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 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
>
>
--
Morri Feldman
Shokat L
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.
Hi,
How can I find out the color of an atom?
Also, how should I call it from a python script?
(Is there a function that will let me access the C variables?)
get , /x///1/CA
does not work. (where is any item in settings.py that has
anything to do with color)
TIA,
Indraneel
--
http://prodata.
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
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
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
Hi,
I can confirm that updating the ATI drivers and using the
antialiasing x2 option for MacPyMOL removes the flicker problem (at
least on my G4 iBook). The lines look much coarser though i.e. not as
nice as usual - seems you win some you lose some..
Brian
On 4 Nov 2005, at 13:15,
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.
Thanks Jesper,
That seems to work!!!
MGM
On 4 Nov 2005, at 13:06, Jesper Karlsen wrote:
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 Display
Warren et al.
I checked, and my Powerbook G4 12" has nVIDIA GeForce4 MX, with 32
Mb memory. Always worked fine before. Realize that there are two
different types of flicker. There is the usual mild flicker as one
rotates a model (seems more than it used to be), and there is a more
gl
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 fin
Just for completeness, I've now checked a 20" G5 iMac with a 128MB
ATI card and it is fine. Also, I can confirm that there is not a
problem whilst using X11 pymol on a 64MB ATI card.
Cheers
MGM
Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under
10.4.3 however, if I l
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 an
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.
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
sti
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 my
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 di
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 la
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 "", line 1, in ?
File "/home/dmitriy/pymol/lib/python2.4/si
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 the
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