightly build download web page has the date for > each > build, and that will not be updated if code checked in during the > day > does not compile. Code changes checked in before about 8 pm makes > it > into that night's build. > > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Tom > > > > ------------------------------ > > _______________________________________________ > 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 15 > ********************************************* >

2 1

Chimera user, about 'turn' command
by Aguang Dai 15 Feb '08

15 Feb '08

Dear Mr./Ms. I'm a Chimera user in FSU. I would like to use Chimera to build some models. I used 'turn' command to rotate the model around the z axis. The command and option was: turn z 27.6923. The model is from a PDB file. But the result was that it should have be, not what I wanted. The atoms should be always in the circle centered in the Z axis, respectively. So my question is: When Chimera open a PDB file recording a protein structure, whether the coordinate axis is exactly the same as that in the PDB file? Thank you for your information in advance. Best, Daniel

3 2

zone tool in volume rendering
by William Jeffrey Triffo 14 Feb '08

14 Feb '08

I've been using the new mask tool to extract features along surfaces, which is useful in its own right for generating separate maps of segmented areas. but, if I wish to color a region around a surface (or between surfaces) without generating a new map, I am not sure how to do this - the 'zone' and 'color zone' tools in Volume viewer expect atoms or marker files. I had thought about loading multiple files of these surface regions after segmenting them out, each with their own color, but loading them together produces the ordering problem with the volume rendering. also, loading multiple volumes consumes a lot of memory and I run short of memory. is there currently a way to color arbitrary regions in a volume rendering? for example, rendering all data within 60 A of a surface with a different color than the rest of the volume, or coloring a region between two surfaces a different color, analogous to the 'sandwich' option of the mask tool. thanks, -Jeff

2 1

save volume histogram transfer function
by William Jeffrey Triffo 14 Feb '08

14 Feb '08

hello, is there a way for me to save the histogram transfer function that is displayed in Volume Viewer? I see that I can write down where the nodes are placed as these values appear in the "Level" dialog, but do not see a place to input magnitude (or write it down) of each node on the line. Ideally, I would just like to save it out, to apply the identical transform to multiple segmented areas of a volume. thanks, -jeff

2 1

Per-model clipping plane flickering
by Tom Goddard 14 Feb '08

14 Feb '08

Hi Jeff, I think you need to increase the "cap to clip plane distance" in the Surface Capping dialog from its default value of 0.001 to maybe 0.01 or 0.1. I guess you have surface capping turned on. Sometimes the clip plane partially clips the surface cap causing a fractured appearance of the cap. The OpenGL clip plane is offset from the cap by a small amount to prevent this but the needed displacement depends on the precision of the OpenGL depth buffer. Chimera should figure out the right value for this offset but currently it is specified by the user. Tom Jeff wrote: > hi Tom, > > I am getting odd output using the per-model clipping plane - I have a > volume loaded w/ precomputed subsamplings, and have generated a > surface depiction of the volume. when I enable the per-model clipping > plane, there is a lot of blinking in the model at the interface with > the per-model clipping plane. > > this volume is a membrane that I masked out using contours (as I > explained a couple of emails ago, where I have a bunch of contours > plotted along a surface, and then use the zone tool along those > contours). this means that there are a lot of zeros where the masked > volume ends; could that be part of the problem? > > I am using Chimera build 2492, MacBookPro 2GB (identical model to > yours), and Leopard with the latest X11 patch. > > best, > > -Jeff >

1 0

Opaque volume planes
by Tom Goddard 12 Feb '08

12 Feb '08

Hi Jeff, The trouble obtaining opaque volume planes is not related to volume plane display being built into the volume dialog. It is related to a change I made in how transparency is handled in solid mode back in Aug 2007. Today I changed transparency in "solid" style volume rendering so it is easier to obtain completely opaque data planes. In tonight's builds (if they succeed, may not since we are switching to Python 2.5 today) you can obtain completely opaque volume planes by using the "Brightness and Transparency" panel of the volume dialog to set transparency to 0. This transparency value represents the fraction (0-1) of the depth of the volume required to produce opacity to the degree indicated by the height of the yellow curve on the histogram. In other words it modulates the overall transparency. But until today it was arbitrarily deciding not to modulate the transparency if this depth was less than one grid spacing. This meaning of the transparency factor was introduced in August 2007, and prior to that the transparency factor just scaled the opacity given by the yellow curve. Tom Jeff wrote: > hi Tom, > > in the older (plug-in) volume planes tool, I was able to generate > images that were opaque planes. I don't seem to be able to do this > anymore, even with transparency = 0. is there a way for me to do this > in the current Chimera?

2 2

Split into models
by Sadler, Evan 12 Feb '08

12 Feb '08

Recent email address change caused the first try to bounce, so I resent it. I've loaded a file (2rjp.pdb) with 4 chains and want to split it into 4 models so I can align them. But "split" returns: unrecognized command: "split" What am I doing wrong? Evan -- J. Evan Sadler, M.D., Ph.D. Howard Hughes Medical Institute Washington University 660 S. Euclid Ave., Box 8022 St. Louis, MO 63110 Tel: 314-362-9067 FAX: 314-454-3012 email: esadler(a)im.wustl.edu

2 1

selection shadow is fixed
by jean-francois menetret 11 Feb '08

11 Feb '08

Recompiling the driver for the graphical card took care of the "selection shadow" Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street On Mon, 11 Feb 2008, 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. selection shadow (jean-francois menetret) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 11 Feb 2008 08:49:42 -0500 (EST) > From: jean-francois menetret <menetret(a)bu.edu> > Subject: [Chimera-users] selection shadow > To: chimera-users <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.A41.4.63.0802110846190.146120(a)acsrs3.bu.edu> > Content-Type: text/plain; charset="x-unknown" > > > I am using the latest nightly build installed on our linux machine. If I > select a PDB and move it around, the selection leaves a "shadow" behind > (see attached snapshot). > Thanks > > > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine > Physiology and Biophysics Department > 700 Albany Street W315 > Boston, MA 02118 > Email: menetret(a)bu.edu > Mailing address: 715 Albany Street >

2 1

Dual display Mac problem moving Chimera window
by Tom Goddard 11 Feb '08

11 Feb '08

Jeff reports that with 2 displays on Mac OS 10.5 the Chimera window gets stuck when being dragged from one display to the other. Fixed by updating X11. Jeff wrote: > hi Tom, > > I thought since you also have a MacBookPro you might know the answer > to this question - I just bought a 24" monitor to extend the display > on my MBP (running Leopard). for all my other applications, I am able > to drag the application window onto the adjacent desktop space that > now exists on the new monitor (am still using the screen on my laptop > as well). however, the chimera window "gets stuck" - after I launch > it, the window spawns on my laptop screen, and when I try to move it > onto the new monitor, it stops halfway and I can't drag it any further. > > is there a properties file or something that Chimera / X uses to set > the bounds on the desktop? I took a screenshot but it saved 2 separate > files (one for each screen); the new 24" screen is set up on the left > side of the MBP. > Jeff wrote: > hi Tom, > > I downloaded the latest X11 update from macosforge (xquartz project) > and this relieved the Chimera window location problem, am now able to > move the window onto my attached 24" screen. > > -Jeff >

1 0

selection shadow
by jean-francois menetret 11 Feb '08

11 Feb '08

I am using the latest nightly build installed on our linux machine. If I select a PDB and move it around, the selection leaves a "shadow" behind (see attached snapshot). Thanks Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

1 0

split-map
by Gatsogiannis, Christos 08 Feb '08

08 Feb '08

Hello chimera team, is there any memory-limitation for the split-map tool? When i perform a segmentation of a density-map larger than ~100MB i always get a chimera-error. In order to perform the segmentation, i have to coarse the density-map with a factor of 2, as example in imagic, and then split-map works fine with the new map. The result is of course density maps with a lower resolution. My Linux-PC has 4GB of memory and my first thought was that this should be enough for the segmentation of the density map as example in 10 parts (10x100=1GB). Is there any way to circumvent this problem and perform the segmentation with the original map? Thanks Christos Gatsogiannis Christos Dipl.Biol. Cryo-EM Lab Institut for Zoology Johannes Gutenberg University 55128, Mainz Germany Tel: +49(0)6131-39-23091

2 1

regd. DMS
by Vinay Kumar 08 Feb '08

08 Feb '08

Hello all, I had installed DMS previously. And recently upgraded my OS to fedora 8. When i try to recompile dms this is the following error i get. I did not face this the previous time!! could anyone guide me?? Regards Vinay Following is the error ----- [hpws@localhost dms]$ make cd libpdb ; make OPT="-O" make[1]: Entering directory `/home/hpws/dms/libpdb' cc -O -c -o pdb_read.o pdb_read.c pdb_read.c:25:20: error: stdio.h: No such file or directory pdb_read.c:26:20: error: ctype.h: No such file or directory pdb_read.c:27:21: error: string.h: No such file or directory In file included from pdb_int.h:20, from pdb_read.c:28: pdb.h:516: error: expected ')' before '*' token pdb.h:518: error: expected ')' before '*' token In file included from pdb_read.c:37: read_format.i:19: error: 'NULL' undeclared here (not in a function) In file included from pdb_read.c:45: pdbrun6_read.i:45: error: initializer element is not constant pdbrun6_read.i:45: error: (near initialization for 'pdbrun6[26]') pdbrun6_read.i:46: error: initializer element is not constant pdbrun6_read.i:46: error: (near initialization for 'pdbrun6[27]') pdbrun6_read.i:47: error: initializer element is not constant pdbrun6_read.i:47: error: (near initialization for 'pdbrun6[28]') pdbrun6_read.i:48: error: initializer element is not constant pdbrun6_read.i:48: error: (near initialization for 'pdbrun6[29]') pdb_read.c:59: error: expected ')' before '*' token pdb_read.c: In function 'pdb_read_string': pdb_read.c:304: warning: incompatible implicit declaration of built-in function 'memset' pdb_read.c:556: warning: incompatible implicit declaration of built-in function 'strncpy' pdb_read.c:913: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:978: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:992: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:1027: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:1047: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:1076: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:1094: warning: incompatible implicit declaration of built-in function 'sscanf' make[1]: *** [pdb_read.o] Error 1 make[1]: Leaving directory `/home/hpws/dms/libpdb' make: *** [pdb] Error 2

2 1

clipping: solids or interior surfaces
by Ian Yarbrough 07 Feb '08

07 Feb '08

Hello, Is there any way to color the interior face of a surface (when exposed by clipping) a different color or shade than the outside surface? Or a way to show the interior as a volume instead of a cavity? Essentially I'm looking for the same thing as this fellow describes in his post on the following date: *Andrew Jewett* aij at physics.ucsb.edu <chimera-users%40cgl.ucsf.edu?Subject=%5BChimera-users%5D%20clipping%20%28interior%20surfaces%20and%20solids%29&In-Reply-To=Pine.LNX.4.44.0502252312570.5796-100000%40localhost.localdomain> *Mon Feb 28 16:56:34 PST 2005* http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-February/000287.html He describes it much more elegantly than I can. Was this feature was ever implemented? Thanks and cheers, Ian Yarbrough Texas A&M University Biochem/Biophysics Dept 832-858-9278

3 2

locating models in maps by unit cell transformations
by Trevor Sewell 07 Feb '08

07 Feb '08

Hi, It often turns out that the atomic model you create in O needs to be transformed by a crystallographic symmetry operation in order to fit into the map created by refmac. In O this is no problem because the map automatically covers the bit of model you put in the center of your screen. However this does not seem to happen in Chimera. Is there an easy way to make the map cover the model (i.e. without working out what the transformation is and then creating a transformed pdb file)? Many thanks Trevor

3 3

using IDLE
by Ben Keshet 07 Feb '08

07 Feb '08

Hi, I am interested in performing the same actions several times on several different structures. For example: open a file, select the histidines, delete them, save and close. Is IDLE the right tool for that? I opened the python shell (Tools-> General Controls-> IDLE) but could not open files or manipulate them using the shell. I have no knowledge in python. What is the best way to write scripts to execute commands repeatedly? If IDLE is the tool, how can use it to do that? Is there a written source for that? Do I need to master python first? Many thanks, Ben

3 7

clipping related models identically
by Eric Pettersen 06 Feb '08

06 Feb '08

Raven Huang asks (paraphrased): > I have four related structures that I want to show in cutaway view, > with the cut being in the same place in all the structures. How > can I do that? The technique varies depending on whether you are clipping using the global clip planes (i.e. the ones shown in the Side View), or with per-model clip planes (from the Per-Model Clipping tool). Both techniques share the same setup step though: open all your models and get the parts you care about superimposed. If the starting coordinates are already "in the same reference frame" then you don't have to do anything but open the models. Otherwise you will have to superimpose them either with the MatchMaker tool or the "match" command. There is a discussion of using those here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ images.html#matching To view just one of the structures at a time, use the Model Panel (Favorites->Model Panel) and use the buttons in the Shown column (or the Show Only button in the button list) to show one structure/ surface. Now for adjusting the clip plane... Global clipping: open the Side View and adjust the near clip plane until it is cutting where you want it to. Per-model clipping: use the Per-Model Clipping tool to adjust the clip plane of the visible model until it is cutting where you want it to. Then choose one of the other models you want to cut from Per- Model Clipping's "Model:" menu. Enable clipping and click the "Align plane" button once you have chosen the original model in the menu next to the button. The model clip planes will now be aligned. Once the models are all clipped, you can either show then individually (the Model Panel again) and save separate images, or move them apart using the "move" command and save one combined image. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Planes feature in the Volume Viewer
by William Jeffrey Triffo 05 Feb '08

05 Feb '08

hi, when using the Planes tool in Volume Viewer, are the planes numbered from 0 or 1? I loaded a contour using the IMOD import, where I had drawn the contour on slice 12 of a volume; however, it appears that the plane that transects the contour in Chimera is '11' when using the Planes tool. I tried to test the enumeration by exceeding bounds (150 slices are in the volume, so was expecting an error for an entry of '150' if it was enumerated from zero), but it appears that slice indices outside the range of the loaded volume just default to the limit in either direction (typing in '200' just sets it to the highest-enumerated slice). -- ------------------------------------------------------------- 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

2 1

Contact/clash detection for HETATMs
by Jonathan Magasin 05 Feb '08

05 Feb '08

Hello, I'm trying to use the clashes/contacts tool to explore valid phi/psi angles for L- and D-Ala (as part of a homework assignment; developing a Ramachandran plot for each). The tool worked great for L-Ala but does not report any contacts for D-Ala. (For each, I've snipped just the relevant sections out of a larger PDB. I'm using default params for collision detection, with detection calculated for any movement.) The difference in the PDB's for L-Ala and D-Ala is that the latter are in HETATM records. I did include the CONNECT info (to explicitly tell Chimera how HETATMs bond) but that did not help. Perhaps there's something else I must include, or some modification I can make to the HETATMS (element labeling?) so that collision detection will work as with peptides? Or is this a known limitation? (Is there a list of known limitations? I'm a new user.) I'm not Note that the distance tool works for D-Ala. If I can get collision detection to work, it take much less time. Thanks in advance. -Jonathan

2 1

Aligning two residues same name
by Elaine Meng 05 Feb '08

05 Feb '08

> Changing residue name works. Deleted membrane, saved pdb without > membrane. > Loaded the two models. Command line: match :XXX :YYY Hi Francesco, You can still use the name without changing it, for example open 4hhb open 4cpp preset apply interactive 1 match #1:hem #0:hem.a ~ribbon This matches the single heme residue of 4cpp (#1) to the chain A heme of 4hbb (#0 - it has four heme residues, in chains A-D). The protein parts are totally different but I just used this as an example because they both have heme. It takes a little time, but I recommend learning about the command- line specification language because it is used in so many commands, and can be very powerful yet flexible. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html Or, for some quick hints see the examples on the second page of the "Quick Reference": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf 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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Re: [Chimera-users] [Dock-fans] How to get the charged mol for the ligand
by cpsosa＠comcast.net 04 Feb '08

04 Feb '08

Thanks. We tried that but after the hydrogens were added. We saved it and "vi" the mol2 file. I'll try this. -- Carlos P. Sosa -------------- Original message ---------------------- From: Eric Pettersen <pett(a)cgl.ucsf.edu> > I forgot, there's actually a fourth thing you can do: change the > atom type directly. Select the oxygen atom and open the command line > (Favorites->Command Line) and type: > > setattr a idatmType O3 sel > > which will set the selected atom's "idatmType" attribute to sp3 > oxygen ("O3"). > > Do this before hydrogens are added. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Feb 3, 2008, at 1:27 PM, Eric Pettersen wrote: > > > Hi Carlos, > > There are basically three things you can do: > > > > 1) Download the latest daily build and try that. I have been > > working hard on atom typing for ring systems recently (and am still > > working on it) and there's a pretty good chance that it will type > > (and therefore protonate) the phenyl oxygen correctly now. You > > get a daily build by going to the Chimera home page > > (www.cgl.ucsf.edu/chimera) and following the "Daily Builds" link. > > > > 2) Directly edit the structure (after adding hydrogens but before > > adding charges). Control-double-click the oxygen and select > > "Modify Atom" from the pop-up menu. In the resulting dialog change > > the element type to O, the geometry to tetrahedral, and the number > > of bonds to 2. You should also probably change the atom name field > > to be the same as what the atom's name is. Then click the Change > > button and the hydrogen will be added. > > > > 3) Before doing any processing, change the bond length. Control > > double-click on the C-O bond and choose "Set Bond Length" from the > > pop-up menu. Type in a bond length appropriate for a C-O single > > bond and then run the rest of your processing. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > > > On Feb 2, 2008, at 5:19 PM, cpsosa(a)comcast.net wrote: > > > >> > >> Hello, > >> > >> We have the opposite problem, our PDB has one oxygen that is part > >> of a phenyl group and after using addH in Chimera, hydrogen does > >> not get added to that oxygen. Is there a way to add hydrogen to a > >> single atom? using Chimera. For Chimera to add a hydrogen to > >> that O... perhaps making the C-O bond larger. > >> > >> Any suggestions? > >> > >> Thanks, > >> > >> -- > >> Carlos P. Sosa > >> > >> -------------- Original message ---------------------- > >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> > >>> I assume this is IMZ from 1rv1? Chimera is adding a proton to > >>> the N3 > >>> nitrogen that it shouldn't. After adding hydrogens and before > >>> saying > >>> OK to the charge calculation, type this command to Chimera's command > >>> line to delete the extra hydrogen: > >>> > >>> del :IMZ@h3 > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> UCSF Computer Graphics Lab > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>>> I could not get the charges for my molecule (ligand in x-crystal > >>>> structure). how to do that? > >>>> I am getting the following error message. > >>>> I am using chimera to do these funtions. > >>>> > >>>> Running ANTECHAMBER command: C:\Program Files\Chimera\bin > >>>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp > >>>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 > >>>> \temp > >>>> \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 > >>>> (IMZ) > >>>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe > >>>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o > >>>> ANTECHAMBER_BOND_TYPE.AC - > >>>> f ac -j part > >>>> (IMZ) > >>>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe > >>>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > >>>> (IMZ) Total number of electrons: 351; net charge: 1 > >>>> (IMZ) INFO: Number of electrons is odd: 351 > >>>> (IMZ) Please check the total charge (-nc flag) and spin > >>>> multiplicity (-m flag) > >>>> Failure running ANTECHAMBER for residue IMZ > >>>> > >>>> > >>>> Thomas > >>> > >>> > >> > >> > >> > >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> > >> Date: January 31, 2008 12:54:24 PM PST > >> To: dock-fans(a)docking.org > >> Subject: Re: [Dock-fans] How to get the charged mol for the ligand > >> > >> > >> I assume this is IMZ from 1rv1? Chimera is adding a proton to the > >> N3 nitrogen that it shouldn't. After adding hydrogens and before > >> saying OK to the charge calculation, type this command to > >> Chimera's command line to delete the extra hydrogen: > >> > >> del :IMZ@h3 > >> > >> --Eric > >> > >> Eric Pettersen > >> UCSF Computer Graphics Lab > >> http://www.cgl.ucsf.edu > >> > >> > >>> I could not get the charges for my molecule (ligand in x-crystal > >>> structure). how to do that? > >>> I am getting the following error message. > >>> I am using chimera to do these funtions. > >>> > >>> Running ANTECHAMBER command: C:\Program Files\Chimera\bin > >>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp > >>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 > >>> \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 > >>> (IMZ) > >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe > >>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o > >>> ANTECHAMBER_BOND_TYPE.AC -f ac -j part > >>> (IMZ) > >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe > >>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > >>> (IMZ) Total number of electrons: 351; net charge: 1 > >>> (IMZ) INFO: Number of electrons is odd: 351 > >>> (IMZ) Please check the total charge (-nc flag) and spin > >>> multiplicity (-m flag) > >>> Failure running ANTECHAMBER for residue IMZ > >>> > >>> > >>> Thomas > >> > >> > >> _______________________________________________ > >> Dock-fans mailing list > >> Dock-fans(a)docking.org > >> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > >> > >> > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

Fwd: Loading prmtop/mdcrd with partial workout
by Francesco Pietra 04 Feb '08

04 Feb '08

What I asked below has no sense. Deleting residues does not freed memory. Of course, because those residues can be resumed. francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Fri, 1 Feb 2008 12:49:22 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Loading prmtop/mdcrd with partial workout > To: chimera <chimera-users(a)cgl.ucsf.edu> > > I am experiencing difficulties with Amber ptraj in removing solvent/lipid/box > (i.e., unexpected problems of prmtop fitting after that, though I used a > prmtop > before creating solvent/lipid/box). > > Otherwise, I have memory problems with Chimera in loading such an extensive > MD > (many ns, in various coordinate files) with all the burden of > solvent/lipid/box. > > My question: is that feasible with Chimera to load a coordinate file, remove > solvent and lipid, load a second coordinate file, remove solvent and lipid, > and > so on for all coordinate files? > > Thanks > > francesco pietra > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Re: [Chimera-users] [Dock-fans] How to get the charged mol for the ligand
by Eric Pettersen 04 Feb '08

04 Feb '08

Hi Carlos, There are basically three things you can do: 1) Download the latest daily build and try that. I have been working hard on atom typing for ring systems recently (and am still working on it) and there's a pretty good chance that it will type (and therefore protonate) the phenyl oxygen correctly now. You get a daily build by going to the Chimera home page (www.cgl.ucsf.edu/ chimera) and following the "Daily Builds" link. 2) Directly edit the structure (after adding hydrogens but before adding charges). Control-double-click the oxygen and select "Modify Atom" from the pop-up menu. In the resulting dialog change the element type to O, the geometry to tetrahedral, and the number of bonds to 2. You should also probably change the atom name field to be the same as what the atom's name is. Then click the Change button and the hydrogen will be added. 3) Before doing any processing, change the bond length. Control double-click on the C-O bond and choose "Set Bond Length" from the pop-up menu. Type in a bond length appropriate for a C-O single bond and then run the rest of your processing. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 2, 2008, at 5:19 PM, cpsosa(a)comcast.net wrote: > > Hello, > > We have the opposite problem, our PDB has one oxygen that is part > of a phenyl group and after using addH in Chimera, hydrogen does > not get added to that oxygen. Is there a way to add hydrogen to a > single atom? using Chimera. For Chimera to add a hydrogen to that > O... perhaps making the C-O bond larger. > > Any suggestions? > > Thanks, > > -- > Carlos P. Sosa > > -------------- Original message ---------------------- > From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> I assume this is IMZ from 1rv1? Chimera is adding a proton to the N3 >> nitrogen that it shouldn't. After adding hydrogens and before saying >> OK to the charge calculation, type this command to Chimera's command >> line to delete the extra hydrogen: >> >> del :IMZ@h3 >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >>> I could not get the charges for my molecule (ligand in x-crystal >>> structure). how to do that? >>> I am getting the following error message. >>> I am using chimera to do these funtions. >>> >>> Running ANTECHAMBER command: C:\Program Files\Chimera\bin >>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp >>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1\temp >>> \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 >>> (IMZ) >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC - >>> f ac -j part >>> (IMZ) >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >>> (IMZ) Total number of electrons: 351; net charge: 1 >>> (IMZ) INFO: Number of electrons is odd: 351 >>> (IMZ) Please check the total charge (-nc flag) and spin >>> multiplicity (-m flag) >>> Failure running ANTECHAMBER for residue IMZ >>> >>> >>> Thomas >> >> > > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: January 31, 2008 12:54:24 PM PST > To: dock-fans(a)docking.org > Subject: Re: [Dock-fans] How to get the charged mol for the ligand > > > I assume this is IMZ from 1rv1? Chimera is adding a proton to the > N3 nitrogen that it shouldn't. After adding hydrogens and before > saying OK to the charge calculation, type this command to Chimera's > command line to delete the extra hydrogen: > > del :IMZ@h3 > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >> I could not get the charges for my molecule (ligand in x-crystal >> structure). how to do that? >> I am getting the following error message. >> I am using chimera to do these funtions. >> >> Running ANTECHAMBER command: C:\Program Files\Chimera\bin >> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp >> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 >> \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 >> (IMZ) >> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC >> -f ac -j part >> (IMZ) >> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >> (IMZ) Total number of electrons: 351; net charge: 1 >> (IMZ) INFO: Number of electrons is odd: 351 >> (IMZ) Please check the total charge (-nc flag) and spin >> multiplicity (-m flag) >> Failure running ANTECHAMBER for residue IMZ >> >> >> Thomas > > > _______________________________________________ > Dock-fans mailing list > Dock-fans(a)docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > >

1 1

Aligning two residues same name
by Francesco Pietra 04 Feb '08

04 Feb '08

Task: compare/align a single-residue molecule before docking (naked molecule, mol2 or pdb file) with same residue as ligand in a protein after docking/MD (pdb file of a snapshot for complex embedded in a bilayer membrane). Should I change the residue name in one of the two models? Same name poses to me problems. Or there is a direct way? Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

2 1

Fwd: Aligning two residues same name
by Francesco Pietra 04 Feb '08

04 Feb '08

Changing residue name works. Deleted membrane, saved pdb without membrane. Loaded the two models. Command line: match :XXX :YYY How to put the difference in quantitative terms (rmsd)? Thanks francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Mon, 4 Feb 2008 06:59:25 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Aligning two residues same name > To: chimera <chimera-users(a)cgl.ucsf.edu> > > Task: compare/align a single-residue molecule before docking (naked molecule, > mol2 or pdb file) with same residue as ligand in a protein after docking/MD > (pdb file of a snapshot for complex embedded in a bilayer membrane). Should I > change the residue name in one of the two models? Same name poses to me > problems. Or there is a direct way? > Thanks > francesco pietra > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

2 1

Permission to use Chimera created image
by Seymour Yang 01 Feb '08

01 Feb '08

Hi, I wish to obtain permission to use one or two of the virus images shown on your Chimera image gallery (Semliki forest Virus and Sindbis Virus). We are writing a feature article about 3D molecular imaging and would like to include some Chimera images. May I ask whom to contact regarding permission and obtaining higher resolution files? Hope you can help. Seymour Seymour Yang Producer - Science Feature Stories Email: seymour(a)sciencephoto.com Website: www.sciencephoto.com Blog:http://sciencephoto.blogspot.com/

3 2

Loading prmtop/mdcrd with partial workout
by Francesco Pietra 01 Feb '08

01 Feb '08

I am experiencing difficulties with Amber ptraj in removing solvent/lipid/box (i.e., unexpected problems of prmtop fitting after that, though I used a prmtop before creating solvent/lipid/box). Otherwise, I have memory problems with Chimera in loading such an extensive MD (many ns, in various coordinate files) with all the burden of solvent/lipid/box. My question: is that feasible with Chimera to load a coordinate file, remove solvent and lipid, load a second coordinate file, remove solvent and lipid, and so on for all coordinate files? Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

1 0

screening
by snoze pa 01 Feb '08

01 Feb '08

In continuation to my previous question, Is it possible to use chimera in virtual screening?

2 1

graphics card question (survey?)
by William Jeffrey Triffo 31 Jan '08

31 Jan '08

hello, anyone out there using a Radeon HD 2600 XT or GeForce 8800 GT? Just wanted to know if there are any driver issues out there that are known - these are the two 'lower-end' options on the current Mac Pro line, and I am evaluating that as a potential purchase (so technically, my question may only be relevant if you are also using a Mac machine). likewise, if you have a current-generation Mac (Tiger/10.4 or Leopard/10.5) and have bought a third-party card that you have had success with, I am all ears. best, -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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fourier transforms
by Matt Shawkey 31 Jan '08

31 Jan '08

Hi, I'm doing fourier transforms of 3d volumes and noticed that they are computed in Chimera using only a small portion of the actual data available (e.g. 128 ^3 pixels rather than the 512^3 pixels in the volume). Is there a way to do a fourier transform using all of the available data? THanks, Matt

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Surface color
by James Fethiere 30 Jan '08

30 Jan '08

Hi, I'm using the volume path tracer and color zone to highlight regions of a map. I would like to display a model within this region but it is not visible when I color the region with color zone. How can I make this zone transparent but still a different color that the rest of the map? Thanks James

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Re: [Chimera-users] mac pro theoretical question
by Tom Goddard 29 Jan '08

29 Jan '08

Hi Jeff, I don't know much about any of the current Apple graphics cards (Radeon HD 2600 XT 256Mb, Nvidia GeForce 8800 GT 512Mb, Nvidia Quadro FX 5600 1.5Gb). My first concern would be whether bugs in the drivers for these cards are going to cause trouble in Chimera. We have a web page that lists problems with graphics drivers observed using Chimera: http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html#cards There was a recently reported problem (squashed atom spheres) with GeForce 8800 GTX (not GT) on Windows. The Apple driver may be much different. The Quadro FX 4500 which was Apple's high-end offering before the 5600 crashed with solid volume rendering. Don't know if the current 5600 would have the same problem -- but there is a fair chance it does. Chimera uses many different OpenGL calls and I'd guess 1 in 10 drivers exhibit bugs of varying severity when using Chimera. Some of Chimera performance is related to graphics card speed and memory, and some is related to CPU speed and memory. When the displayed models rotate slowly that is the graphics card except if you are using transparent volume surfaces or meshes which are sorted by depth on the CPU for every new view angle. Everything else is the CPU, main memory, memory cache performance, and hard-drive speed. Solid style volume rendering makes a lot of textures which usually will be stored in graphics card memory. More graphics card memory could make larger volume rotate faster because they fit on the card. 256^3 volumes (16 million voxels, 4 bytes per voxel) typically rotate at 10 frames per second with graphics memory sizes 128 Mb and up. Textures have to have power of 2 sizes so just knowing that can get you better performance if you trim your 550x550x100 region to 512x512x100 you'll get a factor of 4 speed-up. I don't know if a single application using one display can use more than one graphics card in Apple's multicard options. Chimera has no special code to do that. For large volume data, hard-drive speed, main memory size, and CPU speed are likely to be noticable factors in Chimera performance, each of about equal importance to graphics card speed. Tom > hi Tom, > > if you were considering a Mac Pro at some point in the future, what > graphics card would you pick when thinking of chimera (if you don't > mind peeking at some point at the list at > http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/9354001/wo/… > > > are rendering bottlenecks in chimera largely a processor-limited thing > (and thus one of the 'lower end' cards listed would be fine), or > something that benefits dramatically from spending $2000 on a graphics > card (I am not in that kind of market, just wondering what kind of > decision you would make if evaluating that platform) > > best, > > -Jeff > > >

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average vs ensemble
by Rachel Scherer 29 Jan '08

29 Jan '08

Given that chimera doesn't calculate average NMR structures, this query may be outside the groups interests, but can anyone suggest what the appropriate protocol is when making aa-substitutions into an NMR structure: should an "average" be calculated (by averaging the atom coordinates across all the models in a PDB file that predates inclusion of the average into the database entry) or, should one use a representative from a cluster generated with "ensemble cluster" be chosen? Or an average of the representatives of the clusters? Or, the cluster representative that best matches the calculated average? -- Rachel Scherer rachel(a)bio.umass.edu Biology Department (413)545-2825 vox UMASS Amherst (413)545-3243 fax

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coordinates
by hsosa＠aecom.yu.edu 25 Jan '08

25 Jan '08

Hi, I am trying to rotate a molecule around a 3D density map. I had already saved the coordinates of the molecule relative to the map. However if I rotate the pdb file (creating a new pdb file with the rotated molecule) by rotating the coordinates around the origin (0,0,0) the new molecule is rotated around a a center that does not coincide with the center of the map. So I am confused about what are the relative positions of the origin for the map and pdb file. If I have an atom with pdb coordinates 0,0,0 should this atom appear at the center of the density map ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Re: [Chimera-users] Save a transformed density map
by Thomas Goddard 24 Jan '08

24 Jan '08

Hi Keren, Chimera has a resampling capability for extracting regions of a map that aren't aligned with the axes. It doesn't work well in the case you want. So I've made a Chimera command that will do what you want. If your the map you wish to save in the new orientation has id number 0 (listed next to the name of the map in volume dialog), and the map you fit into has id 1 you would use the command: vop #0 resample onGrid #1 The vop stands for "volume operation". (Use menu Favorites / Command Line to type commands.) This will create the new map which will appear in the volume dialog and can be saved with the volume dialog File / Save map as... (or using a command like "volume #2 save /tmp/newmap.mrc"). The vop command with the resample operation will be in tonight's builds of Chimera (assuming they succeed). http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Keren Lasker wrote: > hey Tom, > > I need to save the transformed map for other calculations. Is there a > resampling option in chimera? if not I guess that I can use the output > transformation matrix generated by fit map2map - right? > > thanks, > Keren. > On Jan 24, 2008, at 3:27 PM, Thomas Goddard wrote: > >> Hi Keren, >> >> You can save the Chimera session to preserve the orientation of one >> map fit into another. >> >> If you want to write a new map so that when it is loaded in Chimera >> and other software it will be at the correct place in the map it was >> fit into that is harder. The problem is that none of the map file >> formats provide for a positioning transformation in the header. So it >> would be necessary to resample the map that you fit on the grid of the >> map you fit into. Resampling interpolates data values and can degrade >> map quality. Do you want to do that? >> >> Tom >

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volume visualization
by Enrico Malito 24 Jan '08

24 Jan '08

Hello, I am trying to visualize a map as Volume (ccp4 format map calculated with VOIDOO in NEWZD then converted with MAPMAN) and somehow the map in chimera results shifted with respect to the corresponding pdb model (in a completely different place). If I open same pdb and map file in other visualization programs they are actual in the right position (map into the cavity of the enzyme). I'm opening the map from the Volume Viewer-->File-->Open map Am I doing something wrong? Thanks, EM -- Enrico Malito Ben-May Department for Cancer Research Center for Integrative Science, W423J The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637 Tel: 773-702-4608 Fax: 773-702-6260 http://home.uchicago.edu/~emalito

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Save a transformed density map
by Keren Lasker 24 Jan '08

24 Jan '08

hello, How can I save a transformed map after using the fit map2map option? The "save map" option saves it in its original transformation. thank you, Keren.

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Chimera batch surface exporter
by Trent Grover 24 Jan '08

24 Jan '08

Hi Everyone, I'm pretty new to Chimera, but I'm working on an animation project that requires quite a few proteins and molecules. To speed up the process, I'd like to create a batch converter/exporter script to do the following: Open a PDB file Generate a multiscale model at a specified resolution Export the model out as a VRML or OBJ file I think I can do this using a Chimera command file, but I was hoping someone could point me in the right direction for some of the relevant command line syntax. Is it possible to control the multiscale model tool via command line (I know I can launch the dialog, but can I change the parameters and execute)? Is there a reference somewhere for the command line parameters for the multiscale models tool? What is the command line export command? Where can I find an OBJ exporter (there are references to it in the mailing list archive)? Any help would be greatly appreciated. Thanks, Trent BTW - I have a suggestion for improvement of Chimera. Add a command history window (or modify the existing one) that echoes out the command line text that is equivalent to any command executed via the Chimera user interface. Maya has this functionality and it is wonderful for anyone who is trying to figure out how to script a process that they know how to execute via the various menus.

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Re: [Chimera-users] Surface representation
by Elaine Meng 24 Jan '08

24 Jan '08

> Hi, > I would like to know if there is a way to build a surface > representation from a pdb file of a dummy atom saxs model in > chimera. The file consist only of CA atoms. I could simulate this > by increasing the vdw radius but the model becomes way to big. > Thanks > James Hi James, You can use Multiscale Models to make a contour surface that encloses the "atoms." The tricky part may be adjusting the contour surface parameters to get the desired smoothness and enclosed total volume. At least in my tests, Chimera did not like the columns in your file after the B-factor column, so I made a version with those removed and opened it with "File... Open" before proceeding. I will send you that file in a separate message. (1) for purposes of comparison to the surface, I displayed the atoms as spheres with the radius 3.75 (this value was given in comments in the file) using the following commands: setattr a radius 3.75 rep sphere You can show the command line with Favorites... Command Line. (2) started Multiscale Models (under Tools... Higher-Order Structure), clicked the "Make models" button near the bottom. This generates the contour surface but hides the spheres. To also show the spheres, Ctrl-click on the surface to select it, and then in the "Style" line of the dialog, choose "Show also.. Spheres". To see spheres inside the surface, make it transparent; set Transparency to some fraction, say 0.3. (3) Then you can fiddle with the contour surface parameters in the Multiscale Models dialog. Many are hidden but can be shown by checking the box next to "..." I got a fairly decent enclosure of the spheres with all default parameters except setting the "Threshold atom density" for "CA only" to 0.0006 instead of the default 0.002. You could also fiddle with the smoothing parameters and resolution if that is not good enough. If you have some idea of what total volume the surface should enclose, that can be evaluated with Measure Volume and Area (under Tools... Volume Data). 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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Re: [Chimera-users] Chimera-users Digest, Vol 57, Issue 24
by Jonathan Hilmer 22 Jan '08

22 Jan '08

POV-Ray also works extremely well as a distributed job. This site has some basic discussion of some of the distributed POV options: http://columbiegg.com/httpov/?p=why Jonathan > Today's Topics: > > 1. (no subject) (jean-francois menetret) > 2. Re: Flip handedness of map (Tom Goddard) > 3. VRML alpha vs 1-alpha (Nils Becker) > 4. Re: VRML alpha vs 1-alpha (Greg Couch) > > > ------------------------------ > > Message: 4 > Date: Tue, 22 Jan 2008 10:37:54 -0800 (PST) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] VRML alpha vs 1-alpha > To: Nils Becker <nils.becker(a)ens-lyon.fr> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0801220934340.1761700(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Tue, 22 Jan 2008, Nils Becker wrote: > > > Hi, > > > > I found information on the web site that VRML models use > > 1-alpha blending for transparency, and that that looks ugly. > > I agree. > > > > Now I have externally generated VRML files including transparency. > > > > Is there a way to get nice (normal) transparency rendering of these > > models in chimera? > > > > e.g. editing the vrml files, converting them to another format or some > > option inside chimera? > > > > Thanks for any help, cheers, Nils > > The VRML transparency is 1-alpha, because alpha is an opacity value. So > that is just an alternative way of saying that same thing, and is not the > reason it is worse. > > The reason VRML transparency is worse is that there is no sorting within > the VRML shapes, so the blending of transparent objects has to be > drawing-order independent, so VRML uses additive blending. > > The simpliest solution would be to live with chimera's current depiction > and use the Save Image dialog to generate a ray-traced version. The > ray-traced version will be much nicer (and take a lot longer to compute, > try using the POV-Ray 3.7 beta on a multi-core computer to speed things > up). > > The other solution, is to write some Python code and use the _surface > module's Surface_Model and Surface_Group classes. That is, convert each > VRML object into a triangulated surface, a Surface_Group, and put all of > the Surface_Groups into one Surface_Model. All surfaces within one > Surface_Model are sorted so that the transparency is correct for more than > one overlapping surface (unlike the transpareny in chimera between > models that only works for one level of transparency). You can see > examples that use the _surface module in the GraspSurface, IMOD, > Icosahedron, and Intersurf modules (and others) in the CHIMERA/share > directory of your installation. > > If you have any questions about the _surface module, please ask them on > the chimera developers mailing list, chimera-dev(a)cgl.ucsf.edu. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > _______________________________________________ > 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 57, Issue 24 > ********************************************* >

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VRML alpha vs 1-alpha
by Nils Becker 22 Jan '08

22 Jan '08

Hi, I found information on the web site that VRML models use 1-alpha blending for transparency, and that that looks ugly. I agree. Now I have externally generated VRML files including transparency. Is there a way to get nice (normal) transparency rendering of these models in chimera? e.g. editing the vrml files, converting them to another format or some option inside chimera? Thanks for any help, cheers, Nils

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(no subject)
by jean-francois menetret 21 Jan '08

21 Jan '08

In older versions of Chimera, it was possible to change the handedness of a map with a minus sign for the pixel size of the axis. How do you do that in the newer version ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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visualizing density map
by francesco zonta 20 Jan '08

20 Jan '08

Good morning. I have some problem in visualizing a ccp4 density map with chimera. I can see only a small slab of the map, but i need to visualize a larger reagion. How can I enlarge the visualized volume? thank you for the help Dr. Francesco Zonta

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Re: [Chimera-users] visualizing density map
by Tom Goddard 18 Jan '08

18 Jan '08

Hi Francesco, Your map contains only the crystal asymmetric unit. Coot is able to replicate that asymmetric unit (using the 4 space group symmetries and unit cell translation symmetries) to show the map for a bigger region of the crystal. http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC… Chimera is not able to do that replication. Chimera can only display the part of the map present in the file. You might be able to export a map from Coot that covers a larger region but I do not know how. This replication of the crystal asymmetric unit is a nice feature and I'll add it to the list of requested features for Chimera. Tom francesco zonta wrote: > Hi thomas, here is how I can see the map with coot > This is a cubic box of 60 angstrom. [Image deleted] > The problem I have is probably that with chimera I can not see a > bigger volume, but I do not know why. > > Francesco

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VRML rendering options?
by Nils Becker 18 Jan '08

18 Jan '08

Hi, I have been using Chimera for a while and find it great software. Now I am trying to include my own VRML models and show them together with PDB data. I succeeded in opening an externally generated VRML 2.0 file. Since the VRML file contains colored boxes, the standard smooth rendering is not appropriate. Is there a way to influence the rendering style? Also, is there a way to switch on a fixed transparency (alpha value) for the whole VRML model, on a per-model basis? Any help would be appreciated! Cheers, Nils

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Fwd: Re: Bug (?) with EnsembleCluster
by Francesco Pietra 17 Jan '08

17 Jan '08

Yes, the two behave differently, and not only as to importing pdb. I had opened my combined trajectories (protein+ligand in a lipid membrane) in VMD while looking at either the ligand or the protein: both highly distorted at each one of the 550 frames. I only got nearly reasonable structure for the ligand by averaging the frames. That was most discouraging in the last few days. Did the same for the equilibration and got the same discouraging results. This last analysis was not fitting the analysis with ptraj, Therefore I have now done the same for the MD trajectories with Chimera, which runs more slowly along the frames, and surprisingly, "at the naked eye" both the ligand and the protein save their correct structure along the 550 frames, with only the internal displacement on/back that one expects from MD. I repeated without hiding the membrane and water, and "at the naked" the ligand was not wandering around. I looked at RMDS Maps(Start frame 1; End 550; Step size 2; RMSD map of trajectory against itself; Lower rmsd threshold 2.9, higher 3.9: RMSD varied from 0.194 to 1.810 for the ligand and from 0.612 to 2.420 for the protein. Is that variation too much for accepting this MD for good (or fair) and continuing it with same settings? If it is a too large a range, that explains why the ligand encountered so many protein residues when the mask was used. I was unable to find how to get a plot of RMSD against time. I would like to do that for the ligand (which is a single big residue) and selected residues of the protein. Thanks francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Tue, 15 Jan 2008 06:44:21 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Re: [Chimera-users] Bug (?) with EnsembleCluster > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > CC: chimera BB <chimera-users(a)cgl.ucsf.edu> > > Got FMI, thanks. That seems a reasonable rationalization. Though, if I > understand, importing pdb files without saturating memory (may be importing > one > "model", analyzing it, and then removing it from memory before importing next > "model", or any other better idea) is something to overcome in order to have > Chimera carrying out cluster analysis. Or I do not understand or cluster > analysis is of minor interest, both equally possible. > > francesco > > --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > Just FYI, when you open a 5000 MODEL structure with Chimera's normal > > File...Open, you get 5000 completely separate models (and will likely > > exhaust memory unless its a small molecule). Each model can be > > colored individually, moved, mutated, closed, etc. individually. > > When you open the same 5000 MODEL file with the MD Movie extension > > you get _one_ model with 5000 sets of coordinates, which takes much > > less memory. On the other hand, each frame shares colors and so > > forth with all the other frames, cannot be moved with respect to the > > other frames, etc. VMD undoubtedly uses the latter approach. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > > On Jan 11, 2008, at 3:04 PM, Francesco Pietra wrote: > > > > > Yes, 5365. What happened will be discovered. Up to the stage on > > > amber_score_everything, all was perfectly OK. Minimization and > > > heating was also > > > OK. As to MD, the situation could not be clarified so far. > > > > > > In view of your comments below, I carried out a check with proven > > > MD. I went to > > > Amber tutorial B3, took equil1.mdcrd.gz, decompressed, took the > > > related prmtop, > > > and fed the two files to Chimera, last Daily Building. After all > > > 5000 steps had > > > been acquired, saved pdb, all frames. Quit MD Movie. Try to open > > > this pdb. > > > Well, with my modest desktop, Debian Linux i386, 1GB ram, this pdb > > > could not be > > > opened: rapidly the memory was exhausted and to get control of the > > > computer I > > > had to kill gnome. With vmd, this pdb developed rapidly with all > > > 5000 frames. > > > Exactly as with the pdb from MD with my protein. This does not mean > > > that my MDs > > > are OK. I'll look for what may be wrong there. > > > > > > Thanks > > > francesco > > > > > > > > > > > > > > > --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > > > >> 5365 atoms? Given average atom counts in protonated protein residues > > >> that means your ligand came in close contact with ~340 residues over > > >> the course of the trajectory -- so it's wandering all over the > > >> place. I can see why you want to use cluster analysis. Oh well, I > > >> guess we're stuck until I have time to coordinate with Conrad and > > >> integrate his clustering code with MD Movie. > > >> > > >> --Eric > > >> > > >> On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote: > > >> > > >>> Eric: I followed previous route from combined mdcrd from ptraj. > > >>> > > >>> Removed remaining water. > > >>> > > >>> select ligand z<2.5 > > >>> > > >>> as Chimera command; (this was the minimum, selecting 244 atoms, 118 > > >>> of which > > >>> for the ligand; with z<2.0 the ligand only is selected) > > >>> > > >>> On playing the pdb (saved for selected atoms only) (with LOOP > > >>> deselected) the > > >>> atom selection increased, reaching 5365 atoms at the last (549) > > >>> frame. In > > >>> another run, with z<4.0 the course of atom selection was similar, > > >>> reaching 5993 > > >>> atoms at frame 549. > > >>> > > >>> This huge number of atoms proved problematic for opening pdb. For > > >>> the z<2.5 > > >>> case I left the computer on for 4h and half, with python occupying > > >>> 98% of the > > >>> available MEM (nearly 1GB). I had to kill gnome to recover command. > > >>> > > >>> May be with much more MEM it will work, though I can't check that > > >>> now. > > >>> > > >>> I did not try to combine the trajectories with Chimera as I have no > > >>> indication > > >>> that those from ptraj are faulty. The pdb files for both z<2.5 and > > >>> z<4.0 open > > >>> in vmd. > > >>> > > >>> francesco > > >>> > > >>> --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > >>> > > >>>> On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote: > > >>>> > > >>>>> In the "Define script.." I defined "select ligand z<10", then OK > > >>>>> and a BUG > > >>>>> window was presented. Attached is the reply log (bug). I tried > > >>>>> with > > >>>>> z<4 with > > >>>>> the same result (actually, I don't remember if attached bug file > > >>>>> refers to z<10 > > >>>>> or z<4). > > >>>> > > >>>> In the script-definition dialog you need to have "Interpret script > > >>>> as" set to "Chimera commands". You had it set to "Python". > > >>>> > > >>>>> Still found difficulties in loading more than one mdcrd, though > > >>>>> this should be > > >>>>> my fault. I was not sure if the list of mdcrd is to be given at > > >>>>> beginning or if > > >>>>> the other mdcrd files after the first one are to be given > > >>>>> subsequently from the > > >>>>> menu. I tried with the "list" option but only the first mdcrd was > > >>>>> opened. > > >>>> > > >>>> When you run MD Movie and the dialog comes up where you specify the > > >>>> prmtop/trajectory files, you can use the "Add..." button to add as > > >>>> many trajectory files as needed. I think this means you "give > > >>>> it at > > >>>> the beginning" rather than "subsequently from the menu" in your > > >>>> terminology. > > >>>> > > >>>> You can also just list the files in a "metafile" for the command > > >>>> line. For instance, this file works for me: > > >>>> > > >>>> amber > > >>>> leap.top > > >>>> md01.crd > > >>>> md02.crd > > >>>> md03.crd > > >>>> md04.crd > > >>>> md05.crd > > >>>> md06.crd > > >>>> > > >>>> Note that there _still_ seems to be something funky with Amber > > >>>> compressed trajectories, so don't use them for now but I should > > >>>> have > > >>>> things fixed in a day or so with that. > > >>>> > > >>>> --Eric > > >>>> > > >>>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> ____________________________________________________________________ > > >>> __ > > >>> ______________ > > >>> Be a better friend, newshound, and > > >>> know-it-all with Yahoo! Mobile. Try it now. http:// > > >>> mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > >>> > > >> > > >> > > > > > > > > > > > > > > > ______________________________________________________________________ > > > ______________ > > > Looking for last minute shopping deals? > > > Find them fast with Yahoo! Search. http://tools.search.yahoo.com/ > > > newsearch/category.php?category=shopping > > > > > > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping

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