pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Mac OS X install, general PyMOL function - badly need overview

[Richard G. <re...@co...>]

>
>
>> I have downloaded the version (0.79.dmg.gz) of the PyMol package 
>> suggested by Luca Jovine, but don't know how to get a working version 
>> of Python installed.  The only links I can find are to Python .exe 
>> files for versions 2.1 and 1.5.2, and I have no idea which of the 
>> other downloads (xx-contrib, ext) are needed.  For that matter, is the 
>> v. 0.79 really the latest for OS X, or is 0.82 or 0.83 options?  Which 
>> Python will run in the Mac Unix environment and how do I invoke it 
>> (presumably from the terminal) if it will?  You (W. Delano) make it 
>> clear that running PyMol within Python is not the way to go, then in 
>> the Mac, what is? I also see no links to documentation, nor do I find 
>> any obviously labeled documentation files in the download.

The Jaguar version of MacOS X (10.2) is supposed to have Python 
installed by default according to
the online technotes 
(http://developer.apple.com/technotes/tn2002/tn2053.html).

   Richard Gillilan
   MacCHESS, Cornell

Re: [PyMOL] Mac OS X install, general PyMOL function - badly need overview

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

Hello Jim,

> I have downloaded the version (0.79.dmg.gz) of the PyMol package 
> suggested by Luca Jovine, but don't know how to get a working version of 
> Python installed.  The only links I can find are to Python .exe files for 
> versions 2.1 and 1.5.2, and I have no idea which of the other downloads 
> (xx-contrib, ext) are needed.  For that matter, is the v. 0.79 really the 
> latest for OS X, or is 0.82 or 0.83 options?  Which Python will run in 
> the Mac Unix environment and how do I invoke it (presumably from the 
> terminal) if it will?  You (W. Delano) make it clear that running PyMol 
> within Python is not the way to go, then in the Mac, what is? I also see 
> no links to documentation, nor do I find any obviously labeled 
> documentation files in the download.

At least in my opinion, the easiest way to get python and many other UNIX/
X11 packages on your machine is to first install Fink. This is a package 
manager that will allow you to first install and then update (when 
required) almost anything else you might ever want to use. To learn how to 
do this, please have a look at: http://fink.sourceforge.net/index.php
After you installed Fink and then python through Fink, you can either 
install and run the Xfree version of pymol, or run the native one, or have 
both and run whichever you like to depending on your particular needs. The 
speed of the native version certainly makes it much more usable than the 
Xfree one, but, the latest version of the native program really is 0.79, 
so (at least for now) you miss out on the latest features of 0.82. Also, 
on my machine native pymol seems to freeze whenever I use the "show 
surface" command, which works just fine on the slower Xfree version (is 
this a problem of my particular setup, or did someone else also stumble 
into this?)

> In general, does anyone have any tips on finding needles of required 
> information in this massive haystack of a website?  If you follow links 
> like "Mac OS X", you get dumped into a 10>n page listing of all 
> imaginable open source apps in reverse chronological order. Are there any 
> search tools or internal pages with links to documentation (maybe 
> something on the download page http://prdownloads.sourceforge.net/pymol 
> that I don't recognize as such?)  Finally, there was a "somebody ought to 
> bell the cat"-type discussion about uploading "How TO?" files and 
> tutorials back in May - did anything come of that?  A basic intro to 
> PyMOL is what I, a confirmed nonprogrammer (and damned proud of it) need,
>  no doubt like many others.  Maybe some academics have already put 
> something like this together to prep strudents in their courses to use 
> PyMOL?

For pymol-specific info, have a look at Carly Huitema's tutorial at:

	http://pymol.sourceforge.net/tutorial/index.html

which I found very useful as it nicely complements the manual:

	http://pymol.sourceforge.net/html/toc.html

For more general information about installing crystallographic/structural 
biology software on OSX, the best page I know is my friend's Bill Scott:

	http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html

his site has a lot of extremely useful information clearly arranged and 
explained. Although it might not be directly related to what you want to 
achieve at the very moment, it will certainly give you an idea of the 
issues involved in installing and running this kind of software on OSX.

I'm sure things can only get better in the future, but in the meanwhile I 
hope these pointers help a bit...

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] Mac OS X install, general PyMOL function - badly need overview

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

>   I have downloaded the version (0.79.dmg.gz) of the PyMol package 
> suggested by Luca Jovine, but don't know how to get a working version of 
> Python installed.  The only links I can find are to Python .exe files 
> for versions 2.1 and 1.5.2, and I have no idea which of the other 
> downloads (xx-contrib, ext) are needed.  For that matter, is the v. 0.79 

It's been a while since I played with the Mac version (0.79), but I recall
it not needing any additional installations.  Python is pretty tightly
integrated into PyMOL in the "default" setup, from what I can tell.
Anyway, the installed application should run with a simple double-click,
though I ended up invoking it from a shell.  I imagine the non-native
version would be considerably more complicated to set up, but I haven't
tried it.

> tutorials back in May - did anything come of that?  A basic intro to 
> PyMOL is what I, a confirmed nonprogrammer (and damned proud of it) 
> need, no doubt like many others.  Maybe some academics have already put 

I've found the manual does an adequate job of introduction, even if it's
very outdated.  My only real complaint is that it barely touches on the
subject of programming with/for PyMOL (I'm a programmer, not a
crystallographer).

There's also this:

http://pymol.sourceforge.net/tutorial/index.html

It's geared towards Windows users, but this shouldn't make too much of a
difference.

-Nat

[PyMOL] Mac OS X install, general PyMOL function - badly need overview

[Jim K. <jki...@ch...>]

  I have downloaded the version (0.79.dmg.gz) of the PyMol package 
suggested by Luca Jovine, but don't know how to get a working version of 
Python installed.  The only links I can find are to Python .exe files 
for versions 2.1 and 1.5.2, and I have no idea which of the other 
downloads (xx-contrib, ext) are needed.  For that matter, is the v. 0.79 
really the latest for OS X, or is 0.82 or 0.83 options?  Which Python 
will run in the Mac Unix environment and how do I invoke it (presumably 
from the terminal) if it will?  You (W. Delano) make it clear that 
running PyMol within Python is not the way to go, then in the Mac, what 
is?   I also see no links to documentation, nor do I find any obviously 
labeled documentation files in the download.    

In general, does anyone have any tips on finding needles of required 
information in this massive haystack of a website?  If you follow links 
like "Mac OS X", you get dumped into a 10>n page listing of all 
imaginable open source apps in reverse chronological order.  Are there 
any search tools or internal pages with links to documentation (maybe 
something on the download page http://prdownloads.sourceforge.net/pymol 
that I don't recognize as such?)  Finally, there was a "somebody ought 
to bell the cat"-type discussion about uploading "How TO?" files and 
tutorials back in May - did anything come of that?  A basic intro to 
PyMOL is what I, a confirmed nonprogrammer (and damned proud of it) 
need, no doubt like many others.  Maybe some academics have already put 
something like this together to prep strudents in their courses to use 
PyMOL?

 

Re: [PyMOL] get_view on native mac os X

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

 >On Friday, August 30, 2002, at 06:05 PM, Timothy Moore wrote:
 >
 >Hi, I was wondering if anyone could explain how to use get_view on the
 >native version - which only has the pymol viewer window - when you don't
 >seem to be able to cut text from that..??

Hello Tim,

This should work:

1) Download and unpack the native pymol distribution so that the native 
PyMOL directory is in the /Applications folder:

	/Applications/PyMOL

2) Then open a Terminal window (by double-click Terminal in /Applications/
Utilities), and type the following:

	sudo ln -s /Applications/PyMOL/Darwin/pymol.com /usr/bin/npymol

(this creates a link called "npymol" to the native version of pymol, to 
avoid problems since you mentioned you also have the Xfree/Fink version on 
your system)

3) Now you can launch the native pymol from the command line (Terminal) by 
simply typing:

	npymol

all the ouput from the program will appear in the shell from which you 
launched it, and you will now be able to copy it. However, note that you 
will NOT be able to input commands to pymol by typing into the Terminal 
window, so you will still need to do that by typing into the graphics 
window.

Hope this helps!

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
--------------------------------------------------------

[PyMOL] get_view on native mac os X

[Timothy M. <mr...@no...>]

Hi, I was wondering if anyone could explain how to use get_view on the
native version - which only has the pymol viewer window - when you don't
seem to be able to cut text from that..??

Perhaps if you start logging from the command line, but I don't know how
to do that either..

ADvice would be greatly appreciated!

Tim

P.S. The fink version didn't seem to work for me (I'm too inexperienced
in these things I guess), so I'd rather stay with the native one.

Re: [PyMOL] Secondary structure assignments

[Peter C.M. <pc...@ra...>]

 I've got a crude interface to the RasMol code which lets you run RasMol's
secondary structure assignment code from PyMOL at:
  http://www.rahul.net/pcm/rasmolapi.tar.gz
 I don't make any promises as to how well it works or whether I will ever
get around to cleaning up the ugly code.
 If there are any other RasMol routines that would be valuable to PyMOL,
it probably wouldn't take much more additional work to make them available.
-- 
------------------------------------------------------------------------------
Peter McCluskey          | Free Jon Johansen!
http://www.rahul.net/pcm | 

Re: [PyMOL] Native OS X versions of Pymol

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

> Bill Scott mentioned using the "native version" of Pymol.  I did some 
> looking about on the Sourceforge page and the Apple website, and couldn't 
> find it.  Where is it posted?  I would love to be able to do the same 
> kind of presentations Bill was talking about.

Here:

	http://prdownloads.sourceforge.net/pymol/pymol-0_79a.dmg.gz

Best 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
--------------------------------------------------------

[PyMOL] Native OS X versions of Pymol

[Lorraine C. <may...@fa...>]

Hi Everyone,

Bill Scott mentioned using the "native version" of Pymol.  I did some 
looking about on the Sourceforge page and the Apple website, and couldn't 
find it.  Where is it posted?  I would love to be able to do the same kind 
of presentations Bill was talking about.

Thanks,
Lorraine Cavanaugh


> I just returned from a conference where I gave my first pymol-based
> presentation on an ibook G3 500MHz using the native version (the
> X-windows version, as previously noted, was impossibly slow).  I have to
> say it was a resounding success.

> Bill Scott
>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Lorraine Cavanaugh
Hughson Lab
Department of Molecular Biology
Princeton University
lca...@mo...
lo...@pr...

[PyMOL] Thoughts

[Frank V. <Fra...@sy...>]

Hi Warren

Really great program already, and great promise.  Here are some
suggestions you may or may not like to know about;  ideally, I'd have
liked to give some code, but until I have bandwidth, I pass on the
ideas.  Seem to be fairly intrinsic things that may need some mulling
over. 

1) There's no way to tell what it is you're actually seeing.  In simple
cases, this is no big deal, but it very soon becomes a real mission to
find out what's showing - to remember which of your 15 objects had the
ribbons, which one the C-alpha trace, and whose surface that is.
Admittedly I'm not completely sure I know a good solution, and it would
probably involve redesigning the layout of the object buttons:  maybe
making what's currently displayed bold in the drop-down for each object?
Or little symbols (*&^%$#) next to the object?

2) One cannot toggle states on and off easily.  E.g., You set up a
ribbon selection with some labour, get it coloured just right, and then
want to turn it off to have a look.  Seems currently you have to make a
pml script, together with an anti-script, and run those alternately.  It
feels like there could be a more clickable way, although once again I
don't know a good answer -- maybe rigorous, multiple, specific undos /
redos would do it?  I guess named selections get you partly there, in
which case, see (1).

3) Labelling should be attached to some mouse button by default, as
opposed to having to activate a wizard.  (Maybe labels are an answer to
point (1)?  But then one must be able to select/click on cartoons,
maps, etc.)

Just some food for thought.

phx.


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request a hard-copy version. 

[PyMOL] pymol on OS 10.1

[<wg...@ch...>]

Hi Warren, et al:

I just returned from a conference where I gave my first pymol-based 
presentation on an ibook G3 500MHz using the native version (the 
X-windows version, as previously noted, was impossibly slow).  I have to 
say it was a resounding success.  I used it to present both structures 
with electron density maps from a variety of viewpoints and then also to 
show several movies of 5 states sampled from the hammerhead ribozyme 
reaction coordinate.  It worked really really well, but I could use 
advice on how to do a couple of things more intelligently:

1.  I used pymol in conjunction with a powerpoint presentation.  I found 
the quickest way to do this was to have pymol open simultaneously with 
powerpoint, and to use the escape key to toggle back and forth.  I tried 
using a hyperlink to a one-line applescript I wrote to launch pymol with 
a script of what I planned to show, but this approach was much slower.  
Has anyone found a better way to do this, so I can get an essentially 
instantaneous hyperlink?

2.  I noticed that the electron density carving seemed a bit buggy, and 
I only got it to work by putting the map in in 3 pieces.  When I tried 
to cover the whole molecule at once the program seg faults.  I used the 
same map, I just covered it in 3 pieces rather than 1 and it seemed to 
work fine.  This happened with two structures having the same sequence, 
yet the approach that worked for the first didn't work for the second, 
so I spent about 2 hours hunting for the magic combination that 
prevented pymol from crashing.  Is this a known bug, my idiocy, or what?

3.  Using RNA, if I try to draw a bond between O2' of one residue and 
O2' (for example) of another, it does not work, but a bond between two 
O2s work fine.  I also found this failed when I edited the pdb file to 
be either some letter to replace the prime or an *.  I tried \ to no 
avail.  Is this a bug or am I doing something stupid again?

Otherwise it was great, and after about 2 or 3 hours of work, I found 
the absence of an external GUI to be more of a help than a hinderance as 
it forced me to learn the command language with all of its functionality.

This is a superb program.  Thank you so much for doing this.  Is it 
possible to buy an academic license as a mechanism for sending some 
financial support from my very modest grant?

Bill Scott

[PyMOL] cgo label orientation matrix

[Bartholomeus K. <bku...@ep...>]

Hello subscribers out there!

Robert Campbell and Warren Delano gave some useful hints to cgo label
orientation a few days ago. But so far, I didn't succed yet to get the
labels in plane of the molecule. It was barely possible to rotate and
translate the cgo label [cmd.rotate/translate, thanks to R. Campbell) but
this way is not very accurate. So I rotated the cgo label in plane and got
its orientation alone [cmd.get_view('label'), thanks to W.Delano]. The idea
was to take this matrix and rotate the molecule in plane to the cgo label or
vice versa (molecule's view matrix applied to the cgo label). Then I wanted
to use 'cmd.set_view' in order to perform the orientation onto the molecule
(or label) alone but this command neither accpets the 18 digit matrix or an
assignment to a specific object to be rotated. Maybe this is only a question
of the wrong syntax. Any suggestions are very welcome.

By the way, what do the different digits in the view matrix represent? Maybe
one can convert them to an other style and rotate the molecule's pdb-file by
this orientation using an external program. This would also overcome
rotation dilemma.

Greetings,
Bartholomeus

[PyMOL] transparency on non-surfaces

[Will S. <wh...@br...>]

Can transparency be applied to representations other than surfaces? It
would be nice to be able to fade cartoons in and out, rof example.  

thanks!

  -Will Sheffler
-------------------
$console> cd /pub
$console> more beer
        [_]3
beer (END)

Re: [PyMOL] Pymol slow on a mac G4 with os 10.1

[Florian N. <fn...@ma...>]

Russell Poyner <rp...@fa...> wrote:

> The machine is a newish G4 733Mhz 256K ram with a radeon 7500 card.  I 
> have
> installed the Fink version of pymol with the Fink supplied Xfree.  It 
> works
> but is noticably slower than pymol on my 500 Mhz K6/lintel box, also 
> with a
> radeon 7500 and Xig xserver.
>
> It would seem that the mac installation is not benefitting from the 
> graphics
> hardware despite claims of full acceleration in the xserver.  If there 
> is a
> trick here that I am missing please let me know.
>

  I suggest you to use the beta of the native MacOS X version:
http://prdownloads.sourceforge.net/pymol/pymol-0_79a.dmg.gz

Although it's a beta, it should be blazingly fast on a G4.
Attention, it's a pre 0.8 version and the last features are not  
implemented.
Moreover, the menus are not implemented at all.

By the way, for some reasons, the prompt in PyMol's window is not 
accessible when using MacOS X version 10.2. So if you want to keep the 
beta functional, either don't upgrade or keep MacOS X.1 as a dual boot 
option.

Hopefully, Warren will fix this soon.

regards,

RE: [PyMOL] Pymol slow on a mac G4 with os 10.1

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

Yes, the Fink and GNU/Darwin versions of PyMOL are unaccelerated.  As =
far as I know, the only way to get access to hardware is to call Apple's =
platform-specific OpenGL libraries from within a platform-specific =
window. =20

I am still working on the native OSX port, but with competition from all =
the other PyMOL priorities: such as new features, bug-fixes, and =
support, not to mention my own career and personal life, it is taking =
far longer to complete than I anticipated. =20

There was an incomplete test version available with acceleration, but OS =
10.2 has reportedly broken it.

If you can put up with software rendering, then X-windows based Fink or =
GNU/Darwin versions are fine.  But if you want fast PyMOL, then an =
x86-based PC with Windows or Linux is the only alternative (we're =
talking about a 10-50X performance difference of hardware over software =
-- huge!).  Plus, PC's can do stereo -- Macs can't.

If you need fast 3D graphics on a Mac, I'd encourage you to look around =
for other 3D viewers for at least the next couple months.  VMD =
reportedly has a native version...though I haven't tried it myself.

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: Russell Poyner [mailto:rp...@fa...]
> Sent: Friday, August 23, 2002 7:56 AM
> To: pym...@li...
> Subject: [PyMOL] Pymol slow on a mac G4 with os 10.1
>=20
>=20
> The machine is a newish G4 733Mhz 256K ram with a radeon 7500=20
> card.  I have=20
> installed the Fink version of pymol with the Fink supplied=20
> Xfree.  It works=20
> but is noticably slower than pymol on my 500 Mhz K6/lintel=20
> box, also with a=20
> radeon 7500 and Xig xserver.
>=20
> It would seem that the mac installation is not benefitting=20
> from the graphics=20
> hardware despite claims of full acceleration in the xserver. =20
> If there is a=20
> trick here that I am missing please let me know.
>=20
> Thanks
>=20
> Russell Poyner
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: OSDN - Tired of that same old
> cell phone?  Get a new here for FREE!
> https://www.inphonic.com/r.asp?r=3Dsourceforge1&refcode1=3Dvs3390
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Pymol slow on a mac G4 with os 10.1

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

The machine is a newish G4 733Mhz 256K ram with a radeon 7500 card.  I have 
installed the Fink version of pymol with the Fink supplied Xfree.  It works 
but is noticably slower than pymol on my 500 Mhz K6/lintel box, also with a 
radeon 7500 and Xig xserver.

It would seem that the mac installation is not benefitting from the graphics 
hardware despite claims of full acceleration in the xserver.  If there is a 
trick here that I am missing please let me know.

Thanks

Russell Poyner

[PyMOL] Sticks background color

[Pavel G. <pgo...@ho...>]

Hi,
I am trying to learn Pymol and have already run into a problem. When I try 
displaying in "Sticks" mode, some of the bonds (about 50% of them) take on 
the background color. The problem is also visible when displaying in "Dots" 
mode, although in this case the amount of glitch is less than 5%. My setup: 
Pymol .83 + Python 2.1, Mandrake 8.1, Radeon 7500 with XiG drivers (I need 
the stereo). I am thinking it might be their libraries, but so far this is 
the only problem, "ono" runs fine. If anyone has successfully resolved this 
problem, I would really appreciate it. Thanks in advance,

Pavel



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Re: [PyMOL] q: dash options, transparency, global setting vs.local settings

[Warren L. D. 1 <wa...@su...>]

On Fri, 16 Aug 2002, Bartholomeus Kuettner wrote:

> Dear all!
>
> I've encountered several questions while playing aroung with PyMOL. Maybe
> there is someone who could provide some help?
>
> 1. dash options
>
> It seems that all the "dash" settings (e.g. "dash_length", "dash_with",
> "dash_radius") are global modifiers and cannot be assigned to specific
> interactions in a way like "set dash_gap=0.7, dist1". A different dash_gap
> would prevent a situation where interactions perpendicular to the plane
> become near solid lines while interactions in plane are looking fine.

Bug tracked down and quashed -- it'll work right in the next version.
Thanks for the report.


> 2. transparency, sphere_transparency
>
> Is it still the case in version 0.82 of PyMOL that transparency setting only
> applies to surface or spheres (using sphere_transparency)?

Yes.

- Warren

Re: [PyMOL] g: cgo label orientation

[Warren L. D. 1 <wa...@su...>]

On Sat, 17 Aug 2002, Bartholomeus Kuettner wrote:

> Hello there!
>
> I followed mailing list instructions to create cgo based labels via a python
> script. Unfortunately, the labels are not in plane but more like
> perpendicular. So is there a way to alter the orientation of such cgo
> labels. I think one could apply pymol's "set_view" matrix to the labels to
> get them in plane. Wrong idea? Anyway, how one can rotate the cgo labels
> without rotating the remaining molecule?

That's the right idea... cmd.get_view() will give you a matrix which you
should be able to transform in order to get a coordinate system "in the
vertical" on the screen.  Now what would be great is if PyMOL would do
this for you...

Warren

Re: [PyMOL] Transparent spheres

[Warren L. D. 1 <wa...@su...>]

On 19 Aug 2002, Gareth Stockwell wrote:
>
> Dear PyMOL users,
>
> Does anybody know of a way to either
>
>   i) Change the radius of a specified atom, or

alter (atom selection), vdw=radius

for example

alter (name ca),vdw=5

>  ii) Make a CGO sphere semi-transparent?

Currently impossibleg (transparency came to PyMOL after CGO's).

Cheers,
Warren

Re: [PyMOL] Secondary structure assignments

[Warren L. D. 1 <wa...@su...>]

On Tue, 20 Aug 2002, Peter C. McCluskey wrote:

> >The other thing I'd find useful is some molecular mechanics tools,
> >particularly energy minimization.  Blending PyMOL with MMTK seems like a
> >good way to do this, since MMTK's license looks fairly liberal.

I think we're all of the same mind on this : )

>  There shouldn't be any licensing problems, and you could probably get
> some help from Konrad Hinsen (the main author of MMTK), but I suspect it
> would be a good deal of work to do it cleanly. It might be fairly easy to
> kludge something up that involved communicating with MMTK mainly via
> pdb files.

Konrad and I have been talking about this for some time, but neither of us
has had enough time to look seriouly at it.  You can jerry-rig a PDB file
interface in a few minutes, but the potential interaction between the two
programs could be much more robust (and bi-directional!).

Warren

Re: [PyMOL] rotation about an arbitrary vector?

[Kristian R. <kri...@be...>]

Dear Will,

You wrote:

> The camera
> movement I would like to do is a little more than simple rotations or
> spirals, so it would be very helpful to me to be able to rotate about
> an arbitrary vector, rather than just the principle axes, in mdo
> commands. Is there a way to do this? 

There is. The movie.py script does exactly this: camera movements. 
Basically, any movement can be achieved by adding x,y and z rotations.
You can specify how quick each axis is to be rotated and so on. Any 
camera movement can be smoothed, if You like.

http://www.rubor.de/bioinf/pymol_movie.html

As You wrote You are making movies of trajectories i assume that Your 
animation uses more than one state. Movie.py doesn't get alongt with 
them at the moment. This is because i don't know what would be useful.
If You want to go with movie.py, write me, and we'll get something on that.

Kristian

Re: [PyMOL] Secondary structure assignments

[Peter C. M. <pc...@ra...>]

 de...@ia... (de...@ia...) writes:
>On Mon, Jul 29, 2002 at 01:12:40PM -0400, Nathaniel Echols wrote:
>
>> How hard would it be to incorporate the DSSP algorithm?  I was looking at
>> the source for RasMol, which has a complete implementation.  My feeling is
>> that this could be ported without too much misery.  However, RasMol's
>> license terms are different, and I suspect even a complete translation

>Copyright and the idea of derivative works applies to very specific
>expressions of an idea.  So, unless the DSSP algorithym is patented, a
>complete re-expression in a language like Python (instead of C or C++ or
>whatever RasMol is written in) could probably be made different enough so as
>to be an original work, distinct from RasMol's implementation.  This is what

 I don't know whether the license that current versions of RasMol use would
cause problems, but older versions of RasMol (up through about 2.6) are
public domain, and it looks like they probably have about the same DSSP
code as the current version. So there's probably no licensing problem as
long as we start with the old version.
 I have done some work with interfacing RasMol to Python, so it might be
fairly easy for me to interface it with PyMOL. I will look at it in the
next few days to see how hard it would be.

 na...@ma... (Nathaniel Echols) writes:
>The other thing I'd find useful is some molecular mechanics tools,
>particularly energy minimization.  Blending PyMOL with MMTK seems like a
>good way to do this, since MMTK's license looks fairly liberal.

 There shouldn't be any licensing problems, and you could probably get
some help from Konrad Hinsen (the main author of MMTK), but I suspect it
would be a good deal of work to do it cleanly. It might be fairly easy to
kludge something up that involved communicating with MMTK mainly via
pdb files.
-- 
------------------------------------------------------------------------------
Peter McCluskey          | Free Jon Johansen!
http://www.rahul.net/pcm | 

Re: [PyMOL] Secondary structure assignments

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

> The best way to avoid "derivative work" concern is to code in a "clean room"
> fashion, without reference to someone else's code.  In principle, this could
> be done working from the original paper(s) that describe an algorithm.

I assume this is what authors of other packages have done in the past.
If there's enough interest, and no one is working on this already, I'd be
willing to take a stab at it.

> Not that I'm volunteering ;-)  Just that I would hate to see someone who was
> willing and interested in implementing secondary structure code for PyMol to
> be frightened off the job if, indeed, it could be done in a way that respects
> others' rights.

The other thing I'd find useful is some molecular mechanics tools,
particularly energy minimization.  Blending PyMOL with MMTK seems like a
good way to do this, since MMTK's license looks fairly liberal.
Personally, I'd have to spend two weeks looking at the code for both
packages before I could even start thinking about how this would need to
be done.  I'm certainly not capable of implementing anything like that
from scratch- I slept through math class in college.

-Nat Echols

[PyMOL] rotation about an arbitrary vector?

[Will S. <wh...@br...>]

PyMOL folks,

I've been putting together movies of molecular trajectories on and off
all summer, and have found pymol to be great for this purpose. I now
need to put together something sexy for an end of the summer, and am
trying to make a movie with alot of camera panning. The camera
movement I would like to do is a little more than simple rotations or
spirals, so it would be very helpful to me to be able to rotate about
an arbitrary vector, rather than just the principle axes, in mdo
commands. Is there a way to do this? 

thanks!

-Will