- Chimera-users - RBVI Mailing Lists

save session stripping TER statements from PDB's
by Pattanayek, Sabuj 13 Mar '04

13 Mar '04

In version 1.1892 (and older possibly), file > save session seems to be stripping TER statements from PDB files. The TER statement is helpful for specifically telling Chimera and other PDB viewers not to connect consecutive residues in a PDB (for example ATP/water molecules at the end of a PDB that are not part of the main protein chain). Re-inserting TER's manually into the .py file can become cumbersome especially when one PDB insertion in the .py is 27000+ columns long. Would it be possible to fix this in future versions? Thanks in advance, Sabuj Pattanayek

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[Chimera-users] chimera-1.1917-linux.exe: Exec format error. Wrong Architecture.
by Pattanayek, Sabuj 12 Mar '04

12 Mar '04

I'm getting this error when I try to run the installation -rwx------ 1 root root 26226504 Mar 12 12:02 chimera-1.1917-linux.exe [root@eglimp]# chimera-1.1917-linux.exe chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. [root@eglimp]# ./chimera-1.1917-linux.exe ./chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. [root@eglimp]# md5sum chimera-1.1917-linux.exe 67e955ce87d000916039d94c7d6d0a56 chimera-1.1917-linux.exe [root@eglimp]# uname -rs Linux 2.4.22-openmosix2smp web page: linux chimera-1.1917-linux.exe Size: 26226504 bytes MD5: 67e955ce87d000916039d94c7d6d0a56 Thanks in advance Sabuj Pattanayek

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mac version of 1.1917 snapshot
by Eric Pettersen 11 Mar '04

11 Mar '04

Hi again, If you downloaded the Mac version of 1.1917 before about 5pm PST today, you should download it again because we updated it to fix a bug. The non-Mac versions are fine. The Mac version was not displaying atoms in stick, ball-and-stick, or sphere modes (wireframe mode was okay). Sorry for the possible inconvenience! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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new snapshot release (1.1917)
by Eric Pettersen 10 Mar '04

10 Mar '04

Hi, We've just put a new snapshot release of Chimera up for download on the web site (http://www.cgl.ucsf.edu/chimera) Here are the highlights of the changes between this snapshot (1.1917) and the previous one (1.1892): tools: Match -> Align can create sequence alignments for multiple matched structures (not just pairs) Multalign Viewer can show/edit sequence annotations for relevant formats (RSF, Stockholm) SimpleSession -- saves label font/size and secondary structure assignments -- compiles to .pyc file: 50% less memory use, 15% less time to restore added Export Surfaces as VRML (in Utilities category) -- save surfaces made by Multiscale Models and Volume Viewer as VRML files added Browser Configuration (also in Utilities) -- configure browsers to send certain file types to Chimera (see also new Web Data preferences) FindHBond and PBReader allow line width to be set Movie has preliminary support for reading GROMOS trajectories newly available commands: bondcolor -- color bonds independent of flanking atoms bonddisplay -- set how bond display depends on flanking atom display bondrepr -- set bond representation to be wire or stick (independent of atoms) hbonds -- command equivalent of FindHBond tool rlabel -- whether residue name/number is included in the first atom label per residue Model Panel new 'render attrs...' button allows coloring by model/residue/atom attributes (e.g. B-factor) The 'render attrs...' interface is in preliminary form and will be changing. It also isn't documented yet but is pretty easy to use. Just pick an attribute of interest and a histogram of values will be displayed. By default there will be three color bars on the histogram that you can grab and move around with the mouse, or add or remove with control-click. You can use the 'Color' color well to set the color of the last bar you picked. The 'No value' color well is used in the rare case of the attribute being missing (or set to None) in the atom/residue/model. Click Apply or OK to make the coloring happen. Several parts of the interface are grayed out since they haven't been implemented yet. In the future you will be able to select by attribute value, and change atom radii or ribbon widths based on attribute values. If you are using the last production release (1.1872) instead of the previous snapshot, then you will also be getting these features when you go to 1.1917: general: additional file formats for saved images (PS, EPS) different lighting scheme in graphics window (over-the-shoulder instead of headlight) tools: added Shininess Control (in Viewing Parameters) -- adjust shininess, brightness, and the color used for shiny highlights Collaboratory section in Preferences allows designation of port number and IP address (for firewalls/NAT) Movie -- allows definition of scripts to be run at each time step -- looping can be turned off Multalign Viewer allows structure selection by arbitrary % residue conservation Volume Viewer options added to subdivide and smooth isosurfaces commands: copy command now offers supersampling and PS/EPS formats new ribbackbone command controls whether ribbon and backbone atoms are shown simultaneously Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Use of Chimera for Trends Plant Sci March 2004...
by John F. Allen 24 Feb '04

24 Feb '04

....for article and issue cover illustration. Final proofs attached. Acknowledged. Great program. Will send reprint(s) and final pdf on request. Many thanks John F. Allen Professor of Plant Cell Biology Plant Biochemistry Center for Chemistry and Chemical Engineering Lund University Box 124 SE-221 00 Lund Sweden Tel: +46 46 222 7788 (Office); +46 46 222 4073 (Laboratory) Fax: +46 46 222 4009 (Direct); +46 46 222 4116 (Departmental) E-mail: john.allen(a)plantbio.lu.se Plant Cell Biology: http://plantcell.lu.se Publications: http://plantcell.lu.se:591/john/

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CHIMERA help - coloring density maps
by Padmaja Natarajan 02 Feb '04

02 Feb '04

Hi, I have just started using CHIMERA to look at volume files in the CCP4 format for virus particles. I would like to color the density as a color ramp continuously changing between ANY two specified colors depending on the radial distance from the center of the virus particle (as shown in the attached figure). How do I achieve this with CHIMERA? thank you very much for your help in advance. -Padma

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Chimera dead after NVidia driver install...
by Patrick Ladam 12 Jan '04

12 Jan '04

Hi all, I had chimera 1.1872 working OK on my MDK 9.2 Linux box until I installed the NVidia driver for my GeFOrce2 card. What happens now is that chimera launches but stops during start-up with an error box indicating this message: "Togl: Couldn't get visual" This sounds like an OpenGL problem to me but I am far from being a specialist on this. Does anyone have a clue how I can debug/fix this ? Bye -- ----------------------------------------------------------------- | Patrick LADAM | | | Laboratoire CSSB | THE BIG BANG THEORY: | | UFR SMBH | | | 74 rue Marcel Cachin | In the begining there was | | 93017 Bobigny CEDEX | nothing at all. | | e-mail: | | | ladam(a)smbh.smbh.univ-paris13.fr | Then, it exploded... | | Tel: 01 48 38 77 26 / 76 85 | | | Fax: 01 48 38 77 77 | | -----------------------------------------------------------------

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hi
by amutha ramaswamy 08 Jan '04

08 Jan '04

Dear Sir It is possible to make movies with PDB structurers in chimera. this would really be helpfull in visualing the conformatinal changes. I know chimera has the option for movie with trajectory files. but i wish to kow the option with PDB files only. Looking forward for your kind reply Sincerely Amutha Dr Amutha Ramaswamy Postdoctoral Fellow, Department of Biomedical Informatics 3184 Graves Hall, 333 West 10th Avenue The Ohio state University, Columbus, OHIO 43210 Phone: 614-688-3236 (Office); 614-291-0071(Residence) Fax: 614-292-7659 (Office) --------------------------------- Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes

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Re: save selected atoms in a pdb file?
by Elaine Meng 08 Jan '04

08 Jan '04

Hi Sabuj, You can make surfaces that surround a set of atoms without making a separate PDB file. For example, if you have those atoms selected already, just use the command: surfcat mygroup sel where "mygroup" could be whatever you choose to name this set of atoms and "sel" means what is currently selected. Then, the command surface mygroup will show surface surrounding that group. There are several ways you could select the atoms of interest, and it sounds like you already figured out that part; the following detailed example is just one possibility: open pdb:2gbp sel :glc z<4.5 ~sel :glc ~sel solvent surfcat nearby sel ~sel surf nearby Here I opened a glucose-binding protein structure, selected all residues with any atom within 4.5 A of the ligand glucose (glc), then subtracted glucose itself and waters from the selection. Then I made the selected atoms a surface category with "surfcat," unselected them, and showed the corresponding surface. If you really want to save the selection to a file, it can be done on unix systems. Chimera can send information on what atoms are displayed to the system, and then the system command "cat" can send the information to a file. In Chimera, if the atoms of interest are selected: show sel pdbrun nouser cat > ~homedir/myfile.pdb (where "homedir" is your username) saves the displayed atoms to a PDB file named myfile.pdb in your home directory. It is necessary to use show (which undisplays everything else) since pdbrun includes all atoms that are displayed. The coordinates are transformed, so will be different from the original coordinates if you have moved the view around. If you want the untransformed coords, use the "reset" command before the "pdbrun" command. This process doesn't work on Windows as there is no cat command. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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save selected atoms in a pdb file?
by Pattanayek, Sabuj 08 Jan '04

08 Jan '04

Hi, Is it possible to save only the currently selected set of atoms/bonds or the atoms/bonds currently shown in the display into a pdb file? This is would be useful when doing surfaces for a particular location (e.g. atoms surrounding a central cavity), since the command "surface selected" seems to leave gaps in inaccessible areas (behind the atoms surrounding the cavity). Thanks, Sabuj Pattanayek

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[Chimera-users] shininess/brightness/specular color of surfnet surfaces
by Pattanayek, Sabuj 05 Jan '04

05 Jan '04

Hi, Is it possible to alter the shininess/brightness/specular color of Surfnet surfaces? Also is it possible to save the surfaces so they don't have to be recreated every time? Thanks, ----------------------------------------------------------------- Sabuj Pattanayek Martin Egli Lab Vanderbilt University Dept. Biochemistry http://linegli.mc.vanderbilt.edu

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Old version for Sparky
by laurent volpon 05 Jan '04

05 Jan '04

Hello, I would like to download an old version of Chimera (1.1442) because I have to use it with the same Python version (2.1) as Sparky. I tried at http://www.cgl.ucsf.edu/chimera/distrib/oldreleases.html but I had this: "Error: The URL you used is malformed". Please can you help me to find this version, or is there a way to use the version I have (1.1872) with the version 2.1 of Python (instead of 2.2). Thank you by advance for your answer. Sincerely Dr Laurent VOLPON ______________________________ Dr Laurent Volpon 3575 Avenue du Parc, Suite 5315 P.O. Box #85 Montréal, Qc, H2X 4A3 tel.: (514) 847-9494 ______________________________ --------------------------------- Lèche-vitrine ou lèche-écran ? Yahoo! Magasinage.

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vdw viewer
by Terry Downing 23 Dec '03

23 Dec '03

Hey CGL, I would like to be able to visualize several different vdw parameter sets on the same molecule. Is there a way to visualize just the vdw surface? Can I change the parameter files easily? As always, thanks in advance for your help. Sincerely, Terry Downing -- P. Therese Downing Chemistry and Chemical Biology Graduate Program Kuntz and James Labs, UCSF Voice: (415)476-3986 Fax: (415)502-1411

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ribbon+atoms
by Eric Pettersen 23 Dec '03

23 Dec '03

Hi, the 1892 snapshot release we just put out allows control over whether backbone atoms can be displayed with ribbons (on a per-model basis). There is a "ribbackbone" command, an entry in the New Molecules preference category, and a control in the attributes panel (reached via the "attributes..." button in the model panel). Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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interactive volume segmentation
by Juha Huiskonen 18 Dec '03

18 Dec '03

Hello, currently it is possible to select only box-shaped subregions in Volume Viewer. I would be especially interested in segmenting electron density maps or their isosurfaces to different subregions with any shape interactively. Is anyone planning to add a feature like this? Regards, Juha Huiskonen

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Re: [Chimera-users] Chimera export to VRML?
by Thomas Goddard 17 Dec '03

17 Dec '03

Hi Morgan, I've written an extension to export Chimera multi-scale and volume surfaces as VRML. I wasn't able to export the molecular (MSMS) surfaces because the code does not provide access to the surface coloring. I've submitted a request to enhance the molecular surface code to make surface colors readable. I'm not sure if the VRML surface exporting will make it into the coming snapshot release. If it doesn't I will provide it to you by email. I'll let you know when we have the snapshot ready, probably later this week. Tom

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Re: [Chimera-users] Chimera export to VRML?
by Thomas Goddard 16 Dec '03

16 Dec '03

Hi Morgan, We hope to have a snapshot Chimera release later this week. I'll try to get VRML output of multi-scale and msms surfaces in that release. Snapshot releases aren't as well tested as production releases, but are intended for trying out new features like this. Tom PS: Your email does not go to chimera-users unless you explicitly CC it to that list. We like to post to that list so others can benefit from it. I've included your email below and CC'ed this to chimera-users. Let me know if you want to keep your email private. > From: Morgan Ryan <mryan1(a)nc.rr.com> > Subject: Re: [Chimera-users] Chimera export to VRML? > Date: Tue, 16 Dec 2003 14:35:27 -0500 > > Thanks, Thomas. (Am I broadcasting to the list? I'm not sure if I'm > talking to a list or just you and Eric Petterson...) > > > For a large structure like a > > ribosome the VRML file ...might have a million triangles, and the file > > will > > at least be 30 megabytes. > > The 3D programs I use have fairly refined mesh management tools for > reducing complexity selectively, although being able to choose the mesh > density directly through MSMS would be pleasing. > > > You can choose the resolution of the multi-scale surfaces. We don't > > currently have VRML output for the multi-scale surfaces but that > > could be added fairly easily. I could look into that. > > The advantage of VRML output (or 3dmf, or dxf, or some other > interchange format) is that you could open the model in Maya, Studio > Max, Strata, Cinema 4D, any of the 3D animation programs, and make > startling movies wiith Hollywood special effects--light sabers! > Atomic-resolution recreations of enzyme reaction mechanisms! (The > latter is what I'm working on...) > > It would be a wonderful extension of Chimera if VRML output were added. > Morgan

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Chimera export to VRML?
by Morgan Ryan 16 Dec '03

16 Dec '03

VRML seems to be a native internal format for (the magnificent) Chimera. Is it possible to export VRML models from Chimera? Or do you worldly folks know of a mechanism for converting msms output into vrml files? Thanks! Morgan Ryan, enthusiastic amateur ____________________ Morgan Ryan Development editor W H Freeman 209 Adams Way Chapel Hill NC 27516 phone: 919 942 4890 fax: 651 846 5265 mryan(a)whfreeman.com

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help
by amutha ramaswamy 16 Dec '03

16 Dec '03

Dear sir I am using the Chimera molecular visualising software. I am not able to color the PDB structure according to the B-factors. could you plase let me know how do i color accroding to the bfactor. i would greatly apprecuate your help in this regard sincerely amutha Dr Amutha Ramaswamy Postdoctoral Fellow, Department of Biomedical Informatics 3184 Graves Hall, 333 West 10th Avenue The Ohio state University, Columbus, OHIO 43210 Phone: 614-688-3236 (Office); 614-291-0071(Residence) Fax: 614-292-7659 (Office) --------------------------------- Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing

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Re: Gaussians
by Thomas Goddard 11 Dec '03

11 Dec '03

Hi Lars, I'm not sure what you mean by visualizing some Gaussians. If you mean you want to make a volume which contains some specified Gaussians then I can give you a separate Python program that will do that. I already wrote it for another user. It is included at the end of this email. It outputs a netcdf format volume file. Tom % ./spots.py Make a volume array that is the sum of specified Gaussians. The first line of the input file has the grid cell size. Each subsequent line has 5 fields giving x, y, z, width, height. A volume grid is made that includes each Gaussian out to 3 widths. The resulting volume is written in netcdf format. Syntax: spots.py <infile> <outfile> % cat spotfile .5 15.49100 7.05000 17.16500 0.38 1.00 14.94600 7.55000 15.88800 0.35 1.00 16.01100 7.60400 14.81400 0.34 1.00 ... % ./spots.py spotfile gspottest.nc The spots.py code follows. Note that it contains a path to your Chimera installation because it needs Chimera modules to write the netcdf volume. #!/usr/bin/env python # ----------------------------------------------------------------------------- # Make a volume array that is the sum of specified Gaussians. # The resulting volume is written in netcdf format. # # Syntax: spots.py <infile> <outfile> # # The input file has a grid cell size on the first line followed by one # line per gaussian with 5 fields specifying x, y, z, width, height. # import os.path import sys # Need Chimera path to use VolumeData and Numeric modules CHIMERA_PATH = '/usr/local/chimera' sys.path.insert(0, os.path.join(CHIMERA_PATH, 'lib')) sys.path.insert(0, os.path.join(CHIMERA_PATH, 'share')) import Numeric # ----------------------------------------------------------------------------- # def make_spot_grid(path): step_size, spot_parameters = read_spots(path) range = 3 # in spot widths xyz_min, xyz_max = bounding_box(spot_parameters, range) xyz_origin = xyz_min xyz_step = (step_size, step_size, step_size) xyz_size = map(lambda a,b: a - b, xyz_max, xyz_min) import math grid_size = map(lambda s, step, math=math: 1 + int(math.ceil(s/step)), xyz_size, xyz_step) a = spot_array(spot_parameters, range, xyz_origin, step_size, grid_size) from VolumeData import Array_Grid_Data g = Array_Grid_Data(a, xyz_origin, xyz_step) return g # ----------------------------------------------------------------------------- # def read_spots(path): f = open(path, 'r') lines = f.readlines() f.close() step_size = float(lines[0]) spot_params = [] for line in lines[1:]: params = map(float, line.split()) spot_params.append(params) return step_size, spot_params # ----------------------------------------------------------------------------- # def bounding_box(spot_parameters, range): xmin = ymin = zmin = None xmax = ymax = zmax = None for x, y, z, w, h in spot_parameters: pad = range * w if xmin == None or x - pad < xmin: xmin = x - pad if ymin == None or y - pad < ymin: ymin = y - pad if zmin == None or z - pad < zmin: zmin = z - pad if xmax == None or x + pad > xmax: xmax = x + pad if ymax == None or y + pad > ymax: ymax = y + pad if zmax == None or z + pad > zmax: zmax = z + pad return (xmin, ymin, zmin), (xmax, ymax, zmax) # ----------------------------------------------------------------------------- # def spot_array(spot_parameters, range, xyz_origin, step_size, grid_size): shape = list(grid_size) shape.reverse() # array indices are z, y, x. array = Numeric.zeros(shape, Numeric.Float) for x, y, z, width, height in spot_parameters: add_spot((x,y,z), width, height, range, xyz_origin, step_size, array) return array # ----------------------------------------------------------------------------- # def add_spot(xyz, width, height, srange, xyz_origin, step_size, array): ijk = map(lambda a,b,s=step_size: (a - b)/s, xyz, xyz_origin) w = width / step_size w2 = w * w r = srange * width / step_size import math imin, jmin, kmin = map(lambda l, r=r, math=math: int(math.floor(l-r)), ijk) imax, jmax, kmax = map(lambda l, r=r, math=math: int(math.ceil(l+r)), ijk) for k in range(kmin, kmax+1): for j in range(jmin, jmax+1): for i in range(imin, imax+1): di, dj, dk = i-ijk[0], j-ijk[1], k-ijk[2] s2 = di*di + dj*dj + dk*dk e = height * math.exp(-s2/(2*w2)) array[k,j,i] += e # ----------------------------------------------------------------------------- # def bfactor_backbone_spots(path, molecule = None): if molecule == None: import chimera molecule = chimera.openModels.list()[0] out = open(path, 'w') out.write('.5\n') # step size import math for a in molecule.atoms: if a.name in ('C', 'N', 'CA') and hasattr(a, 'bfactor'): x, y, z = a.coord().xyz.data() w = math.sqrt(a.bfactor / (8 * math.pi**2)) h = 1 out.write('%8.5f %8.5f %8.5f %6.2f %6.2f\n' % (x,y,z,w,h)) out.close() # ----------------------------------------------------------------------------- # def syntax(): msg = ('Make a volume array that is the sum of specified Gaussians.\n' + 'The first line of the input file has the grid cell size.\n' + 'Each subsequent line has 5 fields giving x, y, z, width, height.\n' + 'A volume grid is made that includes each Gaussian out to 3 widths.\n' + 'The resulting volume is written in netcdf format.\n' + 'Syntax: spots.py <infile> <outfile>\n') sys.stderr.write(msg) sys.exit(1) # ----------------------------------------------------------------------------- # def run_command(): if len(sys.argv) != 3: syntax() inpath = sys.argv[1] outpath = sys.argv[2] grid = make_spot_grid(inpath) from VolumeData.netcdf.netcdf_grid import write_grid_as_netcdf write_grid_as_netcdf(grid, outpath) # ----------------------------------------------------------------------------- # if __name__ == '__main__': run_command()

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B-Factor
by Luis Cuello 09 Dec '03

09 Dec '03

Hello, My name is Luis Cuello and I am a graduate student at the University of Virginia..I started using chimera recently but I have not been able to colored my files by B-factors values, Is there any way to do that with chimera software??? If you could help me in this matter I would appreciated..Sincerely Luis Cuello University of Virginia Molecular Physiology 1(434)9245473 e-mail:lgc4r@virginia.edu

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Re: [Chimera-users] delphi potenital map viewing
by Thomas Goddard 05 Dec '03

05 Dec '03

Hi Klaas, The Delphi Viewer is the only tool that can color a molecular surface according to the potential value. Can you email me the Python traceback you get when the "_cubes error: ..." occurs? This shows exactly where in the code the error happened. You find it by looking at Favorites/Reply Log. Having the traceback alone might be enough for me to figure out and correct the problem. If you could put the phi file on the web so I could download it I would almost certainly be able to figure out the problem. The Delphi Viewer is supposed to be able handle maps of any size. It will be much slower than volume viewer, but it should not generate an error with a large map. Tom > Date: Fri, 05 Dec 2003 21:10:20 +0100 > From: Klaas Decanniere <Klaas.Decanniere(a)pandora.be> > Reply-To: Klaas.Decanniere(a)pandora.be > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] delphi potenital map viewing > > Thomas Goddard wrote: > > >Hi Klaas, > > > > The size of the Delphi potential map Chimera can display is only > >limited by the size of your computer memory. > > > > If you open a large map it does not get shown immediately if the map > >is larger than 1 Mvoxels (~100^3). > > > > > > When I tried using the "delphi viewer" option, I get _cubes error: grid > index out of range > Using the volume viewer I can indeed load everything. > Is there a way to tie the volume viewer thing to a molecular surface? > With a colour gradient showing different levels of potential? (As in the > Molecular surface option in the Delphiviewer) > Or maybe I can save the subsampled map somehow and then read it into the > delphiviewer thing? > > Thanks again for your help. > > Klaas > > P.S.: I like the program more each day. > P.P.S.: If you ever have a day with nothing to do: the automatic > fetching of pdb files doesn't work for me as I'm behind a proxy server.

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delphi potenital map viewing
by Klaas Decanniere 04 Dec '03

04 Dec '03

Hello, Thinking that more is better I ended up with Delphi potential maps on a rather large grid which I would like to visualize with chimera (gsize=213) Chimera seems to think the grid is to large. Is there an easy way to have chimera accept bigger grids (speed is not really an issue)? Alternatively, what is the largest grid that chimera can accept? Thanks for your help. Klaas Decanniere

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ribbon+atoms
by Elaine Meng 25 Nov '03

25 Nov '03

Dear Soren, Thanks for the compliments - we're trying! You're right that in recent versions of Chimera , showing ribbon turns off the backbone atoms. There is an easy workaround: open two copies of the same molecule, use one copy to show ribbon and the other copy to show atoms. The reason for the behavior is when the ribbon is drawn as a smooth curve, it does not exactly pass through the backbone atoms. Often one wants to show just the ribbon and certain side chains, and the current behavior is to extend the side chain to meet the ribbon (even when the backbone atoms are not on the ribbon) so that they are not floating in space. However, we agree that sometimes one will want to display both the ribbon and the backbone atoms, and in the future there will a preference to switch between: (a) show ribbon, not backbone atoms, and extend the side chains to meet the ribbon (b) show ribbon and whatever backbone atoms are displayed by the user, do not extend side chains to meet the ribbon Until this switchable preference becomes available, we hope that the suggested workaround will let you do what you want. Sincerely, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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ribbon+atoms
by Soren M. Kristensen 25 Nov '03

25 Nov '03

Dear Chimera developers You have createdt an absolutely brilliant program. I have a small question/suggestion about displaying atoms and ribbons simultaneously. When displaying a number of backbone atoms and then putting on a ribbon, then some of the atoms dissapear in release 1700 and onwards. Is there a way to avoid this behaviour? It basically means that I am stuck with the pre-1700 version, but maybe there is some parameter I can tweak to make it work in the new versions? I would be grateful for your help. I reproted this as a bug some 6 months ago, but was told that it was supposed to be like this. I measure experimental values for selected backbone atoms and display them as colorcoded spheres on top of a ribbon to indicate what is measured different places in the structure. If you have suggestions to acieve this behaviour in another way I would be grateful. Thank you in anticipation, Søren -- Søren M. Kristensen, Ph.D. Phone: (+45) 3532 0301 University of Copenhagen FAX: (+45) 3535 0609 Department of Chemistry E-mail: smk(a)kl5.ki.ku.dk H. C. Ørsted Institutet http://kl5.ki.ku.dk/~smk Universitetsparken 5 Room: C508 DK-2100 København Ø Denmark

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