- Chimera-users - RBVI Mailing Lists

[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 10 Mar '04

10 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 09 Mar '04

09 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 22 Dec '03

22 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 16 Dec '03

16 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 10 Dec '03

10 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 08 Dec '03

08 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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some CADD tools released
by gentamicin5 19 Nov '03

19 Nov '03

Dear all, I have written some CADD tools, and the details are described below. All of these programs are released under GNU/GPL. You can download them from: http://home.pchome.com.tw/team/gentamicin/mol/mol.htm ------------------------------------------------------------------- CADD tools (linux & irix) pscan_2.2.0 PSCAN is a small but a practical tool for finding any potential binding site of a protein. It can picture the size and appearance of a binding site, and point out the possible pharmacophore.Thus it is helpful for drug design. While running DOCK, QCPE_MS is necessary for autoMS and even the next step sphgen. QCPE_MS, however, is a commercial package. Now, PSCAN and SPHBOX can do the same job. After removing all dots outside of the target binding site by SPDBV (or others), and choosing several positions you are interesting, run SPHBOX to generate sph and box files. pmol2q_2.1.1_rc2 PMOL2Q is a specific file format converter for protein pdb file to mol2 file with adding hydrogens and partial charges. From v2.1.1, PMOL2Q can also output pdbq and pdbqs format. (The pdbqs format is added solvation data according with ADDSOL in AutoDock) It can recognize each amino acid and reconstruct the coordination precisely. The bond length of 109 pm for C-H, 101 pm for N-H, 96 pm for O-H and 134 pm for S-H are used for adding hydrogens.You can choose to add global hydrogens or only polar hydrogens. KOLL and AMBER95 partial charges are available in PMOL2Q. PMOL2Q can also check probabel error of protein coordination, including incomplete atom_missing residues and atom bumps. Hydrogens will not be added on incomplete residues if they exist. You need to fix it by other program before converting file format. (ex. SPDBV can fix the incomplete residues by mutate function) dbfilter_2.2.1 DBFILTER can check the mol2 format database, and pick out any problematic structure which results in "segmentation fault" of DOCK during flexible docking. (for example, salt or structure which contains multi-molecular built in....) And DBFILTER will output a new database which you want. There are also 12 kinds of filters for spotlighting drug-like properties. Including: Common_atoms_only, Molecular_weight, LogP, H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens, Rings, Big_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-. ----------------------------------------------------------------- 每天都 Yahoo!奇摩海的顏色、風的氣息、愛你的溫度，盡在信紙底圖 http://tw.promo.yahoo.com/mail_premium/stationery.html

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Fwd: MidasPlus version 2.1 (1997/02/04)
by Robin Parsons 17 Nov '03

17 Nov '03

Begin forwarded message: > From: Devleena Mazumder <devleena(a)chem.ucsb.edu> > Date: Fri Nov 14, 2003 6:04:37 PM US/Pacific > To: Robin Parsons <rparsons(a)cgl.ucsf.edu> > Subject: Re: MidasPlus version 2.1 (1997/02/04) > > Dear Robin, > Thanks for your email. > I have installed Chimera. Its easier to use than Midas. Unfortunately, > I > dont see the label3d option in it that was available with Midas. So, I > am > unable to get labels in neon. > Thanks > Devleena > > On Thu, 6 Nov 2003, Robin Parsons wrote: > > :>To: Devleena, > :>University of California, Santa Barbara, > :> > :>Thank you for your interest in our MidasPlus molecular modeling > :>software. You should know, however, that MidasPlus 2.1 is the final > :>version of MidasPlus and will not be developed further. You may wish > :>to explore our next generation of molecular modeling software, > Chimera. > :> You can look over Chimera's capabilities on our web site at: > :> > :>www.cgl.ucsf.edu/chimera/ > :> > :>In addition, Chimera is offered at no cost to educational and > :>non-profit institutions. > :> > :>Please contact me if you have any further questions. > :> > :>Robin Parsons > :>UCSF Computer Graphics Lab > :>Resource for Biocomputing, Visualization and Informatics > :>600 16th St., Room N-472B, Box 2240 > :>San Francisco, CA 94143-2240 > :>Commercial Carrier Zip Code: 94107 > :>tel. 415-476-1540 > :>fax 415-502-1755 > :>rparsons(a)cgl.ucsf.edu > :> > :> > > > > _______________________________________________________________ > DEVLEENA MAZUMDER-SHIVAKUMAR > PhD Candidate, Dept of Chemistry & Biochemistry > UNIVERSITY OF CALIFORNIA SANTA BARBARA > http://www.chem.ucsb.edu/~devleena/ > > **Although the past gives us lessons, it does not > give the whole answer to what must be done now.** > > Robin Parsons UCSF Computer Graphics Lab Resource for Biocomputing, Visualization and Informatics Assistant to Thomas Ferrin, PhD 600 16th St., Room N-472B, Box 2240 San Francisco, CA 94143-2240 Commercial Carrier Zip Code: 94158 tel. 415-476-1540 fax 415-502-1755 rparsons(a)cgl.ucsf.edu

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quick question
by vreyes 30 Oct '03

30 Oct '03

To Whom It May Concern: Our system is SUN Solaris 64bit Sparc III. Should I select #4 from the list below when downloading Chimera? 1.) SGI IRIX Platforms 2.) i386 Linux Platforms 3.) Mac OS X using X windows 4.) Tru64 UNIX 5.0/5.1 Platforms 5.) Microsoft Windows Platforms Please let us hear from you ASAP. Thanks very much for your help. V. Reyes San Diego Supercomputer Center Structural Bioinformatics group

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Delphi controller
by Marco Sette 21 Oct '03

21 Oct '03

Dear all, I'm trying to use the Delphi controller but I have problems to interface Delphi to Chimera.I created a link to Delphi under the Chimera directory but it does not seems the correct way. Is there some place to look to solve this problem ? I use Linux RedHat 9.0 Thanks, Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Delphi under Chimera
by Marco Sette 20 Oct '03

20 Oct '03

Dear all, I'm trying to use the Delphi controller but I have problems to interface Delphi to Chimera.I created a link to Delphi under the Chimera directory but it does not seems the correct way. Is there some place to look to solve this problem ? I use Linux RedHat 9.0 Thankks to all. Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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by solomon 15 Oct '03

15 Oct '03

Hi, I'm a new chimera user. Now I have some difficult to use chimera. How can I save the amino acid that I select as a new .pdb file. For example, I select the amino acids that is around the ligand within 10 A,and I want to save these residues as an another .pdb file. How can I do? Best regards, xiaogaokeng

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how to edit pdb file
by solomon 15 Oct '03

15 Oct '03

dear sir, I'm a new chimera user. Now I have some difficult to use chimera. How can I save the amino acid that I select as a new .pdb file. For example, I select the amino acids that is around the ligand within 10 A,and I want to save these residues as an another .pdb file. How can I do? Best regards, xiaogaokeng

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Re: bug? (HETATMs)
by Eric Pettersen 06 Oct '03

06 Oct '03

On Saturday, October 4, 2003, at 10:21 AM, solomon wrote: > when i open a pdb format file like below: > HETATM ................................. > HETATM ................................. > HETATM ................................. > ... > ... > ... > HETATM ................................. > > then I find that all the HETATM type atoms are bonding each other. All > the HETATM need a ter card to split them. As for HETATM type, I think > maybe there is some wrong with chimera. > best regards > gaokeng xiao Dear Gaokeng, As far as know, Chimera will connect HETATM segments of all standard PDB files (i.e. those distributed by the RCSB) correctly. That being said, Chimera has to do a lot of guessing when it comes to connecting non-standard PDB files (which I'm pretty sure is the kind of file you're talking about here). One thing to keep in mind with HETATMs is that they don't necessarily imply a chain break. Also, they are supposed to have CONECT records detailing their connectivity. So for instance, part of PDB entry 1f1j looks like this: ATOM 3688 OG SER B 602 58.714 25.290 29.976 1.00 66.81 O TER 3689 SER B 602 HETATM 3690 C ACE C 701 29.751 29.860 -0.650 1.00 52.20 C HETATM 3691 O ACE C 701 28.552 30.100 -0.812 1.00 55.72 O HETATM 3692 CH3 ACE C 701 30.801 30.183 -1.675 1.00 52.54 C ATOM 3693 N ASP C 702 30.252 29.308 0.427 1.00 51.48 N The ACE residue in the HETATM records is connected to residue 702 (as detailed in the CONECT records for the file). So in summary, you can have sequences like these where the HETATM residues are connected: ATOM ATOM HETATM HETATM HETATM ATOM ATOM -or- HETATM HETATM HETATM ATOM ATOM Now the really big problem is that the SCOP web site returns "PDB" files with just these kinds of sequences but with _no_ CONECT records! So, Chimera guesses as best it can in this situation. The rule of thumb that it uses is that HETATMs are connected unless they occur somewhere after a TER card with no intervening ATOM record. Explicit CONECT records can add connectivity. So for your file of all HETATMs where nothing should be connected, there is a silver lining: in order to get nothing connected you just have to add a _single_ TER card at the beginning of the file, like this: TER HETATM ................................. HETATM ................................. HETATM ................................. --Eric

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graphics accelorator choice of chip
by David Griffiths 02 Oct '03

02 Oct '03

Since Fire GL2 is now discontinued does anybody have experience of latest graphics acceloratots for use on chimera It has been suggested to me that the following should be OK but does anybody have experience of using them ? NVidia Geforce FX 5600/5900 ATI 9700/9500. david griffiths d.g.griffiths(a)herts.ac.uk

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Re: [Chimera-users] how to color ribbons?
by Elaine Meng 20 Aug '03

20 Aug '03

Hi Mario, I'll include two different ways you could do this in Chimera 1.1700: ---------------- with menu ---------------- Actions... Atoms/Bonds... hide Actions... Ribbon... show Actions... Ribbon... edged Actions... Color... white Select... Structure... secondary structure... helix Actions... Color... red Select... Structure... secondary structure... sheet Actions... Color... cyan Select... Clear selection ---------------- with commands ---------------- ~display ribbon ribrepr edged ribcolor white ribcolor red :/isHelix ribcolor cyan :/isSheet ---------------- In both approaches, first the atoms are undisplayed, then the ribbon is turned on. The step setting the ribbon type to "edged" is optional; you could use whichever ribbon type you want. Then, I make everything white before making helices red and strands cyan. The reason I don't use the turn descriptor is that it only applies to explicit PDB TURN records, whereas in most cases, the PDB only contains HELIX and SHEET records. You could just put the commands in a plain text file, for example named "sscolor.com," and then use the command "source sscolor.com" to execute all the commands in the file. (The file must be in the working directory; otherwise you will have to include the whole path in the source 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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how to color ribbons?
by Mario Albrecht 20 Aug '03

20 Aug '03

Hi, I'm new to Chimera but I'm missing a simple script in the menu for the normal display of ribbons. Helices in ribbons should be colored in red, strands in cyan, and the rest in white. May you provide such a script? Thank you much, Mario Albrecht

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background manipulation
by Jacob Schmidt 18 Aug '03

18 Aug '03

Greetings: Can you tell me how to completely get rid of the black background on which structures appear? As you probably know printer ink is not cheap. Thanks - Jakob Schmidt, Dept . Biochem and Cell Biol. SUNY Stony Brook

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saving partial coordinates
by Elaine Meng 21 Jul '03

21 Jul '03

Hi Mark, In the current release of Chimera: if you are on a non-Windows system, you can use the command "pdbrun" to save just the atoms that are displayed. You can see the manual page for this command by typing "help pdbrun" in the Chimera Command Line (by default, Favorites... Command Line). example: pdbrun nouser cat > myzone.pdb Pdbrun literally sends the information for only the displayed atoms in their displayed positions to another command, in this case "cat" to send the information to the file myzone.pdb. If you want the coordinates to be the same as in the original file, first use the command "reset." All the atoms should be in view (i.e. if you are zoomed in and the atoms around the periphery cannot be seen in the Chimera window, they won't be in your output file either). The command "save" (or File... Save Session As... ) doesn't save coordinates, only how they are positioned/colored/displayed, etc. In fact, restarting a saved session will use the original input file(s) for coordinates. The command "write" (same as the function "write PDB" in the Model Panel) saves coordinates into a file. However, these will save the entire coordinates whether displayed or not. If you are on Windows, I am not aware of a solution in the current release. In our working version and thus the next release (late summer or early fall, I believe) there is a delete action. This would allow you to select the atoms/bonds outside a zone, for example, and then actually delete them. (Actions... Atoms/Bonds... delete). Subsequently, a file created with "write" would only contain the atoms/bonds that had not been deleted. 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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I Need Help!
by Mark Cunningham 20 Jul '03

20 Jul '03

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Re: ribbons, chimera, and collagen
by Eric Pettersen 18 Jul '03

18 Jul '03

Hi Randy, You can force Chimera to treat collagen as helical without too much difficulty. First, select a chain or chains (either Select...Chain, or pick an atom or atoms in the graphics window and use up-arrow several times until the chain(s) are selected). Then use the selection inspector (Tools...Inspectors...Selection Inspector, or click the button showing the selection in the lower-right part of the Chimera window). Change what is being inspected to 'Residue' and then set 'in helix' to true. The problem is that the ribbons don't look very good (they're too "twisty") because it's not an alpha helix. Maybe Conrad can suggest something. I don't have any suggestions myself (I tried making them "strands" and that was pretty twisty also). --Eric > I'm trying to make a ribbon plot of collagen using chimera, but it > doesn't > recognize collagen's secondary structure. > Can I just tell it to make a ribbon with the backbone atoms (or peptide > bonds), and not worry about what kind of secondary structure it really > is? > If so, how? > Have a nice day, > Randy

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Delphi and Chimera
by Marco Sette 09 Jul '03

09 Jul '03

Dear all, I have seen Chimera is able to create potential map using Delphi but, in your site, it is stated that this is valid only for unix systems. I have Delphi installed into windows and linux systems: it will be possible in the (near) future to run DelphiController onto these systems ? Thanks a lot for your attention, Best Regards, Marco -- Dr.Marco Sette, Ph.D. Deaprtment of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Re: [Chimera-users] Chimera - Dock grid
by Thomas Goddard 20 Jun '03

20 Jun '03

Hi Joel, The voldata.tar.gz file had a bug. I forgot to do byte swapping on the grid values. So it works on SGI and Mac or on Linux and Windows, but not both. I fixed this problem. The new code is at: http://www.cgl.ucsf.edu/home/goddard/voldata.tar.gz Tom

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Chimera - Dock grid
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi there, I'm quite impressed with chimera and its dock functionality. My query is about dock grid. I can't find any documentation about this ie what the values and their ranges represent. Also I can't seem to turn them off once they are on. And not to be too ungrateful different colours would be handy as well...how can I change those? While I'm at it is there a delete molecule button? Thanks for your help in advance joel -- ________________________________________ Joel Tyndall, PhD Research Officer http://www.imb.uq.edu.au Institute for Molecular Bioscience incorporating Centre for Drug Design and Development Centre for Cellular and Molecular Biology The University of Queensland Brisbane Australia 4072 Tel: +61 7 3346 2988 Fax: +61 7 3346 2101 email: J.Tyndall(a)imb.uq.edu.au

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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writing Mol2 format
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi David, Writing out Mol2 format can in principle be done, but there are a few caveats. If the original format is Mol2, the original information could be retained and written back out. I don't know how simple/hard this would be to implement (feel free to chime in, other members of the team). When the original format is not Mol2, there is less information in the molecule data than is needed to write the file. Chimera uses a fairly rich set of atom types, but there is still not a one-to-one relationship with all Mol2 types. One would need to create a mapping between the types. Also, I believe Chimera currently knows connectivity but not bond orders, and does not retain any point charge information. The online Chimera Programmer's Guide actually includes an example of code required to write out a mol2 file. I had forgotten about this when visiting your office earlier. It discusses a mapping between atom types (if you use this, you should examine this mapping and make sure it works the way you think it should). The example code writes out all bonds as single. Check it out: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html click the "Examples" link and then "Chimera's Object Model" This example is "writeMol2.py" If you have a molecule open in Chimera, you can view the type assignments using Actions... Label... IDATM type (version 1.1700). A listing/explanation of Chimera types can be seen at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html Best, 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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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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Writing to mol2
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Hi, I'm one of your "neighbors" working in the Shoichet lab for the summer. I think it'd be neat if you could output in mol2 format rather than just pdb format, especially if the input is in mol2. Is this in the works? Has it already been done? Is it easy to do? David Minh

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Chimera & dock grids
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Dear Dr. Tyndall, Thanks for your interest - DOCKgrid is indeed undocumented, partly because we have a much more advanced extension for viewing 3D data sets, Volume Viewer. This would let you have multiple contour surfaces or transparent solids in colors of your choosing, with interactively adjustable thresholds. The current hitch is that the DOCK grid formats have not yet been added to the Volume Viewer extension. We are actively looking into this and hope to incorporate it soon (we will let you know when this happens). I believe the values are directly those stored in the grid files, which (for dock 4 at least) are described in http://dock.compbio.ucsf.edu/dock4/html/Manual.1c.html#pgfId=850 The VDW repulsion, VDW attraction, and electrostatic grid values are described in equation 9 (all three are in the *.nrg grid). These are not in energy units until multiplied by ligand atom parameters. I believe the color choices in DOCKGrid are red and red. Display with Volume Viewer should be a vast improvement. To close molecules and also these contour surfaces, one way is to open the Model Panel (Tools... Inspectors... Model Panel in version 1.1700). In the Model Panel, choose the model(s) you want to close on the left side, then click "close" on the right side (not the Model Panel Close button). Unfortunately the contour surfaces created by DOCKgrid are each VRML files without an informative title, so it may be hard to tell which is which. If you only have one, of course, it will be obvious. I hope this helps! Best regards, 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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Re: Chimera graphics card requirements
by chimera-users＠cgl.ucsf.edu 10 Jun '03

10 Jun '03

Hi Jim, I think Chimera will start without an OpenGL stencil buffer. But the outline highlighting of selected atoms/bonds/... will not work. Fill mode highlighting settable with Favorites/Preferences/General/ Selection highlight method will work. With a Quadro4 700 XGL on Linux you should definitely have a stencil buffer available. Below is the output of "glxinfo -t" on my Linux system with Quadro4 500 graphics. It shows half the visuals have 8 bit stencil buffer. It shows I am using the Nvidia 4191 driver OpenGL version string: 1.4.0 NVIDIA 41.91 Check the OpenGL version string on your machine to make sure you are using the Nvidia driver and not Mesa (software opengl). Tom $ glxinfo -t name of display: :0.0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: NVIDIA Corporation server glx version string: 1.3 server glx extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer client glx vendor string: NVIDIA Corporation client glx version string: 1.3 client glx extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_SGI_video_sync, GLX_SGIX_swap_group, GLX_SGIX_swap_barrier, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_NV_float_buffer GLX extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_ARB_get_proc_address OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro4 500 GoGL/AGP/SSE2 OpenGL version string: 1.4.0 NVIDIA 41.91 OpenGL extensions: GL_ARB_imaging, GL_ARB_multitexture, GL_ARB_point_parameters, GL_ARB_texture_compression, GL_ARB_texture_cube_map, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat, GL_ARB_transpose_matrix, GL_ARB_vertex_program, GL_ARB_window_pos, GL_S3_s3tc, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint, GL_EXT_compiled_vertex_array, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels, GL_EXT_paletted_texture, GL_EXT_point_parameters, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shared_texture_palette, GL_EXT_stencil_wrap, GL_EXT_texture_compression_s3tc, GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, GL_EXT_texture_object, GL_EXT_vertex_array, GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, GL_NV_blend_square, GL_NV_fence, GL_NV_fog_distance, GL_NV_light_max_exponent, GL_NV_packed_depth_stencil, GL_NV_pixel_data_range, GL_NV_point_sprite, GL_NV_register_combiners, GL_NV_texgen_reflection, GL_NV_texture_env_combine4, GL_NV_texture_rectangle, GL_NV_vertex_array_range, GL_NV_vertex_array_range2, GL_NV_vertex_program, GL_NV_vertex_program1_1, GL_NVX_ycrcb, GL_SGIS_generate_mipmap, GL_SGIS_multitexture, GL_SGIS_texture_lod glu version: 1.3 glu extensions: GLU_EXT_nurbs_tessellator, GLU_EXT_object_space_tess Vis Vis Visual Trans buff lev render DB ste r g b a aux dep ste accum buffers MS MS ID Depth Type parent size el type reo sz sz sz sz buf th ncl r g b a num bufs ---------------------------------------------------------------------------------------------------- 0x21 24 TrueColor 0 32 0 rgba 1 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x22 24 DirectColor 0 32 0 rgba 1 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x23 24 TrueColor 0 32 0 rgba 1 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x24 24 TrueColor 0 32 0 rgba 0 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x25 24 TrueColor 0 32 0 rgba 0 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x26 24 TrueColor 0 32 0 rgba 1 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x27 24 TrueColor 0 32 0 rgba 1 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x28 24 TrueColor 0 32 0 rgba 0 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x29 24 TrueColor 0 32 0 rgba 0 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x2a 24 DirectColor 0 32 0 rgba 1 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x2b 24 DirectColor 0 32 0 rgba 0 0 8 8 8 0 0 24 8 16 16 16 16 0 0 0x2c 24 DirectColor 0 32 0 rgba 0 0 8 8 8 8 0 24 8 16 16 16 16 0 0 0x2d 24 DirectColor 0 32 0 rgba 1 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x2e 24 DirectColor 0 32 0 rgba 1 0 8 8 8 8 0 0 0 16 16 16 16 0 0 0x2f 24 DirectColor 0 32 0 rgba 0 0 8 8 8 0 0 0 0 16 16 16 16 0 0 0x30 24 DirectColor 0 32 0 rgba 0 0 8 8 8 8 0 0 0 16 16 16 16 0 0 > From: Jim Procter <procter(a)zbh.uni-hamburg.de> > Reply-To: procter(a)zbh.uni-hamburg.de > Organization: Zentrum Bioinformatik Hamburg > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Chimera graphics card requirements > Date: Tue, 10 Jun 2003 10:53:20 +0200 > > Hi. I'm sorry to bother you again - particularly with some trivial hardware > question, but I've been wondering about the minimum specification of OpenGL > graphics driver needed for Chimera. > > We have Quadro4 700 XGL/AGP/SSE2 drivers for our linux-installations, on what > I would expect to be fairly high-end PCs. There doesn't seem to be any way to > force these drivers to generate a stencil buffer - is this what other people > have found ? > > Thanks. > Jim

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Re: Chimera at NCMI
by chimera-users＠cgl.ucsf.edu 09 May '03

09 May '03

Hi Steve, I'll ask the other Chimera developers about making independent mode rotation use the center of the whole model when it is undisplayed. Unfortunately that is a change in the C++ that would not be available for a while. I'll try making a rotation/translation undo button next week. I think it can be done all in Python and I could just email you the code. Tom > Date: Fri, 9 May 2003 20:48:49 -0500 (CDT) > From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> > Reply-To: sludtke(a)bcm.tmc.edu > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Yeah, a rotation/translation undo would be great! The miscentering > problem isn't an issue for what I'm doing right now (at least not much of > one, but a more generic way of setting the center would be nice. Perhaps > using the origin you set for the volume data as a center for rotation. The > manual translations seem to be independent of this value... > > cheers... > > -- > ---------------------------------------------------------------------------- > Steven Ludtke, PhD | Baylor College of Medicine > sludtke(a)bcm.tmc.edu | Co-Director > stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging > V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. > instant messenger: sludtke42 | * Those who do ARE * > http://ncmi.bcm.tmc.edu/~stevel | The converse also holds

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independent rotation mode
by chimera-users＠cgl.ucsf.edu 09 May '03

09 May '03

Date: Fri, 9 May 2003 13:57:27 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi again. I just ran across a bug I thought I'd report. The session file is rather large, so I won't attach it initially. Let me know if you have problems reproducing it. Anyway, I have loaded several volume data sets which represent different versions of the same structure. Then: 1) set 'independent' rotation mode 2) set one model so it is active, but not shown (in the model panel) 3) rotate the models 4) set the model in 2 to be shown again Even though it was active, the model in 2 was not rotated. I have a complex scenario of models where I need to do this operation frequently, so right now all my rotations keep getting messed up unless I make sure all the models are active AND shown before rotating anything. Cheers... PS - This happens with both the current 1700 version and the previous one. -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds Date: Fri, 9 May 2003 15:04:20 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Not THAT big a rush. Whenever you have a chance :^) Anyway, I was trying to avoid having to explain the whole situation, but here goes. I have a PDB model, a density map based on the PDB model and 3 different EM maps of the same molecule (each a little different). All are aligned and centered. What I want to do is have the EM map(s) with overlaid PDB structure on the left side of the screen and the x-ray map with overlaid structure on the right half of the screen. Then I use 'independent mode' to rotate everything about its own center so I can see how the EM map and x-ray map compare. As long as everything is active and displayed, it works beautifully (except the PDB model center seems very slightly off, so you see a very small amount of the centering artifact you described). Anyway, on the 'EM' side, I have 3 models overlaid. Generally I want to turn their display on and off as I rotate each one around and look at them. However, even though all 3 remain active, when I turn off the display of a model (ONLY in independent mode), it no longer gets rotated properly. Hope that helps clarify... cheers. -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds From: Tom Goddard The problem is that indepedent rotation mode only rotates about the the center of the displayed part of the model. If nothing is displayed there is no center to rotate about. Date: Fri, 9 May 2003 20:02:39 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> I understand. I sort of figured it was something like this. Well, I'll give you my perspective as a 'user' from the EM community. As funny as it seems, I would actually want the opposite of the behavior you stated. That is, the molecules would always rotate about their 'true' center even if part wasn't displayed. The best solution from my perspective would either A) have a different 'independent' mode where things always rotated about their true centers or B) Make it so models that aren't displayed at all use their true center. This doesn't seem quirky to me. If the model is active, you assume some sort of rotation will occur. Presumably if part of the molecule is visible, the whole thing still gets rotated, just about a different center. So, it's odd for it not to get rotated at all. >From a user perspective, a problem I keep running into is that I accidentally do a rotation when not all of the molecules are active. This produces a relative rotation that is virtually impossible to undo through the GUI. Translations aren't a problem. They're pretty easy to 'undo' almost perfectly. But rotations are really tricky. When that happens I end up having to revert to my last saved session. So, having the model not rotate at all just because it isn't visible is doubly annoying... Anyway, just my perspective... -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds Hi Steve, I agree it is odd for the undisplayed model not to be rotated at all. It seems reasonable that when the model is undisplayed it should use the center of the whole model if you are using independent rotation mode. There is the additional problem that the centers of the models don't coincide. When you display an isosurface, it uses the center of the bounding box that just contains the surface. It does not use the actual bounds of the whole density map. I see that Chimera has support for fixing the center of rotation for each model. This could be used to get exactly the rotation behaviour you want. But we need a user interface to let you say which models you want to group together with a common center. I could write something like this in Python. This would address both the undisplayed models not rotating, and the not quite right centers of rotation. I realize that accidentally unaligning two models in Chimera is a disaster -- it usually means starting over. I think we need a rotation and translation undo to address this. Tom

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