pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Bug in CGO cylinder drawing code?

[Robert C. <rl...@k2...>]

Warren,

I have found a CGO-drawing problem for which I cannot find a solution.
I've been trying to perfect my script for drawing symmetry axes of
crystal structures. I noticed that the script wasn't drawing all of the
axes that it should have (i.e. not all of those that were listed by the
script). I did some investigating of the behaviour by writing the CGO
objects out to a file and then editing it down to just a few cylinder
objects.

The grand conclusion, is that if you create a CGO cylinder that goes
from 0,0,0 to x,-x,x (or parallel to that direction) apparently no
matter what the value of x, it does not appear in the graphics window.

Here are some samples.

First I was trying to draw the four 3-fold axes of space group P23:

#! /usr/bin/python
from pymol.cgo import *
from pymol import cmd

ax = [
CYLINDER, 0.0, 0.0, 0.0, -30.0, -30.0, 30.0, 0.2, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0, 
CYLINDER, 0.0, 0.0, 0.0, -30.0, 30.0, 30.0, 0.2, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0, 
CYLINDER, 0.0, 0.0, 0.0, 30.0, -30.0, 30.0, 0.2, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0, 
CYLINDER, 0.0, 0.0, 0.0, 30.0, 30.0, 30.0, 0.2, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0, 
]
cmd.load_cgo(ax,'ax')

but the 3rd of these cylinders does not appear.  So I altered one of the
end-point values ever so slightly:

ax2 = [
CYLINDER, 0.0, 0.0, 0.0, -30.0, -30.0, 30.0, 0.2, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 
CYLINDER, 0.0, 0.0, 0.0, -30.0, 30.0, 30.0, 0.2, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 
CYLINDER, 0.0, 0.0, 0.0, 30.00001, -30.0, 30.0, 0.2, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 
CYLINDER, 0.0, 0.0, 0.0, 30.0, 30.0, 30.0, 0.2, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 
]
cmd.load_cgo(ax2,'ax2')

Now the 3rd cylinder appears. Similarly, changing one of the starting
points, (X, Y or Z -- doesn't matter which) and the cylinder will
appear. I tried rearranging the order of the cylinders and it always
seems to be that particular cylinder that is not drawn. So finally I
tried drawing individual cylinders and found that for example, the
following also will not appear:

ax3 = [CYLINDER, 0.0, 0.0, 0.0, 2., -2.0, 2.0, 0.5, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0]
cmd.load_cgo(ax3,'ax3')

Changing any X, Y or Z value for either the starting or end point of
the cylinder will make the cylinder reappear. Finally, cylinders from
(0,0,0) to (-x,x,-x) and from (x,-x,x) to (0,0,0) also do not appear
(i.e. the same direction).  The presence of (0,0,0) as one of the
starting or end points doesn't matter: (2.0, 2.0, 2.0) to (4.0, 0.0, 4.0)
also does not appear.  

There is something strange about this (1,-1, 1) direction!

I have found this to be true with the CVS version as well as the 0.78
version (both running under Linux) and the CVS and 0.68 version under
IRIX. It doesn't appear to matter what display settings are set.

But the cylinder does appear when the image is ray-traced!

I don't think there is anything that I'm doing wrong here, but if you
have a clue, I'd be very interested!

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] GUI problem on Win2000

[J. <j-...@gm...>]

Hello everybody

At home, I run pymol on Debian/Linux without any problems. However, at
university, we only have windows machines. So I downloaded and installed
Python2.2.1, ActiveTCL 8.3.4.3 and, of course, Pymol 0.82.
So far, I can run (and use) pymol giving commands in the OpenGL window, but
the GUI (which depends on Tcl/Tk) does not appear. The startup window gives
the following error message:

    self.root = Tk()
  File "C:\PROGRA~1\PYTHON~1\Lib\lib-tk\Tkinter.py", line 1487, in __init__
    self.tk = _tkinter.create(screenName, baseName, className)
TclError: Can't find a usable init.tcl in the following directories:
    {C:\python21\tcl\tcl8.3 (guessing)} {} {C:\python21\tcl\tcl8.3
(guessing)}
 C:/python21/tcl/tcl8.3 C:/PROGRA~1/PYTHON~1/lib/tcl8.3
c:/programme/lib/tcl8.3
 c:/lib/tcl8.3 c:/lib/tcl8.3/library c:/library c:/../tcl8.3/library
../tcl8.3/
library

So, what can I do to help pymol finding init.tcl and display the GUI?

Thanks, joerg

PS.: Please CC: to me, as I'm not subscribed to this list.

-- 
Did you know that if you play a Windows 2000 cd backwards, you 
will hear the voice of Satan?

That's nothing!  If you play it forward, it'll install Windows 2000.


GMX - Die Kommunikationsplattform im Internet.
http://www.gmx.net

[PyMOL] Fusing objects

[Keith R. <kr...@is...>]

I have created a number of objects using "symexp" to represent a
crystal structure.  I now need to recompute the bonds to display
molecules split across periodic copies.  

1. Am I correct in understanding that I need to "FUSE" all the objects
   into one to display all inter-object bonds?

2. Is there a quick and general way of doing this?  The documentation
   suggests that I have to pick every atom pair to do this, which
   would be cumbersome to say the least.  I'm sure I must be missing
   something.

Thanks

Keith Refson
-- 
Dr Keith Refson, 
Building R3
Rutherford Appleton Laboratory
Chilton
Didcot
Oxfordshire OX11 0QX
T: 01235 446652		K.Refson@
F: 01235 445720		@rl.ac.uk

RE: [PyMOL] How to run PyMol from within Python?

[DeLano, W. <wa...@su...>]

> So there is no way to run and control PyMol from within=20
> another python program?

If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, =
then you can launch PyMOL from an external Python program as shown in =
examples/devel/start_pymol.py. =20

However, this is not recommended because the PyMOL launch sequence is =
not fixed.  If you do use it, be prepared to deal with changes down the =
road.=20

> The reason for asking is that we are working on a python platform to=20
> run and evaluate protein-protein docking calculations. It would be a=20
> nice feature to be able to call up interaction surfaces and=20
> protein-protein clusters for display  in PyMol and then interact with=20
> them from within our program.

> As things are now I'm forced to treat PyMol as I would treat any=20
> molecular graphics program, that is write macros macros for it. This=20
> is of course much less convenient and less flexible compared to=20
> running PyMol from within our python code.

> Has anyone been able to run and quit PyMol from within python without=20
> killing the interpreter? Is it possible? How?

The underlying source of the limitation here is that the GLUT and Tcl/Tk =
libraries which PyMOL uses do not support repeated set-up/take-down -- =
they are both static "global" systems which steal threads and never =
return.  Thus, while PyMOL is not inherently limited in this fashion, =
these building blocks which it employs are.  Eventually there will be =
versions of PyMOL which are both GLUT and TCL/Tk independent -- but not =
today.

Instead, I recommend using some kind of inter-process communication =
along with object serialization to pass data from your program into =
PyMOL.  Python makes this relatively easy, but you are looking at a =
little bit of development.

Sorry the news isn't better!

Warren

Re: [PyMOL] pymol without GL

[Ezequiel H P. <za...@SL...>]

Nathaniel Echols wrote:
> 
> By the way, has anyone else experimented with hardware antialiasing on
> NVidia cards under Linux?  I've had mixed results so far, and I'm not sure
> what I'm doing wrong (this is with a GeForce 4 Ti 4600).

     the nvidia driver (as far as 28.90) does not allow for simultaneous 
use of anti-aliasing and depth-cueing (fog) so you must choose either
one of those, not both from within pymol.

zac

Re: [PyMOL] pymol without GL

[Nathaniel E. <na...@ma...>]

> pymol.com -c scriptname
> But you have to get your view first somehow.

I can't do this until I compile it; if I try running a pre-existing build
I get errors because one of the GL libraries isn't found.  I've ended up
just installing GL on my system, but the crack technical wizards at SuSE
have decided I need Qt and KDE as well. . . on web server. *sigh*  It's
not really important that I be able to do this, and there's plenty of disk
space to spare, but I prefer limited installs on a server.

By the way, has anyone else experimented with hardware antialiasing on
NVidia cards under Linux?  I've had mixed results so far, and I'm not sure
what I'm doing wrong (this is with a GeForce 4 Ti 4600).

-Nat

Re: [PyMOL] pymol without GL

[Jason M. <ja...@bi...>]

Hello:

pymol.com -c scriptname

But you have to get your view first somehow.

Cheers,
JTM

*************************
Jason Thomas Maynes
MD/PhD Program
Faculty of Medicine  
University of Alberta
ja...@bi...
*************************


On Tue, 16 Jul 2002, Nathaniel Echols wrote:

> 
> quick question: I'm trying to do batch jobs on a server.  Obviously,
> there's no X or OpenGL installed.  Is there any way to build PyMOL without
> any graphical frontend, and just use it as a raytracer?  I don't want to
> go through the trouble of adding in these libraries...
> 
> thanks,
> Nat
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by: Jabber - The world's fastest growing 
> real-time communications platform! Don't just IM. Build it in! 
> http://www.jabber.com/osdn/xim
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

*************************
Jason Thomas Maynes
MD/PhD Program
Faculty of Medicine
University of Alberta
ja...@bi...
*************************

[PyMOL] pymol without GL

[Nathaniel E. <na...@ma...>]

quick question: I'm trying to do batch jobs on a server.  Obviously,
there's no X or OpenGL installed.  Is there any way to build PyMOL without
any graphical frontend, and just use it as a raytracer?  I don't want to
go through the trouble of adding in these libraries...

thanks,
Nat

Re: [PyMOL] How to run PyMol from within Python?

[Johan L. <jo...@pa...>]

Hi all,

So there is no way to run and control PyMol from within another python program?

The reason for asking is that we are working on a python platform to 
run and evaluate protein-protein docking calculations. It would be a 
nice feature to be able to call up interaction surfaces and 
protein-protein clusters for display  in PyMol and then interact with 
them from within our program.

As things are now I'm forced to treat PyMol as I would treat any 
molecular graphics program, that is write macros macros for it. This 
is of course much less convenient and less flexible compared to 
running PyMol from within our python code.

Has anyone been able to run and quit PyMol from within python without 
killing the interpreter? Is it possible? How?

Cheers, Johan



>  > I'm having problems running PyMol from within another Python program.
>
>This is not the recommended way to run PyMOL and may lead to 
>problems.  You can run Python programs within PyMOL as follows:
>
>from the command-line:
>
>pymol example.py     # synchronous, in PyMOL module
>pymol -r example.py  # synchronous in __main__ module
>pymol -l example.py  # asychronous in a new module
>
>You can also launch python programs from within PyMOL with the commands:
>
>run example.py        # synchronous in pymol module
>run example.py,main   # synchronous in __main__ module
>
>spawn example.py        # asychronous in a new module
>spawn example.py,global # asychronous in the PyMOL module
>spawn example.py,main   # asychronous in the __main__ module
>
>see:
>
>help launching
>help run
>help spawn
>
>  > Following the examples in /pymol/examples/devel I have been able to
>  > launch and controll PyMOL. The problem occur when I try to quit PyMol
>  > (version. 0.82) however I do it I end up with a fault terminating my
>  > Python interpreter.
>  >
>  > Under Redhat 7.1/Python 2.1 i get a segmentation fault and under
>  > MacOS 10.1.5/Python 2.2.1 I get a Python bus error. I get the same
>  > result both when quitting from the gui or within python with the
>  > command cmd.quit()
>  >
>  > How can I quit PyMol properly?
>
>I know for a fact that the Mac take-down process is currently 
>flawed, and frequently gives a bus error.  Because it only happens 
>after you quit the program, its a low priority issue...
>
>Not sure about Redhat.
>
>Warren
>

RE: [PyMOL] Re: movie -script - conversion from .png to .tga

[DeLano, W. <wa...@su...>]

Trissa,

I think that the line may have been wrapped in your copy of the input =
file. Try making sure that entire Python in the script file appears on a =
single line -- then it should work.

Cheers,
Warren

--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606  FAX:(650)-266-3501=20

-----Original Message-----
From: Pat...@gs... [mailto:Pat...@gs...]
Sent: Monday, July 15, 2002 10:05 AM
To: pym...@li...
Subject: [PyMOL] Re: movie -script - conversion from .png to .tga



I am trying to run the mkmov1.pml script from the Pymol page.=20
I am stopped at the line=20

/for i in glob("png/*"):os.system("convert "+i+"  "re.sub("png", "tga", =
re.sub("_",".",i)))

I get the errors:=20
Traceback (innermost last):
 File "/apps/pymol/modules/pymol/parser.py", line 98, in parse
   exec(com2[nest],pymol_names,pymol_names)
 File "<string>", line 1
    for i in glob("png/*"): os.system("convert "+i+"
                                                   ^
SyntaxError: invalid token
PyMOL>"+re.sub("png","tga",re.sub("_",".",i)))
Traceback (innermost last):
 File "/apps/pymol/modules/pymol/parser.py", line 234, in parse
   exec(com2[nest],pymol_names,pymol_names)
 File "<string>", line 1
    "+re.sub("png","tga",re.sub("_",".",i)))
                ^
SyntaxError: invalid syntax=20

Without knowing python, I haven't been able to figure out what is wrong=20
with the input line.  Can anyone help?=20

Thanks!=20
Trissa

[PyMOL] Re: movie -script - conversion from .png to .tga

[<Pat...@gs...>]

I am trying to run the mkmov1.pml script from the Pymol page.
I am stopped at the line

/for i in glob("png/*"):os.system("convert "+i+"  "re.sub("png", "tga", 
re.sub("_",".",i)))

I get the errors:
Traceback (innermost last):
  File "/apps/pymol/modules/pymol/parser.py", line 98, in parse
    exec(com2[nest],pymol_names,pymol_names)
  File "<string>", line 1
     for i in glob("png/*"): os.system("convert "+i+"
                                                    ^
 SyntaxError: invalid token
PyMOL>"+re.sub("png","tga",re.sub("_",".",i)))
Traceback (innermost last):
  File "/apps/pymol/modules/pymol/parser.py", line 234, in parse
    exec(com2[nest],pymol_names,pymol_names)
  File "<string>", line 1
     "+re.sub("png","tga",re.sub("_",".",i)))
                 ^
 SyntaxError: invalid syntax

Without knowing python, I haven't been able to figure out what is wrong
with the input line.  Can anyone help?

Thanks!
Trissa

[PyMOL] Molecular sculpting video

[<Pat...@gs...>]

I can't find the molecular sculpting video on the home page.
I have looked under "Movies" and "Gallery".  Could someone
point out its location to me please?

Thanks,
Trissa

[PyMOL] electrostatic surface

[Chun T. <ta...@hh...>]

Hi,
I know pymol can do surface. I want to know if the new release of pymol
0.83 can show electrostaic surface. Thanks.

Chun

RE: [PyMOL] color gradient

[DeLano, W. <wa...@su...>]

Jeff,

	It would take a little Python programming, but modules/pymol/util.py =
has the rainbow command which can be modified so as to give a more =
restricted gradient than the current rainbow.

usage:

load prot.pdb
util.rainbow("prot")

(or just select the rainbow option on the color pop-up menu on "prot")

Cheers,
Warren


--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606  FAX:(650)-266-3501=20
-----Original Message-----
From: jeff chao [mailto:ja...@sc...]
Sent: Thursday, July 11, 2002 2:40 PM
To: pym...@li...
Subject: [PyMOL] color gradient


i would like to make a color gradient (something like purple-cyan) from =
N to C.
is there an easy way to do this?  thanks, jeff

=20
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Jeffrey A. Chao

The Scripps Research Institute          PHONE: (858)784-8743
Molecular Biology MB 33                 FAX: (858)784-2903
10550 N. Torrey Pines Road              E-MAIL: ja...@sc...
La Jolla, CA  92037  USA

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 =20

[PyMOL] color gradient

[jeff c. <ja...@sc...>]

i would like to make a color gradient (something like purple-cyan) from N to C.

is there an easy way to do this?  thanks, jeff


^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Jeffrey A. Chao

The Scripps Research Institute          PHONE: (858)784-8743
Molecular Biology MB 33                 FAX: (858)784-2903
10550 N. Torrey Pines Road              E-MAIL: ja...@sc...
La Jolla, CA  92037  USA

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[PyMOL] Reading mol2 and acnt files

[Ingo D. <dra...@Ma...>]

Hi Pymolers,

here is a small pymol extension to support mol2 and acnt files that come 
from Sybyl. 

Installation:

cp io.tgz to $PYMOL_PATH/modules/pymol
cd $PYMOL_PATH/modules/pymol
tar -xvzf io.tgz
mv io/importing.py .

The next time when pymol is started, the new filetypes are supported
by the load command.
Note, that after loading acnt files a contour must be created via
isomesh or isosurf to see something.

have fun,

Ingo.

RE: [PyMOL] How to run PyMol from within Python?

[DeLano, W. <wa...@su...>]

> From: Johan Leckner [mailto:jo...@pa...]
>=20
> I'm having problems running PyMol from within another Python program.

This is not the recommended way to run PyMOL and may lead to problems.  =
You can run Python programs within PyMOL as follows:

from the command-line:

pymol example.py     # synchronous, in PyMOL module
pymol -r example.py  # synchronous in __main__ module
pymol -l example.py  # asychronous in a new module

You can also launch python programs from within PyMOL with the commands:

run example.py        # synchronous in pymol module
run example.py,main   # synchronous in __main__ module

spawn example.py        # asychronous in a new module
spawn example.py,global # asychronous in the PyMOL module
spawn example.py,main   # asychronous in the __main__ module

see:

help launching
help run
help spawn

> Following the examples in /pymol/examples/devel I have been able to=20
> launch and controll PyMOL. The problem occur when I try to quit PyMol=20
> (version. 0.82) however I do it I end up with a fault terminating my=20
> Python interpreter.
>=20
> Under Redhat 7.1/Python 2.1 i get a segmentation fault and under=20
> MacOS 10.1.5/Python 2.2.1 I get a Python bus error. I get the same=20
> result both when quitting from the gui or within python with the=20
> command cmd.quit()
>=20
> How can I quit PyMol properly?

I know for a fact that the Mac take-down process is currently flawed, =
and frequently gives a bus error.  Because it only happens after you =
quit the program, its a low priority issue...

Not sure about Redhat.

Warren




=20

[PyMOL] How to run PyMol from within Python?

[Johan L. <jo...@pa...>]

Hi Pymolers,

I'm having problems running PyMol from within another Python program.

Following the examples in /pymol/examples/devel I have been able to 
launch and controll PyMOL. The problem occur when I try to quit PyMol 
(version. 0.82) however I do it I end up with a fault terminating my 
Python interpreter.

Under Redhat 7.1/Python 2.1 i get a segmentation fault and under 
MacOS 10.1.5/Python 2.2.1 I get a Python bus error. I get the same 
result both when quitting from the gui or within python with the 
command cmd.quit()

How can I quit PyMol properly?

Thanks, Johan

[PyMOL] Hello & Stereo3D

[<de...@ia...>]

This is my first post to the list, so I guess a "hello, world" is in order.

I figured it was time to get serious about PyMOL given that it's the first
application I've been able to get to work with Hardware Stereo on a linux
box:

     * (6/10/2002) Hardware Stereo 3D under Linux! I have personally
       confirmed that PyMOL performs well with quad-buffer hardware
       stereo under Linux. Thus, I can now recommend the following
       configuration, which also works well with the absolute latest
       version of O (8.0.8):
          + Linux RedHat 7.1
          + ATI FireGL2 (unfortunately expensive, and now special-order
            only).
          + Exact drivers: fgl23glk-glc22-4.0.3-1.9.7.i586.rpm +
            fgl23ddx-glc22-4.0.3-1.9.7.i586.rpm
            http://www.ati.com/support/drivers/firegl/linux/cert/linuxfir
            egl4certx403197.html
            Other versions may work, but these are the only RPMs which
            functioned in my hands.
          + Affordable emitters and glasses can be found at
            www.nuvision3d.com.
          + An untested graphics alternative would be to use a Radeon
            8500 card with the XIG driver and a suitable emitter adapter.

I can confirm that PyMOL 0.83 running atop Mandrake 8.1, with a 3DLabs
Oxygen GVX1 video card and the the XIG Platinum WX driver can render
hardware stereo just fine.  We're using the McNaughton (eg, NuVision) stereo
glasses.  The box has dual PIII 500MHz processors on an intel 440BX chipset,
with 512MB of memory.As our test case last week, we were looking at the PDB
file 1FJG, a structure of a 30S ribosomal subunit (a pretty beefy file).

I had to uninstall (rpm -e) XFree86-devel and dependency-related packages,
and had to install the XIG X server rpm with --nodeps, and had to fiddle
with some font path settings (with which XIG provided prompt and useful
help).  

I also have a Radeon 8500 I'll be testing either in the next day or two, or
in a couple of weeks.  A lot of our systems have video cards with nVidia
chipsets in them, which I guess we'll have to replace unless nVidia gets
around to supporting hardware stereo in their driver set before that
happens.

So far, a rewarding experience.

Now, I get to look forward to learning how to put PyMOL through its paces
(I'm a longtime MOLMOL user)!

--Joe

___________________________________________________________________________
D. Joe Anderson, Ph.D             Computing Support for Botany, ZG, & BBMB.
  bot...@ia... | zgs...@ia... | bbs...@ia...
   1210 MBB, ISU, Ames, IA 5001   http://www.bb.iastate.edu/support

Re: [PyMOL] view area

[Warren L. D. <wa...@su...>]

On Sun, 7 Jul 2002, Nathaniel Echols wrote:

> 1. There doesn't seem to be any way to manually speciify the view area.
> Thus, if I want all images to be in the same frame of reference, I need to
> load them all as different states of the same object, e.g. "load
> frame01.pdb, mov" many times over.  This works fine, but even with 4GB of
> memory PyMOL crashes when I load everything in.  I've found a way around
> this, but it would be much simpler if I could specifiy exactly what angle
> and window to use for rendering.  I'm pretty sure this doesn't exist right
> now, but will it in the future?

It exists...see get_view and set_view. 

cmd.get_view() returns a tuple which can be passed to cmd.set_view(...)

ie. 

set_view (\
    -0.745493710,   -0.657504320,   -0.109211229,\
     0.235591769,   -0.413225234,    0.879625380,\
    -0.623487175,    0.630026162,    0.462960035,\
     2.252975464,    1.815253615,  -55.481048584,\
    -3.770999908,   -6.882999897,   18.787000656,\
    43.924808502,   75.804443359,    0.000000000 )

or

cmd.set_view((\
    -0.745493710,   -0.657504320,   -0.109211229,\
     0.235591769,   -0.413225234,    0.879625380,\
    -0.623487175,    0.630026162,    0.462960035,\
     2.252975464,    1.815253615,  -55.481048584,\
    -3.770999908,   -6.882999897,   18.787000656,\
    43.924808502,   75.804443359,    0.000000000 ))

or

vu=cmd.get_view()

...

cmd.set_view(vu)

in vu[...]:

0-8 is the 3x3 rotation matrix
9-11 is the camera location (I think -- been a while...)
12-14 is the origin of rotation
15-16 are the clipping distances
and 17 is the orthoscopic flag.
 
> 2. Using pretty much any method, PyMOL frequently lops off part of the
> molecule.  This has become a large problem; I'm using PyMOL quite a bit to
> make animations (replacing Molscript entirely), and frequently an
> interesting part of the structure will be out of frame.  How can I avoid
> this?  This is all being done on the command line (usually invoked by some
> CGI script), so I have no way of adjusting the zoom.  'zoom' hasn't been
> too much help.

The initial zoom only works on the first frame, so you should issue zoom
again once all of the frames have been loaded.  If you're still losing
parts of the molecule, add an additional buffer to the zoom command:

zoom (all),3

> Any advice would be much appreciated.  I'm trying to do stuff that would
> be messy in pretty much any environment (e.g. I can't even load all the
> structures with less than 1GB of memory), but the viewport problems apply
> to pretty much anything.

Well, ideally it shouldn't be as messy with PyMOL/Python, but we've still
a ways to go...

Cheers,
Warren

[PyMOL] view area

[Nathaniel E. <na...@ma...>]

Hi--

I'm trying to render a large number of images of a trajectory
automatically. I have two problems:

1. There doesn't seem to be any way to manually speciify the view area.
Thus, if I want all images to be in the same frame of reference, I need to
load them all as different states of the same object, e.g. "load
frame01.pdb, mov" many times over.  This works fine, but even with 4GB of
memory PyMOL crashes when I load everything in.  I've found a way around
this, but it would be much simpler if I could specifiy exactly what angle
and window to use for rendering.  I'm pretty sure this doesn't exist right
now, but will it in the future?

2. Using pretty much any method, PyMOL frequently lops off part of the
molecule.  This has become a large problem; I'm using PyMOL quite a bit to
make animations (replacing Molscript entirely), and frequently an
interesting part of the structure will be out of frame.  How can I avoid
this?  This is all being done on the command line (usually invoked by some
CGI script), so I have no way of adjusting the zoom.  'zoom' hasn't been
too much help.

Any advice would be much appreciated.  I'm trying to do stuff that would
be messy in pretty much any environment (e.g. I can't even load all the
structures with less than 1GB of memory), but the viewport problems apply
to pretty much anything.

thanks,
Nat

[PyMOL] Re: NMR ensemble

[Jules J. <jo...@he...>]

OK, got that bit. Now how can you view all the models independently of
one-another as if you had loaded them individually? At present there is
only one structure on the screen even if i have loaded all 20 in the
original file.

thanks

Jules

On Wed, 3 Jul 2002, Warren L. DeLano wrote:

> On Wed, 3 Jul 2002, Jules Jacobsen wrote:
>
> > Does anyone know how to display an ensemble of NMR structures without the
> > entire ensemble being amalgamated into one big mess?
>
> If you have MODEL entries in the PDB file, PyMOL will automatically
> separate them into separate states which can be viewed as a PDB file.
>
> You can achieve the same effect by loading the structures serially into a
> single object.
>
> load sol1.pdb,ens
> load sol2.pdb,ens
> load sol3.pdb,ens
> ...
>
> Cheers,
> Warren
>
>
>

[PyMOL] Re: NMR ensemble

[Warren L. D. <wa...@su...>]

On Wed, 3 Jul 2002, Jules Jacobsen wrote:

> Does anyone know how to display an ensemble of NMR structures without the
> entire ensemble being amalgamated into one big mess?

If you have MODEL entries in the PDB file, PyMOL will automatically
separate them into separate states which can be viewed as a PDB file.  

You can achieve the same effect by loading the structures serially into a
single object.

load sol1.pdb,ens
load sol2.pdb,ens
load sol3.pdb,ens
...

Cheers,
Warren

[PyMOL] NMR ensemble

[Jules J. <jo...@he...>]

Hi,

Does anyone know how to display an ensemble of NMR structures without the
entire ensemble being amalgamated into one big mess?

cheers

Jules

[PyMOL] RE: Linux Binary Test Request

[Eric R. <ej...@bi...>]

The linux 0.83 binary performs well on my laptop and workstations.

Linux Distribution - SUSE 8.0
Video Cards - ATI Mobility4, GeForce2


-- 
Eric Ross
University of Utah
Department of Biochemistry
ej...@bi...