Re: [PyMOL] Nuvision stereo glasses?
Hi David, ATI radeon 8500 works with the xig.com Summit Xserver, with stereographics stereo enabler cable (takes sync from the monitor cable) and infra red emitter box E2 with stereographics infra red shutter glasses. i don't know if this emitter and enabler cable work with nuvision glasses? (this commercial X server seems to break my sound though.confirmed to me by xig as a bug) cheers Dan On Friday, July 18, 2003, at 06:28 AM, pymol-users-requ...@lists.sourceforge.net wrote: --__--__-- Message: 4 Date: Thu, 17 Jul 2003 17:51:27 -0400 From: David A. Horita dhor...@wfubmc.edu To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Nuvision stereo glasses? This is a multi-part message in MIME format. --_=_NextPart_001_01C34CAD.92AD614C Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Is anyone using the Nuvision 60GX stereo glasses with FireGL Z1 or = QuadroFX 500 cards under linux? Or any other non-nVidia card which = supports quad-buffered stereo but doesn't have a mini-din connector = on-board (i.e., not the 256 Mb FireGL X1). It would be nice to avoid = the problems with the nVidia stereo drivers, but I'd rather not buy the = FX1000+/FireGL X1 level card, and FireGL2/4 are getting old (and hard to = find). The Nuvision guys told me that their VGA passthrough (the -100 = model, not the -NSR model), picks up the stereo sync from nVidia cards = coming through the 15-pin VGA connector. Is this signal present on ATI = cards (or even on dual-DVI-I output cards)? =20 Thanks, Dave Horita =20 -=20 David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016=20 Tel: 336 713-4194 Fax: 336 716-7671=20 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/ =20 Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] ChemPy question
Dear PyMOL-ers, I have just started dabbling in the chempy module, and I have a couple of questions: 1. If I load in a molecule using the following code... from chempy import io from chempy import protein m = io.pdb.fromFile(/tmp/x.pdb) # Use the load_object call, specifying the type of object as a chempy # model (index 8) cmd.load_object(8,m,protein) ...there are no bonds displayed. Is there a chempy call I can make on the model object (m) to calculate covalent bonds? 2. I can happily iterate over, or select by index, atoms in a chempy model, using either of the following # Iterate over all atoms for a in m.atom: # do something # Random access a = m.atom[10] Are there corresponding residue and atom arrays, or does chempy represent these aggregates simply by the fields of the Atom object (resn, resi, chain etc)? As far as I can see, the latter is true, but like I said, so far I am only a dabbler. I should mention why I'm doing this, in case anyone has a more elegant solution. Basically I have a C++ library which handles molecules, making selections, identifying h-bonds etc. I wanted a way to dump out a molecule object from my library, and display it in PyMOL with all of its associated selections and bonds. So basically what I do is: 1. Write out a PDB file for my molecule 2. Write out a short Python program which creates PyMOL selections corresponding to my selections, by way of atom indices. Basically this works by grabbing the 'nth' atom from the chempy model, then composing a selection string which is passed to the cmd.select function. Missing out some detail, here is the bare bones: # Function 1: get a PyMOL selection string from a ChemPy atom def atom_sel(a,obj_name): return / + obj_name + // + a.chain + / + a.resi + / + a.name # Function 2: create a PyMOL selection from an array of atom indices def make_atom_sel(sel_name,array,model,obj_name): sel_str = for i in range(len(array)): sel = atom_sel(model.atom[array[i]],obj_name) sel_str += sel if(i len(array)-1): sel_str += or cmd.select(sel_name, sel_str) # Similar functions exist for creating an h-bond between ith and jth # atoms So to put it all together, given these two functions, the program I execute in order to reconstitute my molecule in PyMOL looks like m = io.pdb.fromFile(/tmp/x.pdb) cmd.load_object(8,m,protein) make_atom_sel(my_sel, [0,2,5,8,18,22], m, protein) Gareth -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute
[PyMOL] H-bond display
I am using distance objects at the moment, to display h-bonding contacts. My question is ... is there any easy way to display the direction of an h-bond using distances (i.e. putting a little arrow on the dashed line)? I am prepared to bash out some functions which do this using CGOs, but of course I won't if it's already implemented! Gareth -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute
[PyMOL] mesh question
Hi everyone- I have two interacting monomers, and have selected the contacting resides between them and drawn a solid surface around these selected residues on one monomer. This worked fine and I had no problem. I would now like to draw a mesh surface around the remaining residues in the monomer, that is, everything but the contacting residues. No matter what selection scheme I try to use, the mesh is always drawn around the entire molecule. For instance: select contacts=(byres monA and (monB around 4)) show surface, contacts show mesh, (monA and (!contacts)) mesh is still drawn around whole molecule However, the following command does work to color just the mesh surface that is not in contact with the other monomer: color grey70, (monA and (!contacts)) which leads me to believe that my syntax is correct for the selection. What am I missing? Is there a way to just show the mesh over a certain portion of a molecule? Many thanks in advance- Steve -- Stephen M. Soisson, Ph.D. Senior Research Biochemist X-ray Crystallography / Dept. of Medicinal Chemistry Merck Research Laboratories P.O. Box 2000, RY50-105 Rahway, NJ 07065 Phone: (732) 594-4349 Fax:(732) 594-5042 stephen_sois...@merck.com -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it. --
RE: [PyMOL] H-bond display
Gareth, CGO is currently the way to go... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Gareth Stockwell Sent: Friday, July 18, 2003 2:46 AM To: pymol-users Subject: [PyMOL] H-bond display I am using distance objects at the moment, to display h-bonding contacts. My question is ... is there any easy way to display the direction of an h-bond using distances (i.e. putting a little arrow on the dashed line)? I am prepared to bash out some functions which do this using CGOs, but of course I won't if it's already implemented! Gareth -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute --- This SF.net email is sponsored by: VM Ware With VMware you can run multiple operating systems on a single machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the same time. Free trial click here: http://www.vmware.com/wl/offer/345/0 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
