[PyMOL] Visualisation of APBS maps in pymol compiled for RHEL WS 3.2 (x86_64)
Hi there, I'm having problems visualising apbs .dx maps in pymol. Pymol (0.97) and apbs (0.3.1) compile from source fine and run otherwise normally. apbs_tools launches ok within pymol and the user interface appears fine. On initiating the calculation, pink dots representing charge assignment appear and disappear. apbs_tools output seems fine: This executable compiled on Mar 18 2005 at 18:20:06 Parsing input file pymol-generated.in... Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from pymol-generated.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2145 atoms Centered at (-1.215e-01, 1.816e+00, -1.078e+00) Net charge -2.99e+00 e Preparing to run 2 PBE calculations. CALCULATION #1: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 191.244 MB total, 191.244 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.689 x 0.704 x 0.761 Grid lengths: 66.183 x 67.631 x 73.076 Grid center: (-0.121, 1.833, -1.045) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 4 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 2.000 A-radius, 2.000 e-charge, 0.000 M concentration 2.000 A-radius, -2.000 e-charge, 0.000 M concentration Solute dielectric: 20.000 Solvent dielectric: 80.000 Using molecular surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 310.000 K Surface tension: 0.105 kJ/mol/A^2 Solving PDE (see io.mc* for details)... CALCULATION #2: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 188.714 MB total, 216.587 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.614 x 0.623 x 0.656 Grid lengths: 58.931 x 59.783 x 62.986 Grid center: (-0.121, 1.833, -1.045) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 4 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 2.000 A-radius, 2.000 e-charge, 0.000 M concentration 2.000 A-radius, -2.000 e-charge, 0.000 M concentration Solute dielectric: 20.000 Solvent dielectric: 80.000 Using molecular surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 310.000 K Surface tension: 0.105 kJ/mol/A^2 Potential to be written to pymol-generated.dx Solving PDE (see io.mc* for details)... Writing potential to pymol-generated.dx CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.000 MB total, 216.587 MB high water Thanks for using APBS! ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'. DXStrToMap: Dimensions: 97 97 97 DXStrToMap: Origin -29.587 -28.058 -32.538 DXStrToMap: Grid0.6140.6230.656 DXStrToMap: 912673 data points. ObjectMap: Map Read. Range = -52.501362 to 43.938789 but the following error appears when I try to update under the visualisation tab of apbs_tools: Function: bound method VisualizationGroup.refresh of pmg_tk.startup.apbs_tools.VisualizationGroup instance at 0x11fe808 (type: type 'instance method') Args: () Traceback (innermost last): File /usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib64/python2.2/site-packages/pmg_tk/startup/apbs_tools.py, line 484, in refresh getattr(self,thing).destroy() File /usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwButtonBox.py, line 66, in destroy Pmw.MegaWidget.destroy(self) File /usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, line 386, in destroy del _hullToMegaWidget[self._hull] KeyError: .17266312.17274344.17632616.18843560.17281704.18873128.18870664.18892984 I guess this is prob a more general python error within my setup but was just wondering if anyone else has encountered this problem or has any suggestions? Thanks, Nicola -- Dr Nicola Meenan Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU T: +44 (0) 1865 275773 F: +44 (0) 1865 275253
[PyMOL] Visualisation of APBS maps in pymol compiled for RHEL WS 3.2 (x86_64)
Hi there, I'm having problems visualising apbs .dx maps in pymol. Pymol (0.97) and apbs (0.3.1) compile from source fine and run otherwise normally. apbs_tools launches ok within pymol and the user interface appears fine. On initiating the calculation, pink dots representing charge assignment appear and disappear. apbs_tools output seems fine: This executable compiled on Mar 18 2005 at 18:20:06 Parsing input file pymol-generated.in... Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from pymol-generated.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2145 atoms Centered at (-1.215e-01, 1.816e+00, -1.078e+00) Net charge -2.99e+00 e Preparing to run 2 PBE calculations. CALCULATION #1: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 191.244 MB total, 191.244 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.689 x 0.704 x 0.761 Grid lengths: 66.183 x 67.631 x 73.076 Grid center: (-0.121, 1.833, -1.045) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 4 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 2.000 A-radius, 2.000 e-charge, 0.000 M concentration 2.000 A-radius, -2.000 e-charge, 0.000 M concentration Solute dielectric: 20.000 Solvent dielectric: 80.000 Using molecular surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 310.000 K Surface tension: 0.105 kJ/mol/A^2 Solving PDE (see io.mc* for details)... CALCULATION #2: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 188.714 MB total, 216.587 MB high water Using cubic spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.614 x 0.623 x 0.656 Grid lengths: 58.931 x 59.783 x 62.986 Grid center: (-0.121, 1.833, -1.045) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 4 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 2.000 A-radius, 2.000 e-charge, 0.000 M concentration 2.000 A-radius, -2.000 e-charge, 0.000 M concentration Solute dielectric: 20.000 Solvent dielectric: 80.000 Using molecular surface definition; harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 310.000 K Surface tension: 0.105 kJ/mol/A^2 Potential to be written to pymol-generated.dx Solving PDE (see io.mc* for details)... Writing potential to pymol-generated.dx CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.000 MB total, 216.587 MB high water Thanks for using APBS! ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'. DXStrToMap: Dimensions: 97 97 97 DXStrToMap: Origin -29.587 -28.058 -32.538 DXStrToMap: Grid0.6140.6230.656 DXStrToMap: 912673 data points. ObjectMap: Map Read. Range = -52.501362 to 43.938789 but the following error appears when I try to update under the visualisation tab of apbs_tools: Function: bound method VisualizationGroup.refresh of pmg_tk.startup.apbs_tools.VisualizationGroup instance at 0x11fe808 (type: type 'instance method') Args: () Traceback (innermost last): File /usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib64/python2.2/site-packages/pmg_tk/startup/apbs_tools.py, line 484, in refresh getattr(self,thing).destroy() File /usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwButtonBox.py, line 66, in destroy Pmw.MegaWidget.destroy(self) File /usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, line 386, in destroy del _hullToMegaWidget[self._hull] KeyError: .17266312.17274344.17632616.18843560.17281704.18873128.18870664.18892984 I guess this is prob a more general python error within my setup but was just wondering if anyone else has encountered this problem or has any suggestions? Thanks, Nicola -- Dr Nicola Meenan Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU T: +44 (0) 1865 275773 F: +44 (0) 1865 275253
Re: [PyMOL] Translating and rotating
On Mar 23, 2005, at 17:38, Warren DeLano wrote: Yes, but it is currently awkward because you need to protect the other atoms in the object from moving first (action menu - movement - protect on the inverse selection), then you can drag the object moving just the atoms in the original selection. No problem in my case, I want to move all atoms anyway, relative to an electron density map. But I don't see how I can move the atoms at all using the mouse - all I change is the camera view. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr -
Re: [PyMOL] Reading external grid files
On Mar 23, 2005, at 14:14, Antonio Morreale wrote:
I'm new to pymol, and maybe the question is very basic, but I hope to
have your help. I would like to read grids files generated by in house
program, how can I do this within pymol?
If the data is defined on an equidistant grid, and if you can read
those files into a Python array using Python code, then yes.
Here is an example for a Python script that reads a grid file into
PyMOL. My map object has attributes data (a 3D array containing the
data points) and x_axis, y_axis, z_axis (1D arrays containing the
coordinate values). The script is executed using run from inside
PyMOL.
Konrad.
filename = 'helix/filt-nmsk.map'
mesh_levels = [0.4, 0.5, 0.6]
from MMTK import *
from chempy.brick import Brick
import Numeric as N
map = load(filename)
x = map.x_axis/Units.Ang
y = map.y_axis/Units.Ang
z = map.z_axis/Units.Ang
resolution_x = x[1]-x[0]
resolution_y = y[1]-y[0]
resolution_z = z[1]-z[0]
brik = Brick()
brik.setup_from_min_max(
[x[ 0], y[ 0], z[ 0]],
[x[-1], y[-1], z[-1]],
[resolution_x, resolution_y, resolution_z],
0.01)
print brik.lvl.shape
print map.data.shape
# bring all values into the interval [0..1]
brik.lvl[:, :, :] = map.data/N.maximum.reduce(N.ravel(map.data))
cmd.load_brick(brik,density)
for level in mesh_levels:
cmd.do('isomesh s%d,density,%f' % (int(10.*level), level))
Re: [PyMOL] How to generate a DNA structure with given sequence?
Hi Hyun-Chul, It's easy to use PyMOL to build protein fragments in standard geometries (Build menu in the Tcl/Tk GUI window), but I'm not sure about DNA. Three non-PyMOL methods that I'm aware of are: (1) The program B (aka Biomer) from Dave Case's group at Scripps (http://www.scripps.edu/mb/case/Biomer/). It's a Java-based online biopolymer-building package, and is freely accessible. (2) The utility nucgen that comes with the Amber software package is useful for generating single- or double-stranded DNA and RNA structures in a variety of geometries (see pg. 236 of the Amber v8 manual -- http://amber.scripps.edu/doc8/amber8.pdf). Unlike B, this runs from a unix shell given plaintext input files, so would be more useful for scripting and things like that. However, Amber is not free. (3) There used to be a web-based server known as RBSCM: Rapid Building of Standard 3D-Conformations of DNA/Protein available at http://www.bioinf.co.uk/bsps/bsps_N.html;, and I found it very useful for quickly building standard geometries. The www.bioinf.co.uk site doesn't seem to exist anymore (no redirects), but maybe you can track it down elsewhere... There are probably other ways to go about this too (e.g., InsightII biopolymer builder), but I think they're all proprietary/closed-source/not-free. Good luck, Cam === pymol-users-requ...@lists.sourceforge.net wrote (on 03/23/2005 03:15 PM): === Subject: [PyMOL] How to generate a DNA structure with given sequence? From: HYUN-CHUL KIM sun...@saju.kaist.ac.kr Date: Wed, 23 Mar 2005 19:40:56 +0900 To: pymol-users@lists.sourceforge.net I want to know how to generate a DNA structure with a given sequence. I heard that Pymol can do that but I couldn't find such command. Can you tell me how to do this? Sincerely, Hyun-Chul Kim
Re: [PyMOL] How to generate a DNA structure with given sequence?
To add to what Cameron said: * Cameron Mura cm...@ucsd.edu [2005-03-24 09:44] wrote: Hi Hyun-Chul, It's easy to use PyMOL to build protein fragments in standard geometries (Build menu in the Tcl/Tk GUI window), but I'm not sure about DNA. Three non-PyMOL methods that I'm aware of are: (1) The program B (aka Biomer) from Dave Case's group at Scripps (http://www.scripps.edu/mb/case/Biomer/). It's a Java-based online biopolymer-building package, and is freely accessible. (2) The utility nucgen that comes with the Amber software package is useful for generating single- or double-stranded DNA and RNA structures in a variety of geometries (see pg. 236 of the Amber v8 manual -- http://amber.scripps.edu/doc8/amber8.pdf). Unlike B, this runs from a unix shell given plaintext input files, so would be more useful for scripting and things like that. However, Amber is not free. (3) There used to be a web-based server known as RBSCM: Rapid Building of Standard 3D-Conformations of DNA/Protein available at http://www.bioinf.co.uk/bsps/bsps_N.html;, and I found it very useful for quickly building standard geometries. The www.bioinf.co.uk site doesn't seem to exist anymore (no redirects), but maybe you can track it down elsewhere... There are probably other ways to go about this too (e.g., InsightII biopolymer builder), but I think they're all proprietary/closed-source/not-free. There is an easy to use open-source program called NAMOT (http://namot.lanl.gov/) that allows one to type in a sequence and create a DNA molecule with options for single- or double-stranded and A, B or Z conformations. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
[PyMOL] RE: pdb loader service
is it possible to use the pdb loader in a *.pml style script? With the shipped plugin it may be hard. I wrote the original, but have since written a new/improved one that does not tough the filesystem and adds a remote command that will fetch and load pdbs as well. You can see the code for this newer plugin on the pymol wiki: http://www.pymolwiki.org/index.php/Category:Plugins_Tutorial Using this newer plugin you can make use of the remote command. Warren, would you be opposed to putting this updated plugin in CVS? It has the benefit mentioned above, and the remote command has proven really useful for me at least. Thanks, Charlie
RE: [PyMOL] G5 and pymol flashing
Bill, I've noticed this happens on some machines (G5 imac) and not others (G5 dual, G4 powerbook, G4 tower). I may be a bug in Panther, since the problems seems to have been fixed in the Tiger beta, but...well...that's not out yet. It does seem to depend on whether or not any other programs actively updating the screen at the same time while PyMOL is running. How many other MacPyMOL users out there are experiencing this issue? Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of William Scott Sent: Thursday, March 24, 2005 3:41 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] G5 and pymol flashing Hi folks: I bought a new G5 fairly recently. When using pymol, the screen goes white for brief instances when rotating a molecule, giving rise to a flashing effect that is so off-putting it keeps me from using pymol on this machine. I have a 20 monitor and the following video card: PCI/AGP Cards: GeForce 6800 Ultra: Type: display Bus: AGP Slot: SLOT-1 VRAM (Total): 256 MB Vendor: nVIDIA (0x10de) Device ID: 0x0040 Revision ID: 0x00a1 ROM Revision: 2119 NVDA,Display-A: Type: display Display Type: LCD VRAM (In Use): 256 MB It was a $450 upgrade from the default card. I am running the latest MacPyMOL version. Is there anything that can be done about this? Is the graphics card defective? The same pymol works perfectly fine on my old G4 laptop. Thanks. Bill --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595alloc_id=14396op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
