Re: [PyMOL] Mac OS X 10.4.3

2005-11-04 Thread Brian J Goodfellow
Warren, with 0.99beta25 the problem still exists. After loading a molecule there's no flickering but if I do a ray trace then the flickering starts when I rotate. Shifting the window stops the flickering. By running show cartoon after loading I can also get the flickering. Again, moving

Re: [PyMOL] problem with CASTp plugin

2005-11-04 Thread Sebastien Moretti
Hello, We are running Python v2.2.3 on Red Hat Enterprise 3 which is almost like Red Hat 9 and/or Fedora Core 1. Our RedHat version seems to be choking on the pyc file. The following is the error we get. Exception in plugin 'CASTpyMOL' -- Traceback follows... Traceback (most recent call

[PyMOL] Re: PyMOL-users digest, Vol 1 #1049 - 6 msgs

2005-11-04 Thread Jesper Karlsen
HI Mac users, Brian Goodfellow wrote: has anyone noticed an annoying flickering appearing when rotating a =20 molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present =20 under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If =20 the window is moved then the flickering

[PyMOL] Re: macpymol beta 21 bug?

2005-11-04 Thread Martin Montgomery
Hi Warren, Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that still has a problem. I then booted into

Re: [PyMOL] Re: macpymol beta 21 bug?

2005-11-04 Thread khinsen
On Nov 4, 2005, at 12:38, Martin Montgomery wrote: Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that

Re: [PyMOL] Re: macpymol beta 21 bug?

2005-11-04 Thread Martin Montgomery
I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and macpymol 99beta21/25 and it works fine with 10.4.3. It seems the problem is limited to ATI graphics cards with less than 256 RAM. nVidea cards are not affected. Will try an ATI card with 128MB RAM if I can find one here.

Re: [PyMOL] Re: macpymol beta 21 bug?

2005-11-04 Thread Christopher Yip
Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under 10.4.3 however, if I launch X11 and run PyMol under that - (version 0.97), then there's no problem Chris On Nov 4, 2005, at 7:26 AM, Martin Montgomery wrote: I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM

[PyMOL] Re: PyMOL-users digest, Vol 1 #1050 - 7 msgs

2005-11-04 Thread Jesper Karlsen
Hi Mac users, MGM wrote: Having just read Jesper's email regarding getting drivers at ATI's website, I had a look and there are no mac drivers available as far as I can see. Only the ATI Displays software. After installing this on my machine, nothing has changed. The molecule loads

Re: [PyMOL] Re: macpymol beta 21 bug in 10.4.3?

2005-11-04 Thread Moriarty, Daniel
I've given it a quick run on a new Powerbook with the ATI Radeon 9700 w/128 MB, and I can't reproduce the flicker. Same thing with a G5 with a 9800 with 256 MB. My dual G4 with a Radeon 9000 (128 MB) does show the flicker, however, and Jespers trick does the trick. No more flicker. Dan -- Dr.

[PyMOL] .xyz file loading problem from chempy module

2005-11-04 Thread Dmitriy
Hello everyone It seems to be a problem with loading an .xyz file as a chempy model. For example doing from chempy import io m = io.xyz.fromFile(some.xyz) gives: chempy: reading some.xyz. Traceback (most recent call last): File stdin, line 1, in ? File

RE: [PyMOL] .xyz file loading problem from chempy module

2005-11-04 Thread Warren DeLano
Dmitriy, The very latest beta versions of PyMOL can read .xyz files directly (via the load or load_raw commands). http://delsci.com/beta load_raw usage: my_xyz=open(some.xyz).read() cmd.load_raw(my_xyz, 'xyz', my_xyz) I suspect the chempy XYZ file is limited to reading Tinker's fixed-column

RE: [PyMOL] Independent Rotation axis...

2005-11-04 Thread Warren DeLano
The rotate and translate commands can do this *if* you append the object=object-name to the command: Try typing in the following sequence of commands: fragment arg fragment glu translate [5,0,0], object=arg translate [-5,0,0], object=glu origin arg, object=arg origin glu, object=glu rotate y,

[PyMOL] Superimpose

2005-11-04 Thread Michael Morbious
Hi everyone, I have two similar (closely related) multi-chain structures. I want to merge them and highlight the regions that do not superimpose. However, I do not know how to superimpose these two structures and how to select non-intersecting residues. Any help will be appreciated. Thanks.

Re: [PyMOL] Mac OS X 10.4.3

2005-11-04 Thread Morri Feldman
I see the same flickering problem (iMac G5, OSX 10.4.3). Opening as pymol -M doesn't help. Best, Morri On 11/3/05, Sabuj Pattanayek sabuj.pattana...@vanderbilt.edu wrote: I don't know if it will make a difference (I don't even have a Mac) but try opening it from a console using: pymol -M

[PyMOL] OS 10.4.3

2005-11-04 Thread Mark Collins
Hi I also have the flickering problem with my 15 g4 powerbook (ATI Radeon 9700 card). Some mentioned a pymol -M command but I don't use the x11 window to open pymol...I just click on a pdb file. Anybody know how to setup the pymol command (alias) ? Thanks, Mark Collins