pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Newbie Pymol Developer Seeks Help

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

On Fri, 27 Sep 2002 py...@ru... wrote:

> I am a software developer starting a project for a biology lab doing
> work in protein structure. I am not a biologist. We'll be using Pymol
> as the basis for the visualization component of the application, and I
> am at the beginning stages of understanding how pymol works and is put
> together.

Great, I'm glad to hear that you're thinking about PyMOL! As the principle
author of the program, I do want to make sure that you are going into this
with your eyes open.  PyMOL in its present state is pretty raw -- you'll
be one of a small collection of developers trying to make use of a system
which is still very much in its early days, which is both good and bad:
good because you have the opportunity to influence the project to suit
your needs (in contrast to something like Chime) -- but bad because it
means some things will be difficult or frustratingly slow to accomplish.

> I already have a number of questions but I am going to hold off until
> I have more experience with the package. But there is one issue I need
> settled soon and I'm hoping some of you can point me in the right
> direction.
>
> We are not going to use the existing external UI or the internal GLUT
> UI.  Our application will be doing a bunch of things not related to

Excellent.  This is probably the best approach to take for a project
involving integration right now, given that both of the user interfaces
are immature and subject to change.

> 3-D structure, and my thinking right now is to simply start pymol in a
> separate thread as it is done in examples/devel/start_pymol.py,
> handing it the -x and -i flags. Then our app will use cmd.* calls to
> get protein structures loaded and manipulated.

Sounds reasonable.  However, Python threading performace is poor -- it
is basically fake: the threads are real, but the interpreter itself is
single-threaded, and so multiple thread context switches are required
to get a single context switch for the interpreter.  However, a program
like PyMOL spends most of its processing time at the C level, so the
overall impact is minimal.

My recommendation would be that you build a lightweight Python socket
or RPC listener which runs as a PyMOL thread, but actually write your
software to run as a separate process.  This has a couple of advantages:
(1) you get the full multiprocessing performance of your system (2) if
PyMOL crashes, your application remains intact (3) you maintain a clean
separation between the two projects, which provides you with long-term
flexibility (perhaps even an ability to use other programs besides PyMOL).

> What I don't understand is how I can get notified of events that
> happen when the user uses the mouse to select residues etc. For
> example, once a protein is loaded, our app may color certain residues
> if we know that there have been experiments that mutated that
> position(s). And if a user clicks on one of those residues, our app
> needs to open up another window and present the data by fetching it
> from a relational database. Is there a way that the external GUI can
> be notified of events? I looked through the documentation and didn't
> see anything obvious.

That's because those decisions haven't really been made yet.  The only
facility which currently exists for this is the Wizard API, which is
incomplete in both the development version and the release.

> I looked through the code a bit, and I'm still at a very early stage
> of learning. But I did see that the pmg_tk module sets pymol._ext_gui
> and sets up a FIFO. I can't see that it is used anywhere by the pymol
> module, but I'm thinking that this is the start of a 2-way
> communication mechanism between pymol and an external GUI?

This functionality needs to be flushed out, but I need outside input as
to how to best go about it.  Fortunately, you're not the only one
interested in this right now, so perhaps we get an active dialog going in
this direction?  What would the ideal system look like, and what are you
top three priorities?

> Can anyone tell me how to be notified that selections change? Or even
> just receive raw mouse events?

Version 0.82 has only bare minimum capabilities in this area -- take a
look at the files inside the modules/pymol/wizard directory for examples
of handling CTRL-mouse clicks.

Welcome to PyMOL!

Cheers,
Warren

[PyMOL] Newbie Pymol Developer Seeks Help

[<py...@ru...>]

Greetings All,

I am a software developer starting a project for a biology lab doing
work in protein structure. I am not a biologist. We'll be using Pymol
as the basis for the visualization component of the application, and I
am at the beginning stages of understanding how pymol works and is put
together.

I already have a number of questions but I am going to hold off until
I have more experience with the package. But there is one issue I need
settled soon and I'm hoping some of you can point me in the right
direction.

We are not going to use the existing external UI or the internal GLUT
UI.  Our application will be doing a bunch of things not related to
3-D structure, and my thinking right now is to simply start pymol in a
separate thread as it is done in examples/devel/start_pymol.py,
handing it the -x and -i flags. Then our app will use cmd.* calls to
get protein structures loaded and manipulated.

What I don't understand is how I can get notified of events that
happen when the user uses the mouse to select residues etc. For
example, once a protein is loaded, our app may color certain residues
if we know that there have been experiments that mutated that
position(s). And if a user clicks on one of those residues, our app
needs to open up another window and present the data by fetching it
from a relational database. Is there a way that the external GUI can
be notified of events? I looked through the documentation and didn't
see anything obvious.

I looked through the code a bit, and I'm still at a very early stage
of learning. But I did see that the pmg_tk module sets pymol._ext_gui
and sets up a FIFO. I can't see that it is used anywhere by the pymol
module, but I'm thinking that this is the start of a 2-way
communication mechanism between pymol and an external GUI?

Can anyone tell me how to be notified that selections change? Or even
just receive raw mouse events?

Thanks!

----
Bob Terek
The Quarry, Inc.
http://www.thequarry.com/
rt...@th...

Re: [PyMOL] Stereo3D hardware recommendation

[Malcolm E D. <mal...@bm...>]

We just had a visit from VREX.  They provide a variety of 3D
options.  They have one very low cost entry point for stereo
glasses.  For I believe $35, they have a pair of shutter glasses
which connect via a wire into a pass through plug which goes
between your box and the monitor cable.  I don't know if you
could put multiple of these in series or whether you are limited
to one pair of glasses; you do have to live with being cabled to
your computer; and I haven't actually seen these in action; but
the price is very intriguing.

They are also looking at a very interesting technology for 3D on
a laptop with passive glasses.  It just requires the software to
support an alternate scanline mode for stereo (i.e. even scan
lines one eye, odd scan lines the other).  They even claim to be
willing to pass along the OpenGL code required to implement this
mode.

Anyway, their web site is www.vrex.com, and no I am not a
shareholder or getting any kickback for passing this along. :-)

Malcolm Davis

[PyMOL] Counting from '01' and wildcards

[Evan S. <st...@sa...>]

I'm making figures with hydrogen bonds and I've found that easiest way to
do it is to select two atoms, measure the distance between the two, and
then to hide the label and recolor the dashed lines grey. However, if I do
this in a script, each time I run the script the numbers assigned to the
"dist" objects continue to get incremented. So, if a line in a script is
"color grey, dist01" that command won't work the second time I run the
script. Is there a way to force the counter back to "01"?

Also, since I want all the dashes to be the same color, I've tried "color
grey, dist*"  but PyMol won't accept the wildcard in this context.

On the topic of wildcards, does PyMol accept them in atom selections? When
I've tried to do things like:
color red, */O*
it doesn't work -- no error, just no selection.

I'm using PyMol 0.82 under XP. Thanks for an help.

Evan Stein

[PyMOL] Meaning of the get_view block

[Serge C. <co...@em...>]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi again,

I posted a question few days ago about the way to center on a particular 
zone of a structure without using the zoom command (which would touch a 
lot of view parameters at once).

I've just figured out that I might be able to do more or less what I 
wanted by producing proper get_view blocks. In that respect I need to 
know what the different numbers are good for:

I have the impression that the block correspond to plenty of info: 
orientation, translation position (ie center of view), cliping, 
zooming... (at least from the doc of pymol, and personnal use).



Thanks for any info on that.

Serge.

- ----------------------------------------------------
Serge Cohen

GPG Key ID: 1024D/69B1D346
- ----------------------------------------------------
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.0.7 (Darwin)

iD8DBQE9lFAqMygj1Wmx00YRAlcXAJwLY5hXStpUKyyvklqzxi+NYb0DbgCghTFN
D2nsSa1VJrfsWX17LN42bls=
=niY8
-----END PGP SIGNATURE-----

Re: [PyMOL] Conformation Editing

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

Yu,

The conformational editing features are not fully designed nor well
tested, and the documentation is still incomplete.  Until the PyMOL user
interface is a bit more stabilized, documentation seems premature.
I am resistant to the idea of committing to a user interface which hasn't
really been evaluated or optimized for usability.  However it is quite
frustrating for all of us knowing that there is considerable  power under
the  hood which can't yet be accessed by users : ( .

However, you should at least be able to do a few basic things, such as
manually adjusting bond torsions:

1. put the mouse into editing mode (Mouse menu)
2. ctrl-right click on a bond
3. ctrl-left click and drag atoms on either side of the bond.

Other mouse combinations allow you to move fragments in different
ways...just play around with the different combinations on the mouse
"matrix".

Sculpting is a bit less obvious:  PyMOL will take a snapshot of
bond lenths, angles, and stereochemistry inside a molecule the first time
sculpting is activated on an object.  From then on, no matter what you do,
PyMOL will labor to maintain those constraints while you drag atoms around
or make other conformational changes.

The Sculpting Wizard can help you out in getting started with this
feature.  However, the bottom line is that more work needs to be
done on these aspects of PyMOL, and that's why increasing funding for
PyMOL is essential.  Until I can afford to start paying people to help me
with development and documentation, progress will cotinue to be slow.

So in closing, I wouldn't look to PyMOL as a workhorse conformational
editing tool just yet -- give it another year or so.

Cheers,
Warren


On Thu, 26 Sep 2002, Yu Shao wrote:

> Hello everyone,
>
> Does anyone know how to use the conformation editing of PyMol, or has it
> been implemented? It's unclear from the menual, which just said that
> "Sorry, no documentation yet -- these features won't be too useful until
> PyMOL is coupled up with an energy minimiation engine." Any infomation
> will be highly appreciated.
>
> Best wishes,
> Yu Shao
> R.P.I.
>
>
>
>
> -------------------------------------------------------
> 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
>

[PyMOL] Conformation Editing

[Yu S. <sh...@rp...>]

Hello everyone,

Does anyone know how to use the conformation editing of PyMol, or has it
been implemented? It's unclear from the menual, which just said that
"Sorry, no documentation yet -- these features won't be too useful until
PyMOL is coupled up with an energy minimiation engine." Any infomation
will be highly appreciated.

Best wishes,
Yu Shao
R.P.I.

[PyMOL] Stereo3D hardware recommendation

[lonely l. <gud...@ya...>]

Hello there,

I plan to purchase a new graphics card and a pair of
stereo glasses to be used with PyMOL. My current
system: Dual Althlon 1900XP / 1GB DDR memory /
Geforce4 video card. Could anyone please give me some
suggestions/recommendations on the following
questions?

Because of the mono-performance issue, I decide to
change my graphics card to ATI Fire GL2 (or 3 / 4).
The current price I found:
GL2: $800
GL3: $1300
GL4: $1700
My first question is: how will the different cards
affect the stereo-viewing performance (at 1280x1024)?
Is it necessary to go for a high-end card (and pay
extra cash)?

For the stereo glasses, I called Stereo Graphics and
their CrystalEyes3 + Emitter boundle costs about $900.
I also called NuVision and their 60GX + Emitter cost
about $300. My second question is: what's the
difference between these two? Can the difference
justify the extra $600?

Thanks a lot!

Jiye Shi

__________________________________________________
Do you Yahoo!?
New DSL Internet Access from SBC & Yahoo!
http://sbc.yahoo.com

RE: [PyMOL] pair_fit crashes

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

Hi Jeremy,

If the proteins have significant homology, then you can use the align =
command:

align prot1////ca,prot2

which will perform a sequence alignment of prot1 against prot2, and then =
an optimizing fit using the CA positions.  I'm not sure if the help text =
for align got into 0.82, but the next version will definitely have it.

PyMOL's command length is limit to about 1000 characters, which is =
probably what is causing pair_fit to crash.  However, ideally it should =
complain gracefully instead of crashing, so if you have a sample script =
& input PDB files which cause it to crash, please send them to me as =
attachments.

As far as script options go, you've pointed out a hole which I had =
forgotten about, but Robert's suggestion on defining a function call in =
the script is definitely the way to go for now.

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: Jeremy Craven [mailto:c.j...@sh...]
Sent: Thursday, September 26, 2002 2:00 AM
To: pym...@li...
Subject: [PyMOL] pair_fit crashes


I have been trying to write a script to overlay two arbitrary proteins =
via my own alignment and the 'pair_fit' command.=20
1) After running into the problem I described below I looked through the =
pymol-users mailing list as hard as I could and found a statment that =
such arbitrary alignment should be in pymol anyhow from vsn 0.80.  I am =
using 0.82 but cannot find it. Is it there ?=20
2) Anyhow, (and assuming that I might want to do alignments my own way =
anyhow), I created a script which read in an alignment and created a big =
long pair_fit command of the form ....=20
pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca), =
(tbr and resi 192 and name ca),(bs and resi 175 and name ca), .... etc=20
The script then executed this string with cmd.do=20
If I restricted this to about 10 atom pairs it worked fine.  If I allow =
more atoms it crashes the program.  On linux it gave segmentation =
violation.  On irix it gave bus error.  On irix it gave another message =
that implied that maybe the selections had got truncated.  On linux it =
got as far as giving a sensible 'ExecutiveRMS' message (including a =
value for the rmsd and the number of atoms) and then froze and =
eventually core dumped. It therefore seems that the long selection has =
been accepted properly, but may it corrupts something else as a side =
effect ?=20
Any ideas anyone ??  I wondered about doing all the selections =
invidually into named selections and then create a shorter pair_fit =
command, but decided I would ask here first.=20
A second little quesion is how do you send command line arguments to a =
pymol python script.=20
If I say=20
PyMOL>   run test1.py abcdef=20
it says=20
Traceback (most recent call last):=20
  File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py", =
line=20
186, in parse=20
    execfile(args[nest][0],pymol_names,pymol_names)=20
IOError: [Errno 2] No such file or directory=20
whereas test1.py really does exist, and "run test1.py" works fine.=20
Otherwise pymol is a great joy to have discovered in the last month or =
so, and a project that I hope I can support (e.g. by contributing =
scripts like this one once I can get it to work properly ...)=20
Cheers=20
Jeremy=20
--=20
*************************************************************************=
********

Dr C. Jeremy Craven
Department of Molecular Biology and Biotechnology
University of Sheffield,=20
Firth Court, Western Bank
S10 2TN Sheffield UK

e-mail: c.j...@sh...
http://www.shef.ac.uk/uni/projects/nmr/CJC/CJC.html

Phone:                       x24323=20
From outside Sheffield:      0114 222 4323
From outside UK:             +44 114 2224323
Fax:                         0114 272 8697

*************************************************************************=
********
 =20

Re: [PyMOL] pair_fit crashes

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

* Jeremy Craven <c.j...@sh...> [2002-09-26 09:59] wrote:

> 2) Anyhow, (and assuming that I might want to do alignments my own way anyhow),
> I created a script which read in an alignment and created a big long pair_fit
> command of the form ....
> 
> pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca), (tbr and
> resi 192 and name ca),(bs and resi 175 and name ca), .... etc
> 
> The script then executed this string with cmd.do
> 
<snip>

I'll tackle the second question:

> A second little quesion is how do you send command line arguments to a pymol
> python script.
> 
> If I say
> 
> PyMOL>   run test1.py abcdef
> 
> it says
> 
> Traceback (most recent call last):
>   File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py", line
> 186, in parse
>     execfile(args[nest][0],pymol_names,pymol_names)
> IOError: [Errno 2] No such file or directory
> 
> whereas test1.py really does exist, and "run test1.py" works fine.
> 

If you write test1.py to be a function definition, e.g.:

def make_pair_fit(arg1,arg2,arg3<etc.>):

Then "run test1.py" will read the python script to create the
definition, but not actually run it.  Then you can run it with:

make_pair_fit(YourArg1,YourArg2,YourArg3,...)

where you've filled in the appropriate values for the arguments.  

Hope that helps. 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] pair_fit crashes

[Jeremy C. <c.j...@sh...>]

I have been trying to write a script to overlay two arbitrary proteins
via my own alignment and the 'pair_fit' command.

1) After running into the problem I described below I looked through the
pymol-users mailing list as hard as I could and found a statment that
such arbitrary alignment should be in pymol anyhow from vsn 0.80.  I am
using 0.82 but cannot find it. Is it there ?

2) Anyhow, (and assuming that I might want to do alignments my own way
anyhow), I created a script which read in an alignment and created a big
long pair_fit command of the form ....

pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca),
(tbr and resi 192 and name ca),(bs and resi 175 and name ca), .... etc

The script then executed this string with cmd.do

If I restricted this to about 10 atom pairs it worked fine.  If I allow
more atoms it crashes the program.  On linux it gave segmentation
violation.  On irix it gave bus error.  On irix it gave another message
that implied that maybe the selections had got truncated.  On linux it
got as far as giving a sensible 'ExecutiveRMS' message (including a
value for the rmsd and the number of atoms) and then froze and
eventually core dumped. It therefore seems that the long selection has
been accepted properly, but may it corrupts something else as a side
effect ?

Any ideas anyone ??  I wondered about doing all the selections
invidually into named selections and then create a shorter pair_fit
command, but decided I would ask here first.

A second little quesion is how do you send command line arguments to a
pymol python script.

If I say

PyMOL>   run test1.py abcdef

it says

Traceback (most recent call last):
  File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py",
line
186, in parse
    execfile(args[nest][0],pymol_names,pymol_names)
IOError: [Errno 2] No such file or directory

whereas test1.py really does exist, and "run test1.py" works fine.

Otherwise pymol is a great joy to have discovered in the last month or
so, and a project that I hope I can support (e.g. by contributing
scripts like this one once I can get it to work properly ...)

Cheers

Jeremy

--
*********************************************************************************

Dr C. Jeremy Craven
Department of Molecular Biology and Biotechnology
University of Sheffield,
Firth Court, Western Bank
S10 2TN Sheffield UK

e-mail: c.j...@sh...
http://www.shef.ac.uk/uni/projects/nmr/CJC/CJC.html

Phone:                       x24323
From outside Sheffield:      0114 222 4323
From outside UK:             +44 114 2224323
Fax:                         0114 272 8697

*********************************************************************************

RE: [PyMOL] Question about crystallographic symmetry

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

Hi Michael

You seem to be after the biological assembly;  in theory, pdb files from
the PDB are supposed to have the matrix that will generate this
somewhere in the header (REMARKS lines), and that shouldn't be too hard
to parse out and apply explicitly to the molecule.

Of course, pdb files are not often the way they're supposed to be;
there are, however a few web servers that try to provide you with
complete biological assemblies.  The first one I found was
http://pqs.ebi.ac.uk/, there may be more.  
	


If your question is more general:  it's not hard, although you do need
to qualify "one unit cell" somewhat, because the molecule itself does
not bother to restrict itself to lie within those abstract planes we've
decided to call unit cell edges.  i.e. it is usual for the _intact_
molecule to lie cross unit cell edges.  

So if you want to have all atoms that lie within a unit cell:
	- generate all symmetry copies within a distance of, say, the
longest unit cell edge.
	- test all atoms and see whether they lie within the
parallelopiped of the unit cell.

	(This latter one is very easy if you convert coordinates to
fractional coordinates.  If 	you want details on that, let me know.)
	
	Of course, you'll then probably end up with incomplete bonds and
things at the edges.


If you only want to generate some assembly with the right number of
copies, without caring about borders, it is a bit more arbitary.  Seems
you could again generate lots of symmetry copies within a large radius,
and then test which subset forms the most compact assembly.  Or
something. 

Does that answer your question?  There are external programs that will
do this sort of thing for you, most obviously in the CCP4 suite
(http://www.ccp4.ac.uk), but I don't think it's necessary to reel those
in. 


Hope it helps
phx.


> -----Original Message-----
> From: Michael George Lerner [mailto:ml...@um...]
> Sent: Wednesday, September 25, 2002 9:50 AM
> To: pym...@li...
> Subject: [PyMOL] Question about crystallographic symmetry
> 
> 
> 
> Hi,
> 
> I'm looking at a PDB file which, due to symmetry, only 
> provides me with
> part of the unit cell (in this case I'm looking at 1HHP, which is a
> dimer but only gives coordinates for the monomer, but I've 
> run across the
> problem before).  I'd like to see the full unit cell.  I 
> understand that I
> can use symexp to create symmetry related objects within a certain
> distance, but I'd like to be able to say "give me the unit cell."
> 
> I noticed that the online manual
> (http://pymol.sourceforge.net/html/S0400xtal.html#10) says 
> "Currently that
> information can only be provided to PyMOL as a CRYST1 record 
> in the PDB
> file, which includes the correct space group identifier. 
> However, it would
> be only a minor development task to add a means of assigning 
> unit-cell and
> symmetry to any molecule object directly from the API."
> 
> So, two questions:
> 
> 1) Can PyMOL already do what I want?
> 2) If not, and if it's "only a minor development task," could 
> someone give
> me some pointers for how to do it so that I can code it up myself?
> 
> thanks,
> 
> -michael
> 
> --
> This isn't a democracy;|                        _  |Michael Lerner
>  it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
> -Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
>                        |                       / \ | mlerner@umich
> 
> 
> 
> -------------------------------------------------------
> 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
>


----------
This message contains confidential information and is intended only for
the individual named. If you are not the named addressee you should not
disseminate, distribute or copy this e-mail. Please notify the sender
immediately by e-mail if you have received this e-mail by mistake and
delete this e-mail from your system. E-mail transmission cannot be
guaranteed to be secure or error-free as information could be
intercepted, corrupted, lost, destroyed, arrive late or incomplete, or
contain viruses. The sender therefore does not accept liability for any
errors or omissions in the contents of this message, which arise as a
result of e-mail transmission. If verification is required please
request a hard-copy version. 

[PyMOL] Question about crystallographic symmetry

[Michael G. L. <ml...@um...>]

Hi,

I'm looking at a PDB file which, due to symmetry, only provides me with
part of the unit cell (in this case I'm looking at 1HHP, which is a
dimer but only gives coordinates for the monomer, but I've run across the
problem before).  I'd like to see the full unit cell.  I understand that I
can use symexp to create symmetry related objects within a certain
distance, but I'd like to be able to say "give me the unit cell."

I noticed that the online manual
(http://pymol.sourceforge.net/html/S0400xtal.html#10) says "Currently that
information can only be provided to PyMOL as a CRYST1 record in the PDB
file, which includes the correct space group identifier. However, it would
be only a minor development task to add a means of assigning unit-cell and
symmetry to any molecule object directly from the API."

So, two questions:

1) Can PyMOL already do what I want?
2) If not, and if it's "only a minor development task," could someone give
me some pointers for how to do it so that I can code it up myself?

thanks,

-michael

--
This isn't a democracy;|                        _  |Michael Lerner
 it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
                       |                       / \ | mlerner@umich

[PyMOL] soap-film II

[Ricardo A. <apa...@if...>]

With respect to my previous question,

any option in PyMOL would be useful, not necessarily a polygonal surface.

Any ideas are welcomed.

Thank you,


Ricardo


Ricardo Aparicio wrote:

> Dear PyMOL users:
>
>
>    To make a structural alignment (2  pdb files) more informative, it 
> would be interesting to make an image stressing the areas where the 
> discrepancies between the two structures are more evident.
>    One option is to use a polygonal surface linking the c-alfa atoms 
> of consecutive residues in the superimposed structures (4 atoms), as 
> implemented in the program O (DVD macros).
>
>    Is it possible to create such a surface using  PyMOL?
>
>    I am sorry if this question has been addressed before but I didn't 
> find an answer in my list files.
>
>    Any help is appreciated.
>
>    Thank you in advance,
>
>
>
> Ricardo Aparicio
> PhD Student
> USP - Sao Paulo
> Brazil
>
>

[PyMOL] soap-film

[Ricardo A. <apa...@if...>]

Dear PyMOL users:


    To make a structural alignment (2  pdb files) more informative, it 
would be interesting to make an image stressing the areas where the 
discrepancies between the two structures are more evident.
    One option is to use a polygonal surface linking the c-alfa atoms of 
consecutive residues in the superimposed structures (4 atoms), as 
implemented in the program O (DVD macros).

    Is it possible to create such a surface using  PyMOL?

    I am sorry if this question has been addressed before but I didn't 
find an answer in my list files.

    Any help is appreciated.

    Thank you in advance,



Ricardo Aparicio
PhD Student
USP - Sao Paulo
Brazil

Re: [PyMOL] Latest Apple G4 graphic cards and PyMOL (Luca Jovine) (fwd)

[Nat <nat...@ya...>]

> I have a GeForce4 Ti 4600 on a dual 1GHz PowerMac G4 (the old one with
> 133 MHz bus).

I too am using this, though on a Dell running Linux.  The performance is
unbelievable; unfortunately the graphics card far outpaces the PC!  I have
dual pentium IIIs and 1GB of memory, and the machine will drop dead long
before the geforce does, particularly when dealing with cartoons or
surfaces of large structures (e.g. GroEL rings).  To really get the
maximum mileage out of the card, you'd probably need to buy one heck of a
machine; for smaller structures, I can't really tell the difference
between this and a plain GeForce2.  One thing I haven't really tested,
however, is the performance gain when dealing with trajectories.

The other thing about that card is that you can crank antialiasing all the
way up (at least on Linux- I would expect OS X to support it as well) and
still get very good performance.  I don't actually think it makes much of
a difference when viewing lines, but cartoons are incredibly better.  I
never turn antialiasing off now.

----------------------------------------------------------------------------
Nathaniel Echols                                                  Programmer
na...@bi...                                        Gerstein Lab
203-589-6765                                                 Yale University
----------------------------------------------------------------------------

RE: [PyMOL] transparent CGOs?

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

David,

	I haven't written this into the CGO system, which is pretty rudimentary =
and pretty incomplete at present.  Transparency is actually tough to get =
right, since certain kinds of objects need to be rendered before the =
transparent surface -- others after.  Then there's the issue of =
Z-ordering transparent triangles, which PyMOL isn't doing yet at all...

	I'll add this functionality to the next release, but don't expect the =
results to look good.

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: David [mailto:sp...@xr...]
> Sent: Monday, September 23, 2002 2:38 PM
> To: pym...@li...
> Subject: [PyMOL] transparent CGOs?
>=20
>=20
> Hi,
>=20
> a rephrase of my earlier question: (how do/can) I make my CGO's
> transparent? Isn't it simply a property of the OpenGL object?
>=20
>=20
> --=20
> Groeten, David.
> ______________________________________________________________
> __________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> sp...@xr...	sp...@gr...   http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
>=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] transparent CGOs?

[David <sp...@xr...>]

Hi,

a rephrase of my earlier question: (how do/can) I make my CGO's
transparent? Isn't it simply a property of the OpenGL object?


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
sp...@xr...	sp...@gr...   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

RE: [PyMOL] Zooming in, on an atom

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

Serge,

	The zoom command in the released version is flaky and sometimes causes =
clipping.  I've fixed this in the development version and will be =
preparing a new release shortly.

	The best thing you can do right now is put a large buffer on the zoom =
command...

zoom all,20

etc.

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: Serge Cohen [mailto:co...@em...]
> Sent: Monday, September 23, 2002 11:43 AM
> To: pym...@li...
> Subject: [PyMOL] Zooming in, on an atom
>=20
>=20
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>=20
> Hi again,
>=20
> This is a different question, I though it was better if I put it in a=20
> different eMail:
>=20
> I'm trying to produce a movie showing a metal binding site in my=20
> protein. I'd like to start from the general (cartoon) view, and then=20
> zoom in (or traveling in) to focus on the metal.
>=20
> So far I used a loop looking like:
>=20
> # Traveling in the site
> diam =3D 30.0
> final =3D 6.0
> step =3D 0.0 + (N.exp((N.log(final) - N.log(diam)) * 1/40))
> for a in range (1, 40):
>    cmd.mdo(a,"zoom ((zn expand %2.9f) & (prot1 or zn)); origin (zn &=20
> i;2)"%(diam))
>    diam =3D diam*step
>=20
>=20
> The problem is that because atoms "fall off" the zooming selection un=20
> regularly, the traveling is unstable (wiggly)... Indeed I=20
> have a third=20
> object (not zn neither prot1) in the figure, I had to remove=20
> it from the=20
> zooming because it was only on one side of the site and it was giving=20
> even worse unstabilities...
>=20
> Does anyone knows better ways to do this king of traveling in?
>=20
> Indeed I was first thinking to center each frames on a "moving" point=20
> which get closer to the zinc, and have a "progressive" move z at the=20
> same time. Unfortunately the only command I found to put a given=20
> position in the middle of the screen is to use zoom, and it=20
> also change=20
> the z position... Am I missing some commands?
>=20
> Thanks for any help.
>=20
> Serge.
>=20
>=20
> - ----------------------------------------------------
> Serge Cohen
>=20
> GPG Key ID: 1024D/69B1D346
> - ----------------------------------------------------
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.0.7 (Darwin)
>=20
> iD8DBQE9j2CjMygj1Wmx00YRAi6RAJ45zAsff2DEsKTeNJR2ul5BkFURbACfZFaG
> ho6XobfQPkh/a5/4se9HLkI=3D
> =3DBqTf
> -----END PGP SIGNATURE-----
>=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

RE: [PyMOL] Ray-tracing without display

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

You can't raytrace it the background using threads, but if you have =
everything in a script, you can launch a separate process to do the =
work:

"pymol -c script.pml"=20

or

"pymol -c script.py"

will run PyMOL without a Window.  You do need to like against the X11 =
and OpenGL libs though...

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: Serge Cohen [mailto:co...@em...]
> Sent: Monday, September 23, 2002 11:32 AM
> To: pym...@li...
> Subject: [PyMOL] Ray-tracing without display
>=20
>=20
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>=20
> Hi there,
>=20
> I'm just starting using PyMol, currently making some couple=20
> of movies...
> I'm set to test the movies on my laptop, but I'd like to do the=20
> ray-tracing rendering on a computing server, and if possible=20
> to run that=20
> on the background without having a X11 session... Is that possible in=20
> anyway?
>=20
>=20
> Thanks for this very nice software.
>=20
> Serge.
>=20
>=20
> - ----------------------------------------------------
> Serge Cohen
>=20
> GPG Key ID: 1024D/69B1D346
> - ----------------------------------------------------
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.0.7 (Darwin)
>=20
> iD8DBQE9j14OMygj1Wmx00YRAqU2AJ40IrivKH/R1SLwkBf1vAPxfZYbpwCghiQa
> YcTC3ucvZ6mWlApvww/T9VE=3D
> =3DmY7I
> -----END PGP SIGNATURE-----
>=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] Latest Apple G4 graphic cards and PyMOL (Luca Jovine)

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

On Monday, Sep 23, 2002, at 14:06 America/Chicago, 
pym...@li... wrote:
>
>
> Dear OSX PyMOL users,
>
> I'd like to hear about your experience with PyMOL using either of the
> graphic cards shipping with the latest Apple G4s (ATI Radeon 9000 Pro 
> card
> 64 DDR and NVIDIA GeForce4 Titanium 128 DDR). We are going to get one 
> of
> these new machines soon but I'm not sure which card should we go for. 
> Any
> suggestion?
> Thanks in advance and best regards,

Dear Luca,

I have a GeForce4 Ti 4600 on a dual 1GHz PowerMac G4 (the old one with 
133 MHz bus).
The "lambda" demo run in 68 seconds with PyMOL 0.84 and Jaguar (MacOS 
X.2.1).
I'm also able to get something like 2 frame/s for the line 
representation of a protein (50000 atoms) and 95 of its 
crystallographic symetries in full screen mode (1280x1024).
That is more than  4.5 millions atoms on the screen!!

Best regards,

[PyMOL] Zooming in, on an atom

[Serge C. <co...@em...>]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi again,

This is a different question, I though it was better if I put it in a 
different eMail:

I'm trying to produce a movie showing a metal binding site in my 
protein. I'd like to start from the general (cartoon) view, and then 
zoom in (or traveling in) to focus on the metal.

So far I used a loop looking like:

# Traveling in the site
diam = 30.0
final = 6.0
step = 0.0 + (N.exp((N.log(final) - N.log(diam)) * 1/40))
for a in range (1, 40):
   cmd.mdo(a,"zoom ((zn expand %2.9f) & (prot1 or zn)); origin (zn & 
i;2)"%(diam))
   diam = diam*step


The problem is that because atoms "fall off" the zooming selection un 
regularly, the traveling is unstable (wiggly)... Indeed I have a third 
object (not zn neither prot1) in the figure, I had to remove it from the 
zooming because it was only on one side of the site and it was giving 
even worse unstabilities...

Does anyone knows better ways to do this king of traveling in?

Indeed I was first thinking to center each frames on a "moving" point 
which get closer to the zinc, and have a "progressive" move z at the 
same time. Unfortunately the only command I found to put a given 
position in the middle of the screen is to use zoom, and it also change 
the z position... Am I missing some commands?

Thanks for any help.

Serge.


- ----------------------------------------------------
Serge Cohen

GPG Key ID: 1024D/69B1D346
- ----------------------------------------------------
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.0.7 (Darwin)

iD8DBQE9j2CjMygj1Wmx00YRAi6RAJ45zAsff2DEsKTeNJR2ul5BkFURbACfZFaG
ho6XobfQPkh/a5/4se9HLkI=
=BqTf
-----END PGP SIGNATURE-----

[PyMOL] Ray-tracing without display

[Serge C. <co...@em...>]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi there,

I'm just starting using PyMol, currently making some couple of movies...
I'm set to test the movies on my laptop, but I'd like to do the 
ray-tracing rendering on a computing server, and if possible to run that 
on the background without having a X11 session... Is that possible in 
anyway?


Thanks for this very nice software.

Serge.


- ----------------------------------------------------
Serge Cohen

GPG Key ID: 1024D/69B1D346
- ----------------------------------------------------
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.0.7 (Darwin)

iD8DBQE9j14OMygj1Wmx00YRAqU2AJ40IrivKH/R1SLwkBf1vAPxfZYbpwCghiQa
YcTC3ucvZ6mWlApvww/T9VE=
=mY7I
-----END PGP SIGNATURE-----

[PyMOL] Latest Apple G4 graphic cards and PyMOL

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

Dear OSX PyMOL users,

I'd like to hear about your experience with PyMOL using either of the 
graphic cards shipping with the latest Apple G4s (ATI Radeon 9000 Pro card 
64 DDR and NVIDIA GeForce4 Titanium 128 DDR). We are going to get one of 
these new machines soon but I'm not sure which card should we go for. Any 
suggestion?
Thanks in advance and 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] surfaces

[David <sp...@xr...>]

Hi,

I would like to make an arbitrary surface (e.g. built up from triangles
or squares) and visualise it together with my molecule. I have succeeded
adapting one of the examples into displaying some triangles as compiled
graphics objects. However, now commands like transparency do not apply
to the objects. The menus do not let me change colors either.

I presume pymol doesn't regard these triangles as "surfaces". Is there
any way to make compiled graphics object transparent? Or to create
surfaces in another way than using cgo's?

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
sp...@xr...	sp...@gr...   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++