[PyMOL] Re: hardware stereo in IRIX

2005-04-23 Thread Dr. Daniel James White PhD

Hi Nicolas,

I have the same SGI computer, Indigo 2 Impact 1
running IRIX 6.5.22m (BTW upgrade to this release is free from 
supportfolio at SGI, might have to install patch 5086 first)


I have stereo graphics emitter and glasses,
and stereo works fine,
i just double click a link on my desktop to pymol.com
pymol version 0.97.

then on menus bar
Display-Stero mode- quad buffered.

running at 1024x786_96s is display settings
on SGI grey speckled monitor.

Are all the cables connected properly for the emitter box?

Dan



On 23 Apr 2005, at 06:19, pymol-users-requ...@lists.sourceforge.net 
wrote:



Hello PYMOLers,
=20
I've recently installed Pymol v0.97 on an SGI but the hardware=20
stereo mode was not detected. Is there somebody successfully using 
PyMol=20
with this mode on an SGI ? If yes, could you please help me to fix 
this=20

problem?
=20
My SGI:
- Irix 64 Release 6.5
- Model Indigo 2 Impact 1
- Main Mem: 128 MB
- CPU: 175 MHz
=20
Thanks a lot,
=20
Nicolas Ambert.

--=20

Dr. Daniel James White BSc. (Hons.) PhD
Bioimaging Coordinator
Nanoscience Centre and
Department of Biological and Environmental science
Division of Molecular Recognition
Ambiotica C242
PO Box  35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi




Re: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2

2004-09-17 Thread Dr. Daniel James White PhD

Hi,

I restarted the installation from unix sources as released on pymol 
sourceforge page,


made the appropriate changes to build.com in the ext directory

and now it is compiling away quite happily so far,
there must have been an error i introduced while I was trying to build 
with gcc 2.7 previously...


anyway, with a clean source tree, i'm as far as tkWindow.c so 
far... still going


cheers

Dan




On 16 Sep 2004, at 21:58, Warren DeLano wrote:


Dan,

It's been a decade or so since I've tried to install GCC on a system 
like
that.  It is always tricking getting the correct include paths to be 
used by
the compiler.  In this case, I think you're getting the IRIX includes 
when

you really want the GCC includes, or vice versa, or your getting both
confounded.

Hardware stereo should work with PyMOL if and only if that Indy2 has
hardware stereo support built in to the video option.  I think the 
extreme

does, but you may need to run in 1024x768 in order to enable it.

Cheers,
Warren

--
mailto:war...@delsci.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
Dr. Daniel James White PhD
Sent: Thursday, September 16, 2004 10:41 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2

Hi Warren and all,

I'm trying building pymol on sgi irix 6.2 gcc 2.95.2

(I got root access to that old sgi indigo2 extreme irix 6.2, and got a
13W3 to VGA cable to connect it to my sony g520 monitor, and it works
great.)

I installed gcc2.95.2,
and am building the external dependencies for pymol

but on running build.com I got an error about previous
declaration of memchr and sure enough there is a file on my
system called /usr/include/string.h and line 69 has memchr

is there a way around this?


I edited build.com :

setenv SGI_ABI -n32
setenv MAKE make
setenv CXX /usr/freeware/bin/c++

are these ok?

will the hardware stereo work with pymol?

this is really all I need this machine for, good for students
(unless I can get a new licensed version of insightII on it
... from the csc here in finland)

cheers

Dan




Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology, Ambiotica C242
Department of biological and environmental science PO Box  35
University of Jyväskylä Jyväskylä FIN 40014 Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi


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Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology, Ambiotica C242
Department of biological and environmental science
PO Box  35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi




Re: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2, external sources python build fails

2004-09-17 Thread Dr. Daniel James White PhD

Hi all,

building pymol external sources on irix6.2 with gcc 2.95

tcl and tk and zlib build ok!!!
but python fails at the first hurdle with:

creating Makefile
cd 
/usr/people/dwhite/freestuff/pymolstuff/ext-0_95/src/Python-2.3.3; make
cc -n32 -c -OPT:Olimit=0 -DNDEBUG -O -I. -I./Include  
-DPy_BUILD_CORE -o Python/thread.o Python/thread.c
/usr/include/sys/prctl.h, line 64: error(1020): identifier 
k_sigset_t is

  undefined
k_sigset_t  t_hold; /* Hold signal bit mask */
^

1 error detected in the compilation of Python/thread.c.
*** Error code 2 (bu21)
*** Error code 1 (bu21)
rooster:/usr/people/dwhite/freestuff/pymolstuff/ext-0_95%




the relevant code from /usr/include/sys/prctl.h on the irix 6.2 system 
is:


#define PRDA_PANCAKE_SIZE   5

/* the system portion of the prda */
struct prda_sys {
pid_t   t_pid;  /* epid */
__uint32_t  t_hint; /* Share group scheduling hint */
__uint32_t  t_dlactseq; /* Deadline scheduler activation seq# */
__uint32_t  t_fpflags;  /* Current p_fpflags (SMM, precise) */
__uint32_t  t_prid; /* Processor type */
__uint32_t  t_dlendseq; /* Deadline sched allocation seq # */
__uint64_t  t_pancake[PRDA_PANCAKE_SIZE];/* registers for pancake */
pid_t   t_rpid; /* pid */
__int32_t   t_resched;  /* send pthread resched signal */
__uint32_t  t_unused[8];

/*
 * The following field is used to hold the cpu number that the
 * process is currently or last ran on
 */
__uint32_t  t_cpu;  /* Last/current cpu */

/*
 * The following fields are used by sigprocmask if the hold mask is
 * to be in user space.
 */
__uint32_t  t_flags;/* t_hold mask is being used? */
k_sigset_t  t_hold; /* Hold signal bit mask */
};


any clues anyone?

python2.1 for irix6.5 from sgi freeware won't install (of course, and 
only python 1.5 is available for irix 6.3 on sgi freware)


cheers

Dan


Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology, Ambiotica C242
Department of biological and environmental science
PO Box  35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi




[PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2

2004-09-16 Thread Dr. Daniel James White PhD

Hi Warren and all,

I'm trying building pymol on sgi irix 6.2 gcc 2.95.2

(I got root access to that old sgi indigo2 extreme irix 6.2, and got a 
13W3 to VGA cable to connect it to my sony g520 monitor, and it works 
great.)


I installed gcc2.95.2,
and am building the external dependencies for pymol

but on running build.com I got an error about previous declaration of 
memchr
and sure enough there is a file on my system called 
/usr/include/string.h and line 69 has memchr


is there a way around this?


I edited build.com :

setenv SGI_ABI -n32
setenv MAKE make
setenv CXX /usr/freeware/bin/c++

are these ok?

will the hardware stereo work with pymol?

this is really all I need this machine for, good for students (unless I 
can get a new licensed version of insightII on it ... from the csc 
here in finland)


cheers

Dan




Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology, Ambiotica C242
Department of biological and environmental science
PO Box  35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi



[PyMOL] sony (sgi) monitorGDM-20D11 flashing LEDs, no picture

2004-09-02 Thread Dr. Daniel James White PhD

Hi there,

Just on the off chance that someone might know...

We have a sgi indigo2 that is working, but the monitor seems to have a 
problem

its a sony (sgi) GDM-20D11
There is no picture when it is turned on,
and the green and amber  LEDs next to each other on the bottom right of 
the monitor blink together.


I can use the machine via VNC from my Mac, so I can see it is running 
ok.


any idea what the problem might be?

I can't find the manual here, or any useful info on the internet

just though someone might have seen this before...sometime..

cheers

Dan


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 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi



[PyMOL] ATI fglrx 3.11 drivers for Radeon 8500 LE with linux 2.6 kernel, quad buffered stereo on sony G520???

2004-08-25 Thread Dr. Daniel James White PhD

Hi

has anyone had any luck getting quad buffered stereo with the new ATI 
linux drivers, fglrx 3.11


I wondered if any one has a working XFree86 config file?

my setup is
ATI fglrx 3.11 drivers for Radeon 8500 LE  with linux 2.6 kernel 
(fedora core 2),
trying to get quad buffered stereo on sony G520 monitor , stereo 
graphics enabler cable and e2 emitter box.


or am I flogging a dead horse

cheers

Dan

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 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi



[PyMOL] enable direct rendering DRI on fedora core 2

2004-06-11 Thread Dr. Daniel James White PhD

Hi everyone!

how can I enable direct rendering DRI on fedora core 2?
I have an ATI radeon 8500 LE,

Should I use the redeon driver, or the r200 driver?

I edited my xorg.conf file is  as below, but VMD and pymol tells me I 
am still using indirect mesa rendering, and it is SLOW.


the ATI closed source driver doesn't work on the fedora 2.6 kernel so I 
cant use that.



cheers

Dan



# XFree86 4 configuration created by pyxf86config

Section ServerLayout
Identifier Default Layout
Screen  0  Screen0 0 0
InputDeviceMouse0 CorePointer
InputDeviceKeyboard0 CoreKeyboard
EndSection

Section Files

# RgbPath is the location of the RGB database.  Note, this is the name 
of the

# file minus the extension (like .txt or .db).  There is normally
# no need to change the default.
# Multiple FontPath entries are allowed (they are concatenated together)
# By default, Red Hat 6.0 and later now use a font server independent of
# the X server to render fonts.
RgbPath  /usr/X11R6/lib/X11/rgb
FontPath unix/:7100
EndSection

Section Module
Load  dbe
Load  extmod
Load  fbdevhw
Load  glx
Load  record
Load  freetype
Load  type1
Load  dri
EndSection

Section InputDevice

# Specify which keyboard LEDs can be user-controlled (eg, with xset(1))
#   Option  Xleds 1 2 3
# To disable the XKEYBOARD extension, uncomment XkbDisable.
#   Option  XkbDisable
# To customise the XKB settings to suit your keyboard, modify the
# lines below (which are the defaults).  For example, for a non-U.S.
# keyboard, you will probably want to use:
#   Option  XkbModel  pc102
# If you have a US Microsoft Natural keyboard, you can use:
#   Option  XkbModel  microsoft
#
# Then to change the language, change the Layout setting.
# For example, a german layout can be obtained with:
#   Option  XkbLayout de
# or:
#   Option  XkbLayout de
#   Option  XkbVariantnodeadkeys
#
# If you'd like to switch the positions of your capslock and
# control keys, use:
#   Option  XkbOptionsctrl:swapcaps
# Or if you just want both to be control, use:
#   Option  XkbOptionsctrl:nocaps
#
Identifier  Keyboard0
Driver  keyboard
Option  XkbModel pc105
Option  XkbLayout fi
EndSection

Section InputDevice
Identifier  Mouse0
Driver  mouse
Option  Protocol IMPS/2
Option  Device /dev/input/mice
Option  ZAxisMapping 4 5
Option  Emulate3Buttons yes
EndSection

Section Monitor
Identifier   Monitor0
VendorName   Monitor Vendor
ModelNameCPD-G520
DisplaySize  400300
HorizSync30.0 - 130.0
VertRefresh  48.0 - 170.0
Option  dpms
EndSection

Section Device
Identifier  Videocard0
Driver  radeon
VendorName  Videocard vendor
BoardName   ATI Radeon 8500LE
EndSection

Section Screen
Identifier Screen0
Device Videocard0
MonitorMonitor0
DefaultDepth 24
DefaultDepth 24
SubSection Display
Viewport   0 0
Depth 24
Modes1280x1024 1280x960 1152x864 1024x768 
800x600 640x480

EndSubSection
EndSection

Section DRI
Group0
Mode 0666
EndSection



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 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi



[PyMOL] Re: give unique chain identifiers

2004-04-14 Thread Dr. Daniel James White PhD

Hi Warren,

OK, that works just as you say it does.

however, what I really need is each chain to have a unique chain 
identifier in the pdb file written out.


I see there might be a problem here as there are 60 molecules, and only 
24 letters in the alphabet
I actually only want to have 15 of them in my model, so we could get 
round it that way, by deleting the ones I dont want

but then how to give them unique pdb chain identifiers?

I want to load the 15 molecule model in Bodil to do my actual modelling.

cheers

Dan


On 6 Apr 2004, at 21:36, Warren DeLano wrote:


Dan,

That's the not expected result, but indeed you have a problem --
each of those subunits will have identical atoms.  To resolve this, 
assign a

unique segment identifier to each subunit:

load 1c8e.pdb1, 1c8e
split_states 1c8e
delete 1c8e
alter all, segi = model[-4:]
rewind
save test.pdb, all

dele all
load test.pdb

The reason why you were getting a PDB file with just END is that you 
didn't
return the viewer ro frame/state 1 after moving all of the data to 
state 1.


After the above, you'll now be able to address each subunit indepently 
as:


hide
show ribbon
color red, segi 0001
zoom segi 0001

http://delsci.com/img/1c8e-subunit.jpg

Cheers,
Warren



-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Dr. Daniel James White PhD
Sent: Tuesday, April 06, 2004 6:22 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] save all not working for multiple objects
from split_states?

Hi all,

I opened a biological unit pdb file of a viral capsid
protein containing the 60 states or models making up the
whole viral capsid structure.

I did
split_states
to get all 60 molecules as individual objects

sweet!

then I deleted the ones I didnt want, leaving 15 molecules
around one of the 5 fold symmetry axes.

now I want to save these molecules to a pdb file.

so I did

save 5fold.pdb, all

this gave no errors, but the pdb file written only contains

END

what am I doing wrong? I expect it is my simple mistake?

cheers

Dan


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 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi


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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 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi




[PyMOL] Re: split_states

2004-04-06 Thread Dr. Daniel James White PhD

Warren,

Exactly what I needed!

cheers

Dan


On 5 Apr 2004, at 23:08, pymol-users-requ...@lists.sourceforge.net 
wrote:



Message: 10
From: Warren DeLano war...@delanoscientific.com
To: 'Todd Geders' ged...@purdue.edu,
'Ann Mullin' amul...@tulane.edu
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] biological unit question
Date: Mon, 5 Apr 2004 13:07:13 -0700

Todd,

Try MacPyMOL for the full PYMOL effect.  http://delsci.com/macpymol

There is also a new command in the 0.95 series:

   split_states object-name

which will spread a PDB biological unit (or any multi-state object --
including SD files) over a series of independent objects.  This makes 
it
possible to interact with such objects more naturally than with 
all_states

= 1.

   load 1c8e.pdb1, 1c8e
   split_states 1c8e
   delete 1c8e
   zoom
   spectrum b
   hide lines
   set cartoon_sampling,3
   show cartoon
   bg_color grey70
   set hash_max, 150
   ray
...
   orient
   zoom complete=1
   ray

image  screen-shot at:

  http://delsci.com/img/1c8e.jpg
  http://delsci.com/img/1c8e-screen.jpg

Note that looking at large systems such as this (255300 atoms) may 
take some
extra RAM -- 1.5 GB is recommended for this task, and it still takes a 
dual

2 Ghz G5 85 seconds to render...

Cheers,
Warren



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 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi




[PyMOL] save all not working for multiple objects from split_states?

2004-04-06 Thread Dr. Daniel James White PhD

Hi all,

I opened a biological unit pdb file of a viral capsid protein 
containing the 60 states or models making up the whole viral capsid 
structure.


I did
split_states
to get all 60 molecules as individual objects

sweet!

then I deleted the ones I didnt want, leaving 15 molecules around one 
of the 5 fold symmetry axes.


now I want to save these molecules to a pdb file.

so I did

save 5fold.pdb, all

this gave no errors, but the pdb file written only contains

END

what am I doing wrong? I expect it is my simple mistake?

cheers

Dan


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 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi



[PyMOL] rebuilding icosohedral virus structure - symexp?

2004-04-02 Thread Dr. Daniel James White PhD

Hi,

I have a virus envelope protein structure pdb entry,
and I want to rebuild the whole virus protein shell
using the symmetry transformations given in the 180 (60 trimers)

REMARK 350   BIOMT1  1  1.0 0.0 0.0
REMARK 350   BIOMT2  1  0.0 1.0 0.0
REMARK 350   BIOMT3  1  0.0 0.0 1.0
REMARK 350   BIOMT1  2  0.80900 0.30900 0.5
REMARK 350   BIOMT2  2  etc...
REMARK 350   BIOMT3  2  etc...
etc..

lines of the pdb file. These lines give the transformations to give the 
complete protein spherical capsid structure.


can I use pymol
symexp command to do this?

I tried loading the file then doing
symexp sym=1ch8h,(1ch8h),20

but nothing seemed to happen?
I'm doing it wrong i'm sure.


I did manage to do this in SwissPDBViewer, but I cant save the complete 
capsid structure as a file that Bodil reads properly. Pymol of course 
reads the file ok... So suppose it is a bodil problem...


anyway, can i use symexp to do this automatically. you have to do it by 
hand 1 by 1 in SwissPDBviewer (and the linux version is a bit funny...i 
did it on a mac)


cheers

Dan

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



Re: [PyMOL] save icosohedral virus structure with all subunits present?

2004-04-02 Thread Dr. Daniel James White PhD

Ok, biological unit, thats great!

but now,
 how do I save this virus capsid as a a pdb or mol file
where each of the many subunits have a different chain identifier.

When I save the virus caspid structure with all subunits visible, the 
pdb file still only has on subunit in it, not all of them...


I want to open it in Bodil (or Pymol or whatever) and only view the 
chains I want to see.


I just want to see the subunits around one of the 5 fold symmetry axes,
ie with the 5 fold axis in the middle surrounded by the 5 
trimers/triangles that surround the 5 fold axis.


cheers

Dan

On 2 Apr 2004, at 17:57, Todd Geders wrote:


I've found the easiest way to do this under PyMOL is to download the
Biological Unit version of the PDB file.  They've already regenerated
the virus particle for you.  It will only show one of the particles at 
a

time unless you check Movie-Show All States.

~Todd Geders

On Fri, 2004-04-02 at 07:14, Dr. Daniel James White PhD wrote:

Hi,

I have a virus envelope protein structure pdb entry,
and I want to rebuild the whole virus protein shell
using the symmetry transformations given in the 180 (60 trimers)

REMARK 350   BIOMT1  1  1.0 0.0 0.0
REMARK 350   BIOMT2  1  0.0 1.0 0.0
REMARK 350   BIOMT3  1  0.0 0.0 1.0
REMARK 350   BIOMT1  2  0.80900 0.30900 0.5
REMARK 350   BIOMT2  2  etc...
REMARK 350   BIOMT3  2  etc...
etc..

lines of the pdb file. These lines give the transformations to give 
the

complete protein spherical capsid structure.

can I use pymol
symexp command to do this?

I tried loading the file then doing
symexp sym=1ch8h,(1ch8h),20

but nothing seemed to happen?
I'm doing it wrong i'm sure.


I did manage to do this in SwissPDBViewer, but I cant save the 
complete

capsid structure as a file that Bodil reads properly. Pymol of course
reads the file ok... So suppose it is a bodil problem...

anyway, can i use symexp to do this automatically. you have to do it 
by
hand 1 by 1 in SwissPDBviewer (and the linux version is a bit 
funny...i

did it on a mac)

cheers

Dan

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


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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] Re: Need advice on graphic card

2003-11-12 Thread Dr. Daniel James White PhD

Hi,

I have 2 monitors running out of an ATI Radeon 8500 on redhat 8.0 using 
the summit accelerated Xserver from Xig.com for hardware stereo on one 
of the monitors.


I use the dual view function, so 1 big desktop (1 screen on 2 
monitors)


Very hardware accelerated!

cheers

Dan


On 12 Nov 2003, at 06:25, pymol-users-requ...@lists.sourceforge.net 
wrote:



--__--__--

Message: 3
Date: Tue, 11 Nov 2003 12:17:20 -0500 (EST)
From: Yu Chen c...@hhmi.umbc.edu
To: Marc Saric marc.sa...@gmx.de
cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Need advice on graphic card

the merged mode is just one framebuffer for both display, so fool the
system thinking it's only a single-head presented.
No, Xinerama won't work with DRI. That's why i used merged mode, but it
messed up nmrview's font.

Seems nobody else out there using two screens?

Thanks anyway, Marc
Chen

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] energy minimisation in python

2003-09-10 Thread Dr. Daniel James White PhD

Warren ,

Are you aware of the python MMTK molecular dynamics package?
AMBER force field and energy minimisation are there!
Could this be easily interfaced with pymol?

http://starship.python.net/crew/hinsen/MMTK/

I had a play with it but I don't really know what I am doing and need 
to learn


Dan


On Tuesday, September 9, 2003, at 09:08 PM, 
pymol-users-requ...@lists.sourceforge.net wrote:




We'd all like to see a real forcefield in PyMOL, but no one has written
the code yet.

Cheers,
Warren

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] Re: ATI radeon 8500 and Linux quad buffered stereo

2003-09-02 Thread Dr. Daniel James White PhD

Hi,

Indeed you should just need the enabler cable from stereographics.
This is compatible with emitter box E-2, and not other emitters I 
think?


with the hardware browser in gnome menu - system tools
my card is listed as
Radeon R200 QL (Radeon 8500 LE)

and in the Xig.com Xserver  Xsetup program as
ATI RADEON 8500, 64MB

The enabler cable fits into the normal (not digital / flat panel...?) 
monitor socket in the back of the card
inbetween the monitor cable and the card. Also the emitter box is 
powered from the keyboard port.weird, but seems to work.
The enabler cable acts as kind of a splitter for the keyboard port, so 
you can plug in the keyboard and the emitter box.


I have a second CRT monitor running out of the digital/flat panel port 
of the card, using the converter that came with the card.
In Xsetup I have enabled dual view in horizontal mode... and it works. 
I think the stereo display is a little slower of course since the card 
is doing more work,
but I can have a 3D window covering all my big monitor, and control 
windows on the other smaller monitor, making up I large rectangular 
screen.

both monitors are running at 1280x1024. millions of colours.

good luck!

Dan

On Monday, September 1, 2003, at 09:41 PM, Ulrich Englich wrote:


Dear Daniel:

Googlegoogle...
Now I found this at the PyMol discussion group...
I guess that answers pretty much my quetions. I presume we are talking 
about
the exact same graphics card? The connector to the left is a digital 
video

output and I need to shop for the stereo enabler cable...

ulrich



Re: [PyMOL] Nuvision stereo glasses?

* From: Dr. Daniel James White PhD d...@removethischalkie.org.uk
* Date: Fri, 18 Jul 2003 11:59:17 +0300
* In-reply-to: e19dlwr-0005zt...@sc8-sf-list2.sourceforge.net
* List-archive:
http://sourceforge.net/mailarchive/forum.php?forum=pymol-users
* List-id: PyMOL Users Group pymol-users.lists.sourceforge.net
* List-post: mailto:pymol-users@lists.sourceforge.net

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


--
--
   \|/
  (o o)
--oOO--(_)--OOo-

www.macchess.cornell.edu
Dr. Ulrich Englich   Tel: 607-255 9386
209 Biotechnology Building   Fax: 607-255 6249
Ithaca, New York 14853E-mail: u...@cornell.edu


*** This message was written entirely with recycled electrons ***



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] pymol crash on linux opening a .pse saved session file

2003-08-06 Thread Dr. Daniel James White PhD

Hi Warren and all,

My student is experiencing a crash every time she attempts to open a 
.pse saved session file.
The file is of a large trimeric molecule in a cartoon and space fill 
representation with different coloured domains


Hardware: PC, Athalon, 1gb ram, ATI radeon 8500 video card, 2 monitors 
dual head.

OS: Redhat 8.0, Xig.com Summit 2.2 X-server for hardware stereo.
software: pymol-0.90-1.rh8.0.py22  RPM installation

On loading the .pse file the computer thinks for a bit, and it looks 
like when it attempts to display the molecule
the viewing window resizes to that which was saved, then the screen 
goes weird on the monitor the viewing window is on,

the mouse pointer vanished and the keyboard is non responsive,
forcing us to press the reset button to reboot. Looks like a big 
Xserver crash.


Any ideas?

cheers

Dan


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



Re: [PyMOL] Nuvision stereo glasses?

2003-07-18 Thread Dr. Daniel James White PhD

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] Re:2 questions about Summit drivers w/ Radeon8500 card for stereo...

2003-06-04 Thread Dr. Daniel James White PhD

Hi,

Sounds line you didn't have a correct installation of the Xig 
summit2.2???
I thought the installation was supposed to move all the old mesa/GL 
stugff to a back up and replace them with

the acellerated xig ones?

Have you contacted the guys at Xig?
If you have paid the 99 dollars or whatever it costs,
then their support is usually prompt and effective!

Lack of DRI means your graphics hardware is not being used at full 
speed!


On my RH8.0 box, the radeon 8500 64MB with Xig summit 2.2 is working 
really well for quad buffered stereo.

Haven't are upgrade to RH9 yet. I keep hearing about problems!

cheers

Dan




On Wednesday, June 4, 2003, at 01:03 AM, 
pymol-users-requ...@lists.sourceforge.net wrote:



Message: 10
Date: Mon, 02 Jun 2003 14:31:08 -0700
From: Cameron Mura cm...@ucsd.edu
Reply-To: cm...@ucsd.edu
Organization: UCSD
To: pymol-users@lists.sourceforge.net, o-i...@origo.imsb.au.dk
CC: Cameron Mura cm...@mccammon.ucsd.edu
Subject: [PyMOL] 2 questions about Summit drivers w/ Radeon8500 card 
for stereo...


Dear PyMOL and O list members,

I just got stereo working on my machine (PC, Red Hat 9, Radeon8500
(64MB) video card) after installing Xi Graphic's Summit v2.2 
DX-Platinum

drivers to enable quad-buffered software stereo, but I noticed that 3D
stereo rendering in 'PyMOL' and 'O' seems a lot slower than it used to
be (same hardware, but w/ Mandrake and v2.1 Summit drivers). So, I have
2 questions (that may or may not be related to the sluggishness):

(1) After installing xvsc and summit drivers, is any further
configuration required to insure proper usage of the Accelerated-X
openGL libraries, include files, etc.? I ask this because I noticed 
that

GL-based programs such as PyMOL are NOT using the Accelerated-X library
libXda.so.1...
For example, if I type ldd /usr/X11R6/bin/xglinfo I get the 
following:


[r...@cm1 etc]# ldd /usr/X11R6/bin/xglinfo
libGLU.so.1 = /usr/lib/libGLU.so.1 (0x4002d000)
libGL.so.1 = /usr/X11R6/lib/sav-GL/libGL.so.1 (0x400b2000)
libXext.so.6 = /usr/X11R6/lib/libXext.so.6 (0x40125000)
libX11.so.6 = /usr/X11R6/lib/libX11.so.6 (0x40134000)
libm.so.6 = /lib/tls/libm.so.6 (0x40213000)
libc.so.6 = /lib/tls/libc.so.6 (0x4200)
libpthread.so.0 = /lib/tls/libpthread.so.0 (0x40235000)
libdl.so.2 = /lib/libdl.so.2 (0x40243000)
/lib/ld-linux.so.2 = /lib/ld-linux.so.2 (0x4000)

I guess I could remove the paths to the old mesa GL libraries and
include files (/usr/include/GL/sav-GLinc/ and
/usr/X11R6/lib/sav-GL/) from /etc/ld.so.conf, but then other GL-based
applications don't seem to work?? So, is there anything special i need
to do in order to make the libXda.so.1 module used instead of the
standard Mesa openGL ones???

(2) Upon start-up, GL-based applications give the following line:
   Xlib:  extension XFree86-DRI missing on display :0.0.
I'm wondering what this problem means (if anything), and how it may be
corrected??

Thanks for any advice!
 Cameron



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