pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] selection in python script

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

Dear pymolers,

I can select some residues in my protein in the command prompt
by saying for example
 select prot = (////VAL or ////PRO or ////GLY)
but now I have trouble translating this into python script.
I tried many varieties including something like
 cmd.select( prot, (////VAL or ////PRO or ////GLY) )
but by far nothing works.
I did not try to write .pml script because I thought that
I need to use python script so that I can do some
string and file processing (iterating through my pdb files).
Any suggestion?

Regards,
K.K.Liang

[PyMOL] Coloring by B-factors

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

Dear PyMOLers,

I've revised the B-factor colouring script that I published on this list
back on May 24th. The function now allows you to choose the style of
colour ramp (blue-magenta-red or rainbow), the way in which the B-value
ranges are chosen (histogram or smooth ramp) plus the number of colours
to use (nbins). I include it here as an attachment. The documentation at
the top of the file says:

USAGE

  color_b(selection='sel',ramp=0 or 1, rainbow=0 or 1, nbins=10)

  or

  color_b selection='sel',ramp=0 or 1, rainbow=0 or 1, nbins=10


  This function allows coloring of a selection as a function of B-value,
  either in a range of hues from blue through magenta to red (rainbow=0,
  the default) or in the colors of the rainbow (rainbow=1). The division
  of B-value ranges can either be as a histogram (equal-sized B-value
  increments leading to unequal numbers of atoms in each bin: ramp=0)
  or as a ramp of B-value ranges with an equal number of atoms in each
  group (ramp=1).

The module must first be imported into PyMOL, either by including it
in the contrib.py module in the modules/pymol directory of your pymol
distribution, or by importing it from another directory or by using the
"run color_b.py" command. If you then just say "color_b", it will color
all of your molecular objects with ten colors ranging from blue to red
(via magenta).

Because I included the line: 

  cmd.extend("color_b",color_b)

Then you don't need the parentheses around the arguments, but if you
"import" the color_b.py module, then you'll need to say, for example:

color_b.color_b(arguments...)

or just

color_b arguments...

One question for the gurus. Is pymol/modules/pymol/contrib.py the
accepted place to put new (or personal) functions? I noticed that if I
include my function within the contrib.py module, it is ready for use
as soon as I start up PyMOL (i.e. I don't have to explicitly "import"
it or "run" it (although with parenthese, it needs to be called as
"contrib.color_b(...)"). I couldn't find any other python module that
imports from contrib.py, so I wasn't sure.

Cheers and happy colo(u)ring,
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

RE: [PyMOL] lines same color as background

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

Results:

on geforce4 ti 4400 from PNY
	WORKS:
		line_smooth=0
		depth_cue=1   

		line_smooth=1
		depth_cue=0

		line_smooth=0
		depth_cue=0

	WORKS NOT
		line_smooth=1
		depth_cue=1
 


On Thu, 30 May 2002, DeLano, Warren wrote:

> Zac,
> 
>    Thanks for the report.
> 
>    The fact that it happens with Ono too indicates that it is a
> driver/openGL-level bug.  You can try some things like disabling
> depth cuing (set depth_cue=0) or smoothing (set line_smooth=0), but
> most likely you will need to wait for a driver upgrade.  Please do
> report the problem to nVidia tech support and clearly state that the
> problem occurs across multiple OpenGL programs.
> 
>   Also, you might try using an older version of the driver.  AFAICR, nVidia uses a unified driver architecture which is both backwards and forwards compatible.  If you do find a robust solution, please pass it along!
> 
> Cheers,
> Warren
> 
> --
> mailto:wa...@su...
> Warren L. DeLano, Ph.D.
> 
> 
> 
> > -----Original Message-----
> > From: Ezequiel Panepucci [mailto:za...@SL...]
> > Sent: Thursday, May 30, 2002 1:39 PM
> > To: PyM...@li...
> > Subject: [PyMOL] lines same color as background
> > 
> > 
> > Hello There,
> > 
> > I have this geforce4 ti 4400 with the latest nvidia
> > drivers and xfree86 4.2
> > 
> > Problem: The lines are always colored the same color as the
> > background. If I change the background to white the lines become
> > white.
> > 
> > all other representaions (sticks, spheres surface) work
> > fine. So as a workaround I am using stick_radius really small
> > but this is not the same, lines are way better for interactive work.
> > 
> > Weird thing is, the same happens under Win2k (dual boot machine
> > here so exactly the same hardware).
> > 
> > More weirdness: also happens with Ono under both OSes.
> > 
> > My feeling is that this has to do with the z-buffer/fog
> > thingy. I did run a program drawing (GL_LINES) with GL_DEPTH_TEST
> > enabled and that worked fine.
> > 
> > any clues?
> > 	Zac
> > 
> > --
> >  Ezequiel Panepucci - Laboratory of Prof. Axel Brunger
> >  HHMI - Stanford University
> >  Phone: 650-926-5127
> >  Cell:  650-714-9414
> > 
> > 
> > _______________________________________________________________
> > 
> > Don't miss the 2002 Sprint PCS Application Developer's Conference
> > August 25-28 in Las Vegas -- http://devcon.sprintpcs.com/adp/index.cfm
> > 
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > 
> 

--
 Ezequiel Panepucci - Laboratory of Prof. Axel Brunger
 HHMI - Stanford University
 Phone: 650-926-5127
 Cell:  650-714-9414

RE: [PyMOL] lines same color as background

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

Zac,

   Thanks for the report.

   The fact that it happens with Ono too indicates that it is a =
driver/openGL-level bug.  You can try some things like disabling depth =
cuing (set depth_cue=3D0) or smoothing (set line_smooth=3D0), but most =
likely you will need to wait for a driver upgrade.  Please do report the =
problem to nVidia tech support and clearly state that the problem occurs =
across multiple OpenGL programs.

  Also, you might try using an older version of the driver.  AFAICR, =
nVidia uses a unified driver architecture which is both backwards and =
forwards compatible.  If you do find a robust solution, please pass it =
along!

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.



> -----Original Message-----
> From: Ezequiel Panepucci [mailto:za...@SL...]
> Sent: Thursday, May 30, 2002 1:39 PM
> To: PyM...@li...
> Subject: [PyMOL] lines same color as background
>=20
>=20
> Hello There,
>=20
> I have this geforce4 ti 4400 with the latest nvidia
> drivers and xfree86 4.2
>=20
> Problem: The lines are always colored the same color as the
> background. If I change the background to white the lines become
> white.
>=20
> all other representaions (sticks, spheres surface) work
> fine. So as a workaround I am using stick_radius really small
> but this is not the same, lines are way better for interactive work.
>=20
> Weird thing is, the same happens under Win2k (dual boot machine
> here so exactly the same hardware).
>=20
> More weirdness: also happens with Ono under both OSes.
>=20
> My feeling is that this has to do with the z-buffer/fog
> thingy. I did run a program drawing (GL_LINES) with GL_DEPTH_TEST
> enabled and that worked fine.
>=20
> any clues?
> 	Zac
>=20
> --
>  Ezequiel Panepucci - Laboratory of Prof. Axel Brunger
>  HHMI - Stanford University
>  Phone: 650-926-5127
>  Cell:  650-714-9414
>=20
>=20
> _______________________________________________________________
>=20
> Don't miss the 2002 Sprint PCS Application Developer's Conference
> August 25-28 in Las Vegas -- http://devcon.sprintpcs.com/adp/index.cfm
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] lines same color as background

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

Hello There,

I have this geforce4 ti 4400 with the latest nvidia
drivers and xfree86 4.2

Problem: The lines are always colored the same color as the
background. If I change the background to white the lines become
white.

all other representaions (sticks, spheres surface) work
fine. So as a workaround I am using stick_radius really small
but this is not the same, lines are way better for interactive work.

Weird thing is, the same happens under Win2k (dual boot machine
here so exactly the same hardware).

More weirdness: also happens with Ono under both OSes.

My feeling is that this has to do with the z-buffer/fog
thingy. I did run a program drawing (GL_LINES) with GL_DEPTH_TEST
enabled and that worked fine.

any clues?
	Zac

--
 Ezequiel Panepucci - Laboratory of Prof. Axel Brunger
 HHMI - Stanford University
 Phone: 650-926-5127
 Cell:  650-714-9414

RE: [PyMOL] Colors and ray-tracing

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

My guess is that you may still be showing sticks in the original object, =
instead of just cartoons.  If you have the same overlapping =
representation in two objects, it isn't predictable which will show up =
in the ray-tracer, and you can get exactly this behavior, where you see =
one color in OpenGL and a different one in the raytracer.

Here is the general sequence of steps you'll want to follow to insure =
success:

load prot.pdb
create cpy,prot
hide
show cartoon,prot
show sticks,cpy
color red,prot
color green,cpy
ray

--
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: Peter Stogios [mailto:pst...@uh...]
> Sent: Tuesday, May 28, 2002 9:08 AM
> To: pym...@li...
> Subject: [PyMOL] Colors and ray-tracing
>=20
>=20
> This topic was touched on before but I'm still having=20
> problems with it.
>=20
> Somebody asked how to color sticks differently from cartoons=20
> and Warren
> explained that this can be done by creating duplicate=20
> objects.  I managed
> to accomplish that, but when I ray-trace the image the=20
> cartoon takes the
> same color as the stick does.  As soon as I move the=20
> ray-traced image, it
> restores back to the different colors, as I want them.
>=20
> For example, I colored the cartoons in one object green,=20
> while I showed
> only sticks in the duplicate object and colored a specific=20
> residue stick
> blue.  When I ray-trace the image, the cartoon at that residue turns
> green, instead of staying blue.
>=20
> Is this a bug or how can I get around this?  Thanks in advance.
>=20
> --=20
> Peter Stogios
> Dept. of Medical Biophysics, Univ. of Toronto
>=20
>=20
> _______________________________________________________________
>=20
> Don't miss the 2002 Sprint PCS Application Developer's Conference
> August 25-28 in Las Vegas -- http://devcon.sprintpcs.com/adp/index.cfm
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Colors and ray-tracing

[Peter S. <pst...@uh...>]

This topic was touched on before but I'm still having problems with it.

Somebody asked how to color sticks differently from cartoons and Warren
explained that this can be done by creating duplicate objects.  I managed
to accomplish that, but when I ray-trace the image the cartoon takes the
same color as the stick does.  As soon as I move the ray-traced image, it
restores back to the different colors, as I want them.

For example, I colored the cartoons in one object green, while I showed
only sticks in the duplicate object and colored a specific residue stick
blue.  When I ray-trace the image, the cartoon at that residue turns
green, instead of staying blue.

Is this a bug or how can I get around this?  Thanks in advance.

-- 
Peter Stogios
Dept. of Medical Biophysics, Univ. of Toronto

Re: [PyMOL] Water problem

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

Dear Warren,

Just to tell you the good news,
I have got version 0.80 installed and everything looks just great.
(I have got well-behaved water molecules flowing now)
I have to study the manual better to play with other functions now.

Thanks again for the great program.

Regards,
K.K.Liang

Re: [PyMOL] Water problem

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

Dear Warren,

Thanks for the message and thanks for the pymol program.
It is one of the most interesting programs that I worked with.

I tried to make all of the atoms in the waters HETATM,
and after all of the records of the atoms, I put CONECT
for all of the water molecules.
In the Win version, I could not 'see' a mistake.
But there are so many waters that I am not 100% sure.
However, in the Linux version I installed,
(I am on the process of making the program out of the source myself,
but I am not very sure which make rule I should use.
I am trying Rules.linux-rpm-rh72-py21n right now.)
pymol does not connect any of the water molecules.
All of the oxygen and hydrogen atoms are not connected to anything.

I hope that I can get some breakthrough myself.
Of course I will be glad if you can check my pdb files for me
but I prepared so many different versions and I am not sure
which version should I send you.
I will do that if I still could not get out of it.

Thanks again.

Regards,
K.K.Liang

Re: [PyMOL] Water problem

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

On Sun, 26 May 2002 kk...@ga... wrote:

> Now the problem is, when I tried to load some of the PDB files
> into a movie, pymol will link the water molecules wrongly.

> Some oxygen atoms are linked to more than two hydrogens.
> What's more, I tested the data both on the Windows version
> and the LINUX (redhat) version (both are the latest just downloaded
> and installed last Thursday), there are many more mistakes in
> the LINUX version than in the Windows version,
> although both versions make mistakes.
> I dig out the test data file of water (water.pdb) from the
> package, which uses HETATM instead of ATOM for the atom records,
> and again I tried it on both versions.

That's the right idea - PyMOL doesn't currently use residue dictionaries
for connectivity except for HETATM waters (in latest windows version I
think).  Residue-based connectivity is planned as a option for the
future...

> This time, there is no mistakes in the Windows version,

Good. That means we've made some progress...

> but still there are several mistakes in the LINUX version.

Which is an older version, if you're using the binary (RPM, etc).

> I was wondering whether there is anything we can do
> to prevent pymol from linking the atoms wildly?

If you compile from the CVS source code, you can get PyMOL working under
linux right away with the HETATM water solution.  Otherwise, just wait for
the next linux binary release.

> In my datafile, there are TER records after the protein
> and after each molecule.
> I also tried to add CONNECT records for waters,
> but these do not provent pymol from making extra links.

It should if the waters are HETATMs *and* you provide CONECT records (even
on the older versions).

To be absolutely sure that PyMOL can handle your structures, you might
want to send me (wa...@de...) a tar archive with 5-10
frames of your trajectory...

Cheers,
Warren

[PyMOL] Water problem

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

Dear pymolers,

I have to study the outcome from our MD calculations on
a protein surrounded by about 1700 water molecules.
There are 12000 such PDB files, each for one specific moment of time.

Now the problem is, when I tried to load some of the PDB files
into a movie, pymol will link the water molecules wrongly.
Some oxygen atoms are linked to more than two hydrogens.
What's more, I tested the data both on the Windows version
and the LINUX (redhat) version (both are the latest just downloaded
and installed last Thursday), there are many more mistakes in
the LINUX version than in the Windows version,
although both versions make mistakes.
I dig out the test data file of water (water.pdb) from the
package, which uses HETATM instead of ATOM for the atom records,
and again I tried it on both versions.
This time, there is no mistakes in the Windows version,
but still there are several mistakes in the LINUX version.

I was wondering whether there is anything we can do
to prevent pymol from linking the atoms wildly?

In my datafile, there are TER records after the protein
and after each molecule.
I also tried to add CONNECT records for waters,
but these do not provent pymol from making extra links.

It will be highly appreciated if you have any concrete suggestion.

K.K.Liang

Re: [PyMOL] b-factors?

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

Dear PyMOLers,

Nat Echols <na...@ma...> [2002-05-23 10:25] wrote:
> >=20
> > Can PyMOL do coloring by B-factors?  I didn't see anything=20
> > about this in
> > the manual.  If not, I'll go ahead and write a new function, unless
> > someone else is working on this.
> >=20
* DeLano, Warren <wa...@su...> [2002-05-23 13:45] replied:
> This can only be done over discrete ranges, as follows:
>=20
> color br0,b>5
> color br1,b>10
> color br2,b>15
> color br3,b>20
> color br4,b>25
> color br5,b>30
> color br6,b>35
> color br7,b>40
> color br8,b>45
> color br9,b>50

Or you could do it with the following python script (which I called
color_b.py). Read this file into pymol using "run color_b.py" and then
you can color your selection by doing:

  color_hist_b("prot and not resn HOH")
  color_ramp_b("all")

or

  color_hist_b (prot and not resn HOH)
  color_ramp_b all

The color_hist_b function colours the model in bins of equal ranges of
B-values (so outliers would tend to have a colour all to themselves),=20
while color_ramp_b colours the model in bins of equal numbers
of atoms in each colour, so the model is coloured in a more even
gradation of all the colours.

If you prefer the "rainbow" type of colour ramp (blue, cyan, green,
yellow, orange, red) then one could easily modify this script to use
those colours instead of br0 through br9 and by changing the number of
bins from 10 to 6.  That's the way I originally wrote this, until I
reread what Warren had written above.

###########################################################################=
###
from pymol.cgo import *
from pymol import cmd

def color_hist_b(model):
    """color model (which could be a selection) in bins of equal range of
    B-factor values
    """
    m =3D cmd.get_model(model)
    b_list =3D []

    if len(m.atom) =3D=3D 0:
        print "No atoms selected"

    else:
        for i in range(len(m.atom)):
            b_list.append(m.atom[i].b)

        max_b =3D max(b_list)
        min_b =3D min(b_list)
        bin_width =3D (max_b - min_b)/10.0

        # subtract 1 from the lowest B in order to ensure that the single
        # atom with the lowest B value doesn't get omitted

        sel0 =3D model + " and b > " + str(min_b - 1.0)
        sel1 =3D model + " and b > " + str(min_b + bin_width)
        sel2 =3D model + " and b > " + str(min_b + 2*bin_width)
        sel3 =3D model + " and b > " + str(min_b + 3*bin_width)
        sel4 =3D model + " and b > " + str(min_b + 4*bin_width)
        sel5 =3D model + " and b > " + str(min_b + 5*bin_width)
        sel6 =3D model + " and b > " + str(min_b + 6*bin_width)
        sel7 =3D model + " and b > " + str(min_b + 7*bin_width)
        sel8 =3D model + " and b > " + str(min_b + 8*bin_width)
        sel9 =3D model + " and b > " + str(min_b + 9*bin_width)

        cmd.color("br0",sel0)
        cmd.color("br1",sel1)
        cmd.color("br2",sel2)
        cmd.color("br3",sel3)
        cmd.color("br4",sel4)
        cmd.color("br5",sel5)
        cmd.color("br6",sel6)
        cmd.color("br7",sel7)
        cmd.color("br8",sel8)
        cmd.color("br9",sel9)

def color_ramp_b(model):
    """color model (which could be a selection) in bins of equal numbers of
    B-factor values
    """
    m =3D cmd.get_model(model)
    b_list =3D []

    if len(m.atom) =3D=3D 0:
        print "No atoms selected"

    else:
        for i in range(len(m.atom)):
            b_list.append(m.atom[i].b)

        b_list.sort()
        bin_num =3D int(len(b_list))/10

        # subtract 1 from the lowest B in order to ensure that the single
        # atom with the lowest B value doesn't get omitted
        sel0 =3D model + " and b > " + str(b_list[0] - 1.0)
        sel1 =3D model + " and b > " + str(b_list[bin_num])
        sel2 =3D model + " and b > " + str(b_list[2*bin_num])
        sel3 =3D model + " and b > " + str(b_list[3*bin_num])
        sel4 =3D model + " and b > " + str(b_list[4*bin_num])
        sel5 =3D model + " and b > " + str(b_list[5*bin_num])
        sel6 =3D model + " and b > " + str(b_list[5*bin_num])
        sel7 =3D model + " and b > " + str(b_list[7*bin_num])
        sel8 =3D model + " and b > " + str(b_list[8*bin_num])
        sel9 =3D model + " and b > " + str(b_list[9*bin_num])

        cmd.color("br0",sel0)
        cmd.color("br1",sel1)
        cmd.color("br2",sel2)
        cmd.color("br3",sel3)
        cmd.color("br4",sel4)
        cmd.color("br5",sel5)
        cmd.color("br6",sel6)
        cmd.color("br7",sel7)
        cmd.color("br8",sel8)
        cmd.color("br9",sel9)

# allow calling without parentheses: color_hist_b <selection>
cmd.extend("color_hist_b",color_hist_b)
cmd.extend("color_ramp_b",color_ramp_b)

###########################################################################=
###

Please let me know if you find any bugs!

Cheers,
Robert
--=20
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] glut headache

[Michal K. <mi...@ge...>]

Hi,

I went the hard way and have compiled the pymol distribution myself on
my linux box. I only had to do some small changes to "Rules" file (
wiping out "ext" dependencies basically).

The only problem I have is that I cannot start pymol ;-).

The glut library is definitially the culprit. I give my error message
in the attachment.

I am on a Slackware linux 8.0 with X 4.2.0 (compiled in house), ATI
Radeon 7500 and libglut 3.7 (distribution version).

Pymol is the first program I install that requires glut and I cannot
say much about quality/versioning of that software.

I just would like to ask: what should I do ?

-- 
Michal Kurowski
<mi...@ge...>

[PyMOL] RE: pymol-on-linux questions

[Marc S. <mar...@mp...>]

> - Any idea what the practical difference between a GeForce 3 and
> a Quadro 2 would be?  I have the GeForce right now, using NVidia's
> drivers; I'm planning on yanking the Quadro 2 from a machine we bought as
> a server.  Would I see any actual performance gain?  Which chip is
> actually faster, at least for what I'd be using it for?

As far as I know, the only differences between a GeForce2 and a Quadro 2 
can be:

-Different memory clock, but this depends on the actual board you have. 
Many "high-end" GeForce2-boards have a even higher mem-clock than the 
Quadro-boards if I recall it correctly
-OpenGL-hardware-stereo (at least under Windows)
-Accelerated drawing of antialiased lines (which is by default crippled 
or disabled on the GeForce2). Would make sense if you are looking at 
chicken-wire-electron-density maps or line-drawings of your molecule a 
lot, or if you are using CAD. Otherwise it would not make much sense.

The underlying hardware (i.e. the GPU itself) should be identical except 
for some patched registers which identify one as a GeForce and the other 
as a Quadro (enabling the above-mentioned features).

Performance-differences (at least in the consumer-sector) normaly arise 
from the surrounding stuff, i.e. type of graphics-memory, clockspeeds 
(memspeed beeing more important than GPU-speed, as the GeForce is 
bandwith-limited) etc.

Bottomline: I would not expect a huge performance-improvement.

Hope this helps.

-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

RE: [PyMOL] b-factors?

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

This can only be done over discrete ranges, as follows:

color br0,b>5
color br1,b>10
color br2,b>15
color br3,b>20
color br4,b>25
color br5,b>30
color br6,b>35
color br7,b>40
color br8,b>45
color br9,b>50

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: Nat Echols [mailto:na...@ma...]
> Sent: Thursday, May 23, 2002 10:25 AM
> To: pym...@li...
> Subject: [PyMOL] b-factors?
>=20
>=20
>=20
> Can PyMOL do coloring by B-factors?  I didn't see anything=20
> about this in
> the manual.  If not, I'll go ahead and write a new function, unless
> someone else is working on this.
>=20
> thanks,
> Nat Echols
>=20
>=20
> _______________________________________________________________
>=20
> Don't miss the 2002 Sprint PCS Application Developer's Conference
> August 25-28 in Las Vegas -- http://devcon.sprintpcs.com/adp/index.cfm
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] pymol-on-linux (some answers)

[Tony H. <ton...@ia...>]

I have compiled pymol on linux with icc (Intel's compiler), and it works
wonderfully.  You simply need to make sure that you set 
CC=icc -I<path to Intel's includes>

I also had to make a directory in the pymol directory called
intel_includes to which I needed to copy float.h from Intel's
substitute_headers directory.  Then of course, you need to add
-I<pymol_path>/intell_includes to CC.

I have not attempted to compile the extras pymol needs without gcc.  So,
python and all the rest are compiled with gcc.  Even so, I've noticed a
substantial speed improvement.

As far as the cards go, I don't know which offers better performance. 
I'm currently running on a Quadro 2, at pymol has good performance, but
I don't know about a GeForce 3.

Tony Hill
Iowa State University

[PyMOL] b-factors?

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

Can PyMOL do coloring by B-factors?  I didn't see anything about this in
the manual.  If not, I'll go ahead and write a new function, unless
someone else is working on this.

thanks,
Nat Echols

[PyMOL] pymol-on-linux questions

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

Hi--

I've been pushing PyMOL beyond the limits of my computer(s)- mainly
dealing with trajectories for massive (>50000 atoms) structures.  A couple
of questions relating to performance:

- Has anyone tried compiling PyMOL on Linux with something other than gcc?
Specifically, I'm interested in using Intel's compiler, which we have a
license for.  I don't mind messing with makefiles, but some software seems
to depend on GCC.

- Any idea what the practical difference between a GeForce 3 and
a Quadro 2 would be?  I have the GeForce right now, using NVidia's
drivers; I'm planning on yanking the Quadro 2 from a machine we bought as
a server.  Would I see any actual performance gain?  Which chip is
actually faster, at least for what I'd be using it for?

thanks,
Nat Echols
Gerstein Lab
Yale University

RE: [PyMOL] Babel and File Format Conversion

[Sherwood, P (Paul) <P.S...@dl...>]

All,

In terms of python implementations there is also PyBabel from Scripps. 
On the web site (http://www.scripps.edu/pub/olson-web/share/python/pybabel/)
it says

" The PyBabel package is a Python re-implementation of some of Babel v1.6
functionalities...."

but I don't have any experience of it myself.

Paul

-----Original Message-----
From: Richard Gillilan [mailto:re...@co...]
Sent: 21 May 2002 13:20
To: Bob Havlin
Cc: pym...@li...
Subject: Re: [PyMOL] Babel and File Format Conversion



I've been working with the OpenBabel code for about a
week now and I'm pretty impressed with the internal OOP
design of the code ... though I would have done a 
few things differently (performance and memory consumption
are always on my mind). If it had existed when I began my 
OrderFour project a number of years ago, I would have used it rather 
than independently invent all the molecule data structures and 
substructure searching code. The SMARTS/SMILES
notation is very cool but a bit complex. OpenBabel would
be a fantastic foundation for a molecular builder ... everything
is there, even features needed for fairly advanced forcefield
assignment though I'm not sure yet how much work it would be to
re-implement MMFF94 with those tools. Anyhow, I urge you guys
to take a look. You might be able to interface to the project in
some way or even Pythonize their objects. 

http://openbabel.sourceforge.net


Richard Gillilan
MacCHESS, Cornell

Bob Havlin wrote:
> 
> Great software!  You have done a wonderful job.
> 
> You probably know about this already, but incorporating the file format
> converter
> named babel
> 
> http://www.eyesopen.com/babel.html
> 
> would make PyMol universal for nearly all file formats.
> 
> Just a suggestion to try to help make PyMol even better.
> 
> Bob
>

_______________________________________________________________

Don't miss the 2002 Sprint PCS Application Developer's Conference
August 25-28 in Las Vegas -- http://devcon.sprintpcs.com/adp/index.cfm

_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Babel and File Format Conversion

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

I've been working with the OpenBabel code for about a
week now and I'm pretty impressed with the internal OOP
design of the code ... though I would have done a 
few things differently (performance and memory consumption
are always on my mind). If it had existed when I began my 
OrderFour project a number of years ago, I would have used it rather 
than independently invent all the molecule data structures and 
substructure searching code. The SMARTS/SMILES
notation is very cool but a bit complex. OpenBabel would
be a fantastic foundation for a molecular builder ... everything
is there, even features needed for fairly advanced forcefield
assignment though I'm not sure yet how much work it would be to
re-implement MMFF94 with those tools. Anyhow, I urge you guys
to take a look. You might be able to interface to the project in
some way or even Pythonize their objects. 

http://openbabel.sourceforge.net


Richard Gillilan
MacCHESS, Cornell

Bob Havlin wrote:
> 
> Great software!  You have done a wonderful job.
> 
> You probably know about this already, but incorporating the file format
> converter
> named babel
> 
> http://www.eyesopen.com/babel.html
> 
> would make PyMol universal for nearly all file formats.
> 
> Just a suggestion to try to help make PyMol even better.
> 
> Bob
>

Re: [PyMOL] Babel and File Format Conversion

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

Bob Havlin wrote:
> You probably know about this already, but incorporating the file format
> converter
> named babel
> 
> http://www.eyesopen.com/babel.html
> 
> would make PyMol universal for nearly all file formats.

The development of Babel is being continued in the OpenBabel
project at <http://openbabel.sourceforge.net/>.

-- 
Lieven Buts
Brussels Free University

[PyMOL] Babel and File Format Conversion

[Bob H. <bo...@ra...>]

Great software!  You have done a wonderful job.

You probably know about this already, but incorporating the file format
converter
named babel

http://www.eyesopen.com/babel.html

would make PyMol universal for nearly all file formats.

Just a suggestion to try to help make PyMol even better.

Bob

[PyMOL] RE: Surfacing Heme's (ie. HETATMS)

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

Hi Michel,

   PyMOL doesn't surface HETATM's by default.  A HEME is labeled a =
hetero-group in the PDB and is ignored by the surfacing routine (the =
ignore flag is set for those atoms).  To fix that, you need to clear the =
ignore flag for the HEM atoms:

flag ignore, hem/, clear
rebuild

Alternatively, if you didn't mind surfacing the waters as well, you =
could simply "set surface_mode=3D1" which tells it to surface atoms =
irrespective of the ignore flag.

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: Michel Guertin=20

Dear Dr DeLano: A colleague showed me the possibilities of PyMol and I =
have been really impressed. However, before purchasing a license I have =
a question. I'm working on bacterial hemoglobins that displayed a tunnel =
connecting the surface of the protein to the heme distal site. With this =
colleague we asked PyMol to show the surface of myoglobin (test). I was =
surprised to find out that it showed the heme completely exposed to =
solvent: this is wrong. We looked at the manual, but found nothing about =
how PyMol build surfaces and if its possible to modify parameters.

RE: [PyMOL] Wizard and External GUI documenation

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

No, not yet.  The best thing to do is just study the code for those that =
currently exist.  The wizard functionality is really a stop-gap =
measure...in the future we'll build a more robust user interface.

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: Michael Sorich [mailto:mik...@ho...]
Sent: Thursday, May 09, 2002 12:46 AM
To: pym...@li...
Subject: [PyMOL] Wizard and External GUI documenation


Is there any documentation (or self-explanatory examples) on how to make =
a Wizard and/or External GUI?
=20
Thanks
=20
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
=20


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[PyMOL] Labels

[Wood C. <C.M...@li...>]

FAO: Chris Rife.

Chris,

To get labels on ray-traced images use the method that follows.

*	Before ray-tracing decide what labels you want
*	Hide everything of the current image
*	Select show labels
*	You will need to change the colour of the labels, as they adopt the
same colour as the object - make them some darker colour
*	Save this image as a png file. Thus you will have an image of just
labels
*	Run ray-tracing and save image
*	Import the labels image into Photo-editor (or other). Photo-editor
has a transparency facility. Render the background transparent and save the
new image.
*	Adjust the size of the transparent labels image and the ray traced
image to be exactly the same and overlay them.


This procedure will give you perfect labels. However, if the the image is
made too small, such as in a stereo image, then the default font of Pymol
becomes very small. 

Chris Wood

Biomolecular Research Group John Moores University, Liverpool