- Chimera-users - RBVI Mailing Lists

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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