pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Questions about atom properties

[<kk...@ga...>]

Dear Pymolers,

In the on-line help (of `iterate_state'), I found examples that
one can iterate through atoms and obtain their x value.
But I tried on my local installations (both Win and Linux),
an error was there when I tried to access 'x' value, for example.
But I can access other properties like partial charge, etc.

Is there an exaust list of atom properties that I can obtain
through pymol?
Or is there a way to know what properties are there
in a python class?

Thanks for your help in advance.

Regards,
K.K.Liang

Re: [PyMOL] Re: fitting residues

[Gareth S. <ga...@eb...>]

Jason,

I think the solution is to create a copy of the object, then render one 
copy as cartoon, and the other as sticks.  The colouring will then be 
independent.

By the way, does anyone kwow if it is possible to invoke the command 
window after startup?  I normally launch PyMOL with -x, but sometimes 
later need the command window, and have to restart the program.

Gareth


On Thu, 25 Jul 2002, Jason Maynes wrote:

> Hello:
> 
> I am trying to color residues off a cartoon loop and want to color the
> sticks version of the residue down to the Ca, but not the Ca itself
> (ie. the residue and the cartoon are different colors).  The
> problem is that if I color the Ca, then that section of the cartoon also
> gets colored.  If I don't color the Ca, then the cartoon loop color comes
> halfway up the bond to the Cbeta.  Does anybody have any suggestions, that
> is if I haven't made the question so convoluted you can understand it.
> 
> Thanks in advance.
> 
> Cheers,
> JTM
> 
> *************************
> Jason Thomas Maynes
> MD/PhD Program
> Faculty of Medicine
> University of Alberta
> ja...@bi...
> *************************
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by: Jabber - The world's fastest growing 
> real-time communications platform! Don't just IM. Build it in! 
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> 

-------------------------------------------------------------------------------
 Gareth Stockwell
 PhD student, Thornton Group
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                         ga...@eb...
 Tel 01223 492548                               http://www.ebi.ac.uk/~gareth

[PyMOL] Re: Suppress some output

[<kk...@ga...>]

Dear Nat,

Thanks for the trick.
This sounds like a good method, in general.
I will do this when I finish debugging my code
and start to work on many files.
I was just curious if we can do this in a program.
Perhaps this is actually a Python problem,
not a Pymol specific problem.

Regards,
K.K.Liang

> Message: 3
> From: Nathaniel Echols <na...@ma...>
> Subject: Re: [PyMOL] Suppress some output
> > Is there a way to keep my program 'quiet',
> > or I can customize the output message myself?
> Depending on your OS and shell, something like this may work:
> denethor:~ > /usr/local/pymol/pymol.com >/dev/null 2>/dev/null
> This works under Bash in any modern Linux distribution, from what I've
> seen.  I suspect it would work on Irix too (still using Bash).  I've had
> the exact same problem- mainly with util.rainbow().
> -Nat

[PyMOL] Re: fitting residues

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

Hello:

I am trying to color residues off a cartoon loop and want to color the
sticks version of the residue down to the Ca, but not the Ca itself
(ie. the residue and the cartoon are different colors).  The
problem is that if I color the Ca, then that section of the cartoon also
gets colored.  If I don't color the Ca, then the cartoon loop color comes
halfway up the bond to the Cbeta.  Does anybody have any suggestions, that
is if I haven't made the question so convoluted you can understand it.

Thanks in advance.

Cheers,
JTM

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

Re: [PyMOL] Suppress some output

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

> Is there a way to keep my program 'quiet',
> or I can customize the output message myself?

Depending on your OS and shell, something like this may work:

denethor:~ > /usr/local/pymol/pymol.com >/dev/null 2>/dev/null

This works under Bash in any modern Linux distribution, from what I've
seen.  I suspect it would work on Irix too (still using Bash).  I've had
the exact same problem- mainly with util.rainbow().

-Nat

[PyMOL] Object-specific transparency

[Gareth S. <ga...@eb...>]

I would like to make one isosurface transparent, and leave another solid
(or set different levels of transparency for each).  I know
object-specific transparency works for molecule objects, e.g.

  load molA.pdb, A
  load molB.pdb, B
  show surface, A
  show surface, B
  set transparency, 0.5, A

(object B remains solidly-rendered)

But if I try the same for isosurfaces, e.g.

  load mapA.ccp4, mapA
  load mapB.ccp4, mapB
  isosurface surfA, A, 1
  isosurface surfB, B, 1
  set transparency, 0.5, surfA

...the transparency of BOTH isosurfaces changes, as reflected by the
messages in the console:

PyMOL>set transparency, 0.5, surfA
 Setting: transparency set to 0.50000 in object 'mapA'.
 Setting: transparency set to 0.50000 in object 'mapB'.
 Setting: transparency set to 0.50000 in object 'surfA'.
 Setting: transparency set to 0.50000 in object 'surfB'.

Is there a way to make isosurface objects behave in the same way as the
molecule objects?

Gareth

-- 
-----------------------------------------------------------------------------
 Gareth Stockwell
 PhD student, Thornton Group
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                        
ga...@eb...
 Tel 01223 492548            Personal homepage:
http://www.ebi.ac.uk/~gareth

[PyMOL] Suppress some output

[<kk...@ga...>]

Dear Pymolers,

I have studied how to use selections and I have done some
very interesting analysis for my own research.
However, there is one thing that I wish to be able to improve.
Since I have to deal with thousands of PDB files,
do about ten to twenty selections on each of them,
and then count the atoms I selected, and save them into data file.
Everytime I select something, the terminal through which I issue
pymol program will echo a line of the selection result.
This is good when I am debugging.
But when I really start to run the program over my PDBs,
I think console output becomes the most time-consuming procedure.
Is there a way to keep my program 'quiet',
or I can customize the output message myself?

Thanks for any suggestion in advance, and happy pymoling!

Regards,
K.K.Liang

[PyMOL] =?ISO-8859-1?B?UulmLjogW1B5TU9MXSBVcCAmIGRvd24gYXJyb3cgcHJvYmxlbSB1bmRlciBPU1gg?=

[<jo...@al...>]

Hi

This is just the same for me using 0.82 under Linux. As Brian Swalla mentio=
ned
before, Up/Down-arrows only work in the GL window. Would be nice though, to=
 have
it working in the external window, too, because typing response is faster i=
n this
window

joerg

Le Tue, 23 July 2002, Luca Jovine a =E9crit

>=20
> Hello,
>=20
> I have started playing with PyMol a couple of days ago and vary truly=20
> impressed! But there's one very useful feature I don't seem to have=20
> working in my installation (version 0.8 installed through Fink on Mac OSX=
=20
> 10.1.5), which is the ability to recall previously issued commands within=
=20
> the external GUI by using the up and down arrows (this feature is=20
> mentioned in the tutorial by Carl Huitema). Is this a problem of my syste=
m=20
> only, or does this feature simply not work onder OSX?
>=20
> Thanks in advance for the help and kind regards,
>=20
> Luca
=0D
Internet et mail gratuit AltaVista http://www.altavista.fr

[PyMOL] Re: PyMOL-users digest, Vol 1 #124 - 1 msg

[Brian S. <bs...@op...>]

> I have started playing with PyMol a couple of days ago and vary truly
> impressed! But there's one very useful feature I don't seem to have
> working in my installation (version 0.8 installed through Fink on Mac OSX
> 10.1.5), which is the ability to recall previously issued commands within
> the external GUI by using the up and down arrows (this feature is
> mentioned in the tutorial by Carl Huitema). Is this a problem of my system
> only, or does this feature simply not work onder OSX?
> 
> Thanks in advance for the help and kind regards,
> 
> Luca

Hi Luca, 

I too am using the fink version of PyMOL under OS X.  You can use the arrow
keys to access your command history, but ONLY if you type the commands
directly into the openGL graphics window, not the top window with the menu
buttons.  Did you try that yet?  I've noticed that there is a miniscule
delay when typing in the graphics window before the characters show up --
you may or may not find that an issue.

cheers!
Brian
-- 
Brian M. Swalla, Ph.D.
Senior Scientist
Optigenix, Inc.
1 Innovation Way, Suite 303
Delaware Technology Park
Newark, DE. 19702-5449

[PyMOL] Up & down arrow problem under OSX

[Luca J. <luc...@ma...>]

Hello,

I have started playing with PyMol a couple of days ago and vary truly 
impressed! But there's one very useful feature I don't seem to have 
working in my installation (version 0.8 installed through Fink on Mac OSX 
10.1.5), which is the ability to recall previously issued commands within 
the external GUI by using the up and down arrows (this feature is 
mentioned in the tutorial by Carl Huitema). Is this a problem of my system 
only, or does this feature simply not work onder OSX?

Thanks in advance for the help and kind regards,

Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620  FAX: +1.509.356-2832
E-Mail: luc...@ma...
W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------

Re: [PyMOL] show spheres

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

> I have iron atoms in the ligand.  When I ask PyMol to show spheres of the ligand, the iron atoms don't show up.  Is it because the radius for iron hasn't been defined?  If so, how can I define it?

Whoops...PyMOL has a goofed up value for Fe.  For now,

load yourfile.pdb
alter (elem Fe),vdw=1.8
rebuild

show sph

[PyMOL] show spheres

[Tom L. <to...@ms...>]

Hi,

I have iron atoms in the ligand.  When I ask PyMol to show spheres of =
the ligand, the iron atoms don't show up.  Is it because the radius for =
iron hasn't been defined?  If so, how can I define it?

Tom Lee

RE: [PyMOL] trouble making movie on linux

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

At first I thought this was a bug, but after Russel sent me the files, =
it turns out that this reveals an important concept for movie-making =
with PyMOL...

In order to make movies which associate atom identities through a =
trajectory , you must specify unique identifiers for each atom.  Just =
the atomic elements aren't usually good enough since how will PyMOL know =
which carbon in one from is associated with which carbon in the next?  =
Instead, each atom must have a unique combination of =
(segi,chain,resn,resi,name). =20

An easy solution with small molecular systems is to simple load the =
movie into discrete objects, where PyMOL doesn't attempt to associate =
atoms and bonds between states.  This is done with an optional argument =
"discrete=3D1" on the first state which is loaded...

load subnoh00.pdb,mov,discrete=3D1
load subnoh01.pdb,mov
load subnoh02.pdb,mov
load subnoh03.pdb,mov

With discrete objects, if you click on a atom in one state, then PyMOL =
won't know which atom corresponds to what in the next state, and so =
you'll have to manually setup representation within each state if you =
want anything fancy. =20

Also note that with discrete objects, atom and bond information is =
replicated for every state.  In contrast, normal objects share one pool =
of atom, bond, and connectivity information across all states (but not =
every atom needs to appear in each state), and normal objects only store =
unique coordinates for each state.  So, if you're using PyMOL to view =
250 frames of a 50,000 atom MD simulation, discrete objects would be =
memory inefficient.  However, if bonds are made/broken between states, =
then you'll need to use a discrete object, or split the trajectory =
across multiple objects.

Take home lessons:

- For trajectories with abiguous atom names, use discrete objects
- For trajectories where bonds are made/broken, use discrete objects
- For trajectories with static connectivity and unique names, use =
discrete objects.
- For large MD-simulations, use normal objects
- For view docking results, use discrete objects=20

Cheers,
Warren


> I am attempting to make a movie from a series of 50 pdb=20
> files.  When I load=20
> the files individually they work fine, however when I load=20
> the files into a=20
> movie using a series of "load file.pdb,mov" commands only the=20
> first 2 frames=20
> are correct.  In frames 3 and higher the connections between=20
> atoms are drawn=20
> apparently randomly so that the effect is that of a pile of=20
> "pixie sticks"=20
> rather than a molecule.
>=20
> I get this effect on two different machines running redhat=20
> 7.3, one using=20
> pymol 0.78, and another using the "easy install" pymol 0.83=20
> package for=20
> linux.
>=20
> I have though about adding CONNECT records to the pdb files=20
> to force proper=20
> bonding, or perhaps I can use babel to put them into some=20
> other format that=20
> will work.

Re: [PyMOL] molecular sculpting

[Lieven B. <li...@ul...>]

"DeLano, Warren" wrote:
> Right now I'm not sure the sculpting feature is more than entertainment, but 
> my expectation is that it >will become part of PyMOL's crystallographic model 
> building system in the future.

I agree. I think it has great potential there, as it allows for a more
"physical" or
"intuitive" way of manipulating the model than moving individual atoms
or turning
torsion angles.

-- 
Lieven Buts
Brussels Free University

[PyMOL] trouble making movie on linux

[Russell P. <rp...@fa...>]

HI,

I am attempting to make a movie from a series of 50 pdb files.  When I load 
the files individually they work fine, however when I load the files into a 
movie using a series of "load file.pdb,mov" commands only the first 2 frames 
are correct.  In frames 3 and higher the connections between atoms are drawn 
apparently randomly so that the effect is that of a pile of "pixie sticks" 
rather than a molecule.

I get this effect on two different machines running redhat 7.3, one using 
pymol 0.78, and another using the "easy install" pymol 0.83 package for 
linux.

I have though about adding CONNECT records to the pdb files to force proper 
bonding, or perhaps I can use babel to put them into some other format that 
will work.

Thanks in Advance

Russell Poyner

RE: [PyMOL] fitting residues

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

Jason,

Try turning off "Smooth Loops" in the Cartoon menu.

or

   set cartoon_smooth_loops=3D0

Also potentially useful is

   set cartoon_flat_sheets=3D0

Cheers,
Warren

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



> -----Original Message-----
> From: Jason Maynes [mailto:ja...@bi...]
> Sent: Thursday, July 18, 2002 11:27 AM
> To: pym...@li...
> Subject: [PyMOL] fitting residues
>=20
>=20
> Hello:
>=20
> I was wondering if there was anyway to make the cartoon backbone match
> the real backbone to a greater extent.  Now I have residues=20
> displayed as
> sticks and a backbone displayed as loop and the loop doesn't=20
> really come
> near the residue so it looks like the residue is floating in=20
> space.  I am
> looking for a command similar to defining the secondary structure as
> "turn" in molscript which forces the cartoon through the=20
> actual backbone.
>=20
> Thanks in advance.
>=20
> Cheers,
> JTM
>=20
> *************************
> Jason Thomas Maynes
> MD/PhD Program
> Faculty of Medicine
> University of Alberta
> ja...@bi...
> *************************
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] fitting residues

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

Hello:

I was wondering if there was anyway to make the cartoon backbone match
the real backbone to a greater extent.  Now I have residues displayed as
sticks and a backbone displayed as loop and the loop doesn't really come
near the residue so it looks like the residue is floating in space.  I am
looking for a command similar to defining the secondary structure as
"turn" in molscript which forces the cartoon through the actual backbone.

Thanks in advance.

Cheers,
JTM

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

Re: [PyMOL] pymol without GL

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

Oops!
I forgot to mention that this is related to the GeForce4 Ti 4400
that we have in our lab. So I am guessing it also applies to the
Ti4600.

On the other hand, the Quadro4 700 XGL works fine, except for the
annoying stereo-good mono-bad performance glitch.

Zac

DeLano, Warren wrote:
> Zac, 
> 
>    Is this a new limitation? I've been using both antialiasing 
 >    and depth cue with nVidia cards for years...

Zac wrote:
>>   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.

RE: [PyMOL] molecular sculpting

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

Molecular sculpting works like a real-time energy minimizer, except that =
it isn't minimizing the energy.  Instead, its just trying to return =
local atomic geometries (bonds, angles, chirality, planarity) to the =
configuration the molecules possess when they were first loaded into =
PyMOL. =20

To actually use this feature:

1. load a PDB file

2. configure the mouse for editing (Mouse menu)
   or click in the mouse/key matrix box

3. select "auto-sculpting" from the Sculpting menu

4. select Sculpting from the Wizard menu

5. ctrl-middle-click on any atom in your protein to activate sculpting
   the green part will be free to move
   the cyan part will be a fixed cushion to provide context
   the grey part will be excluded

6. now perform any conformational editing operation in the green region
   such as:=20

     ctrl-left-click-and-drag on an atom

     ctrl-right-click on a bond, then ctrl-left-click-and-drag about =
that
     bond

You can adjust the radius and cushion using the blue pop-up menus.

Right now I'm not sure the sculpting feature is more than entertainment, =
but my expectation is that it will become part of PyMOL's =
crystallographic model building system in the future.

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: Thursday, July 18, 2002 4:04 AM
To: pym...@li...
Subject: [PyMOL] molecular sculpting



I would like to understand the molecular sculpting possibilities of =
pymol=20
but haven't been able to figure it out yet.  When using the wizard, the=20
first request is to click and atom but how to proceed from there?=20

I have used the bit of script provided on the web page and deformed=20
the benzene ring but have not been clever enough to see the =
possibilities=20
from that.=20

Could anyone provide just enough of a step-by-step push-this, click-that =
lead into the=20
molecular sculpting to get me started?

Thanks!=20
Trissa

Re: [PyMOL] molecular sculpting

[Lieven B. <li...@ul...>]

Pat...@gs... wrote:
> I would like to understand the molecular sculpting possibilities of pymol
> but haven't been able to figure it out yet.  When using the wizard, the
> first request is to click and atom but how to proceed from there?
>
> I have used the bit of script provided on the web page and deformed
> the benzene ring but have not been clever enough to see the
> possibilities
> from that.
>
> Could anyone provide just enough of a step-by-step push-this,
> click-that lead into the
> molecular sculpting to get me started?

I don't know about the script or the wizard (yet), but I did try the
sculpting demo in the Demo menu. You can then just drag atoms
by left-clicking them while holding down the control key. The
dragged atom moves, everything it is connected to is dragged along,
and the structure tries to minimize its energy. Great fun!

-- 
Lieven Buts
Department of Ultrastructure
Brussels Free University

[PyMOL] molecular sculpting

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

I would like to understand the molecular sculpting possibilities of pymol 
but haven't been able to figure it out yet.  When using the wizard, the 
first request is to click and atom but how to proceed from there? 

I have used the bit of script provided on the web page and deformed 
the benzene ring but have not been clever enough to see the possibilities 
from that. 

Could anyone provide just enough of a step-by-step push-this, click-that 
lead into the 
molecular sculpting to get me started?

Thanks! 
Trissa

RE: [PyMOL] pymol without GL

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

Not right now...

In order to build PyMOL without linking to real GL libraries, you'd =
either need a fake copy of the GL API, or "#define" out all of the gl =
calls in PyMOL (many hours of work).

Sorry!
Warren

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



> -----Original Message-----
> From: Nathaniel Echols [mailto:na...@ma...]
> Sent: Tuesday, July 16, 2002 12:09 PM
> To: pym...@li...
> Subject: [PyMOL] pymol without GL
>=20
>=20
>=20
> 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=20
> PyMOL without
> any graphical frontend, and just use it as a raytracer?  I=20
> don't want to
> go through the trouble of adding in these libraries...
>=20
> thanks,
> Nat
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: Jabber - The world's=20
> fastest growing=20
> real-time communications platform! Don't just IM. Build it in!=20
> http://www.jabber.com/osdn/xim
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[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