pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] PPP : Puzzle Patch Picture

[Aldo T. <ald...@if...>]

I would like to draw the surface of a protein with the contribution of
each residue clearly shown. In other words when two adjacent triangles
are assigned to different residues, those and only those triangles should
be drawn in -say- black.

I have no idea how to do it.
Aldo
-- 

[PyMOL] align/fit

[Enrico M. <em...@ui...>]

Hi all,
I'm using macPyMOL 0.99rc1 and found very useful the commands  
align&pair_fit to do superposition. I'm just wondering which specific  
algorithm they use, if somebody never used them to do superposition  
of Ca trace for publications, and if there is a specific reference to  
them.
Thanks in advance,
Enrico.

--
Enrico Malito
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1116
Chicago, IL 60607 - U.S.A.
Tel (312) 996-6299
Fax (312) 355-4535

[PyMOL] Re: invoking pymol the unix way on os x

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

You can call the executable inside an application and it will work in the 
normal unix way, eg

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL

You might want to make an alias or a function or a symbolic link like

alias pymol=/Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL

or

pymol() { /Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL "$@" ; }

or

ln -s  /Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL 
/usr/local/bin/pymol


more here, on the wiki:

http://www.pymolwiki.org/index.php/Launching_PyMOL#MacOS_X:


HTH,

Bill



> From: "Andrew Wollacott" <sen...@gm...>
> To: pym...@li...
> Subject: [PyMOL] running macpymol in the background from the terminal
>
> ------=_Part_19022_27230051.1140672389773
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> hello,
>
> I'm running MacPyMol 0.99.  I typically open pymol from the terminal (
> terminal.app) using the "open" command.
>
>> open test.pdb
>
> I have .pdb files set to open with MacPyMol, so graphicConverter doesn't
> open when I do this.  The problem I have when doing this is that when
> entering the "pwd" command into pymol, I get the following:
>
> PyMOL> pwd
> /
>
> so pymol thinks it's running from the root directory.  This makes it tough
> for me to load more pdbfiles into pymol using the "load" command as I must
> first "cd" into the directory with pymol.  Just a note, that in version 0.9=
> 8,
> using the "open" command, pymol would recognize what directory it was opene=
> d
> from.
>
> Now, I can use the "pymol test.pdb" to open pdbfiles, but then the terminal
> gets the output from pymol.  I've tried to run pymol in the background so
> that I can continue to use this terminal window while stilll having pymol
> open.  Using "pymol test.pdb &" I still get pymol output to the terminal.  =
> I
> could use "pymol test.pdb >& /dev/null &" but that seems quite a bit more
> verbose compared to "open test.pdb"
>
> I guess I could alias pymol to essentially pipe it's output to /dev/null bu=
> t
> since version 0.98 worked fine, I was wondering if anyone has a workaround
> for this inconvenience.
>
> Thanks.
>
> - Andrew Wollacott

RE: [PyMOL] label positions, centered, left, or right

[Warren D. <wa...@de...>]

Seth,

Yes, via the "label_position" setting which specifies x,y, and z
alignment of labels.

Values in the range [-1,1] imply alignment.  Beyond that, it is a
translation along camera axes in model-space dimensions. =20

# for left alignment 0.75 A in front of atom

set label_position, [-1,0,1.75]

# for right alignment directly on atom

set label_position, [1,0,0]

# for left alignment 1 A to right of atom

set label_position, [2,0,0]

# for center alignment 2 A below atom

set label_position, [0,-3,0]

# centered 3 A in front of atom

set label_position, [0,0,4]

etc.

Cheers,
Waren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Seth Harris
> Sent: Thursday, February 23, 2006 10:45 AM
> To: pym...@li...
> Subject: [PyMOL] label positions, centered, left, or right
>=20
> Hi all,
>=20
> Minor thing, but thought I'd ask...
>=20
> Labels now appear to be centered on whatever atom they are=20
> labeling. Previously, the left-hand side of the label was on=20
> the atom (left-anchored). Is there a way to choose whether=20
> the label is left-anchored, centered, or right-anchored?=20
>=20
> I find that it's hard to offset the label sufficiently with=20
> commands like:
>=20
> label myprot and name ca, "    %s%s" % (resn,resi)
>=20
> which used to get the label to float nicely just to the right=20
> of the atom.=20
> Now that the label is centered the spaces don't help push the=20
> labels over as much as they used to, and the obvious route of=20
> adding twice as many spaces somehow isn't getting me there. I=20
> thought there might be an anchor, align, or justification=20
> flag on the labels.=20
>=20
> I did also notice that in editing mode you can drag the=20
> labels to whatever position you wanted in recent betas.  Very nice!
>=20
> Cheers,
> Seth
>=20
>=20

[PyMOL] label positions, centered, left, or right

[Seth H. <se...@gm...>]

Hi all,

Minor thing, but thought I'd ask...

Labels now appear to be centered on whatever atom they are labeling.
Previously, the left-hand side of the label was on the atom (left-anchored)=
.
Is there a way to choose whether the label is left-anchored, centered, or
right-anchored?

I find that it's hard to offset the label sufficiently with commands like:

label myprot and name ca, "    %s%s" % (resn,resi)

which used to get the label to float nicely just to the right of the atom.
Now that the label is centered the spaces don't help push the labels over a=
s
much as they used to, and the obvious route of adding twice as many spaces
somehow isn't getting me there. I thought there might be an anchor, align,
or justification flag on the labels.

I did also notice that in editing mode you can drag the labels to whatever
position you wanted in recent betas.  Very nice!

Cheers,
Seth

[PyMOL] running macpymol in the background from the terminal

[Andrew W. <sen...@gm...>]

hello,

I'm running MacPyMol 0.99.  I typically open pymol from the terminal (
terminal.app) using the "open" command.

> open test.pdb

I have .pdb files set to open with MacPyMol, so graphicConverter doesn't
open when I do this.  The problem I have when doing this is that when
entering the "pwd" command into pymol, I get the following:

PyMOL> pwd
/

so pymol thinks it's running from the root directory.  This makes it tough
for me to load more pdbfiles into pymol using the "load" command as I must
first "cd" into the directory with pymol.  Just a note, that in version 0.9=
8,
using the "open" command, pymol would recognize what directory it was opene=
d
from.

Now, I can use the "pymol test.pdb" to open pdbfiles, but then the terminal
gets the output from pymol.  I've tried to run pymol in the background so
that I can continue to use this terminal window while stilll having pymol
open.  Using "pymol test.pdb &" I still get pymol output to the terminal.  =
I
could use "pymol test.pdb >& /dev/null &" but that seems quite a bit more
verbose compared to "open test.pdb"

I guess I could alias pymol to essentially pipe it's output to /dev/null bu=
t
since version 0.98 worked fine, I was wondering if anyone has a workaround
for this inconvenience.

Thanks.

- Andrew Wollacott

RE: [PyMOL] animate angle bending

[Warren D. <wa...@de...>]

Here's an example script that scratch-builds such an animation.  Note
that the "rotate" command seems broken in terms of the selections it
currently accepts -- selection macros don't currently work, so you'll
need to write them out long-hand as I have done below.

# create a 4 state molecule

fragment asp,mov
fragment asp,mov
fragment asp,mov
fragment asp,mov

# orient the camera parallel to the plane of motion

reset
turn x,-50
orient mov////CG+OD1+OD2

# get coordinates of the CG atom

crd =3D [0,0,0]

iterate_state 1,mov////CG, crd[0:3]=3D(x,y,z)

# now rotate atoms in states 2-4

frame 2
cmd.rotate("z",-4,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 4,"mov and name OD2",origin=3Dcrd)

frame 3
cmd.rotate("z",-8,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 8,"mov and name OD2",origin=3Dcrd)

frame 4
cmd.rotate("z",-4,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 4,"mov and name OD2",origin=3Dcrd)

as sticks
set sphere_quality,2
set stick_radius, 0.1
show spheres
set sphere_scale, 0.25
mplay

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Sven Lammers
> Sent: Wednesday, February 22, 2006 5:05 AM
> To: pym...@li...
> Subject: [PyMOL] animate angle bending
>=20
> Dear pymol users,
>=20
> I'm struggling to figure out how to create an animation of an=20
> angle bending vibration with pymol, like this one=20
> http://www.ch.embnet.org/MD_tutorial/Images/Part2/a.gif
> My question is how do I correctly set the origin and axis so=20
> that I could use the rotate command to rotate one bond with=20
> respect to the other.
>=20
> Thanks a lot in advance and best regards, Sven
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
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>=20
>=20
>=20
>=20

RE: [PyMOL] load_png doesn't support alpha (transparency)?

[Warren D. <wa...@de...>]

Peter,

PyMOL does read the alpha, but it doesn't support compositition with the
software at present, so there is no practical use for this capability.

set show_alpha_checker
load transparent.png

Will demonstrate that the alpha is read by adding a checker pattern to
the background.  It sounds, you'd like it superimposed over the existing
scene for purposes of alignment. =20

Thanks for the suggestion!

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Peter Adrian Meyer
> Sent: Wednesday, February 22, 2006 7:43 AM
> To: pym...@li...
> Subject: [PyMOL] load_png doesn't support alpha (transparency)?
>=20
> Hi all,
>=20
> I noticed today that when reading a png file using load_png,=20
> the alpha channel does not appear to be respected (regions of=20
> the png that should be transparent are not transparent but=20
> show up as white).
>=20
> Does anyone know if this by design, a bug, or something I'm=20
> doing incorrectly setting my alpha channel in the png file?
>=20
> If you're wondering why I'm trying to do this; I'm attempting=20
> to generate two aligned figures from models that are in=20
> crystallographic origins.  The end goal is to have maps in=20
> each of these figures also aligned for comparison, so I can't=20
> just transform the models to get them aligned (use of the=20
> align command is out for similar reasons; unless there's a=20
> way to get the transformation matrix generated by model=20
> alignment and apply it to a map that I'm not aware of).
>=20
> Thanks,
>=20
> Pete
>=20
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>=20
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
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>=20
>=20
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RE: [PyMOL] (kein Betreff)

[Warren D. <wa...@de...>]

Marc,

Not exactly, but you can get pretty close with something like this:

load protA.pdb
load protB.pdb

select siteA_res, byres (((protA & donors) within 3.45 of (protB &
acceptors)) or ((protA & acceptors) within 3.45 of (protB & donors)))

select siteB_res, byres (((protB & donors) within 3.45 of (protA &
acceptors)) or ((protB & acceptors) within 3.45 of (protA & donors)))

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Marc Bruning
> Sent: Wednesday, February 22, 2006 5:05 AM
> To: pym...@li...
> Subject: Re: [PyMOL] (kein Betreff)
>=20
> hello,
>=20
> is there a way to only select residues that are involved in=20
> polar contacts?
> thanks,
>=20
> marc
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
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>=20
>=20
>=20
>=20

[PyMOL] load_png doesn't support alpha (transparency)?

[Peter A. M. <pa...@co...>]

Hi all,

I noticed today that when reading a png file using load_png, the alpha
channel does not appear to be respected (regions of the png that should be
transparent are not transparent but show up as white).

Does anyone know if this by design, a bug, or something I'm doing
incorrectly setting my alpha channel in the png file?

If you're wondering why I'm trying to do this; I'm attempting to generate
two aligned figures from models that are in crystallographic origins.  The
end goal is to have maps in each of these figures also aligned for
comparison, so I can't just transform the models to get them aligned (use
of the align command is out for similar reasons; unless there's a way to
get the transformation matrix generated by model alignment and apply it to
a map that I'm not aware of).

Thanks,

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] animate angle bending

[Sven L. <sve...@un...>]

Dear pymol users,

I'm struggling to figure out how to create an animation of an angle 
bending vibration
with pymol, like this one 
http://www.ch.embnet.org/MD_tutorial/Images/Part2/a.gif
My question is how do I correctly set the origin and axis so that I 
could use the rotate command
to rotate one bond with respect to the other.

Thanks a lot in advance and best regards,
Sven

Re: [PyMOL] (kein Betreff)

[Marc B. <br...@mp...>]

hello,

is there a way to only select residues that are involved in polar contacts?
thanks,

marc

[PyMOL] (kein Betreff)

[Milan G. <mil...@gm...>]

RE: [PyMOL] Multiple origins possible?

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

I was going to suggest the same thing.

FWIW, I have a version that you can run from your .pymolrc on my webpage=20
here:

http://www-personal.umich.edu/~mlerner/PyMOL/mg_pymol_utils.py

-michael

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

On Mon, 20 Feb 2006, Gr=E9gori Gerebtzoff wrote:

> Hi Jon,
>
> I don't know if this is possible, but Warren posted some weeks ago two
> scripts you can run on two PyMOL sessions, in order to synchronize the vi=
ew
> on both visualization windows.
> Have a look at these two links:
> http://sourceforge.net/mailarchive/message.php?msg_id=3D14392630
> and
> http://sourceforge.net/mailarchive/message.php?msg_id=3D14394927
>
> It might do the trick for you.
>
> Cheers,
>
> Greg
>
>
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Jon Manning
> Sent: vendredi, 17. f=E9vrier 2006 19:59
> To: pym...@li...
> Subject: [PyMOL] Multiple origins possible?
>
> Hi all,
>
> I'm new new to PyMol, but have a question so would appreciate any
> pointers people have. I currently read in a molecule to pymol, 'copy'
> it, and color the two copies at different positions. I set a single
> origin, being the centre of gravity of the combined molecules. Ideally,
> I'd like to be able to set two origins, and have the molecules rotate
> synchronously side-by-side rather than as one object, so I can compare
> more easily. Is this possible with PyMol?
>
> Thanks,
>
> Jon
>
> --=20
>
> Smart Bomb: "Cogito Ergo Boom."
>
>
> ###########
>
> Jonathan Manning
> PhD Student
> Barton Group
> School of Life Sciences
> University of Dundee
> Scotland, UK
> Tel +44 1382 388707
>
>
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log fi=
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>
>
>

Re: [PyMOL] ball-and-sticks, controlling bond color

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

set stick_color, grey

the image looks a little more like

set stick_color, grey90

but I can't quite tell.

-michael

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

On Wed, 15 Feb 2006, Mat...@im... wrote:

> pym...@li... wrote on 02/15/2006 05:36:51 PM:
>
>> Hi all,
>>
>> There is a beautiful ball-and-stick image on pymol-wiki that I am
>> trying to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick).
>>
>> The wiki image has grey bonds and light blue balls for carbon, dark
>> blue for nitrogen, and red balls for oxygen.  My problem is that all
>> my bonds and balls are the same color, and I can't figure out how to
>> make the bonds a grey color, distinct from the atom ball colors.
>> And I'm trying to script this.
>>
>
>
>
> Hi Marilyn -
>
> You probably can't do it all with one object.  Create another object which
> is a duplicate of the one you're working with, then show spheres on object
> #1 and sticks on object #2.  You can then color the balls and the sticks
> separately, since each object gets its own set of colors.
>
> For example:
>
> PyMOL>create obj1, 1FLT and chain w
> Selector: found 797 atoms.
> Executive: object "obj1" created.
> PyMOL>create obj2, 1FLT and chain w
> Selector: found 797 atoms.
> Executive: object "obj2" created.
> PyMOL>color gray, obj2
> Executive: Colored 797 atoms and 1 object.
> PyMOL>color green, obj1
> Executive: Colored 797 atoms and 1 object.
> PyMOL>show spheres, obj1
> PyMOL>show sticks, obj2
> PyMOL>set stick_radius, 0.1
> Setting: stick_radius set to 0.10000.
> PyMOL>set sphere_scale, 0.25
> Setting: sphere_scale set to 0.25000.
>
>
> This gives a ball-and-stick of one chain where the balls are all green and
> the sticks are all gray.  Modify as needed....
>
> - Matt
>
>
> --
> Matthew Franklin                     phone:(917)606-4116
> Senior Scientist, ImClone Systems      fax:(212)645-2054
> 180 Varick Street, 6th floor
> New York, NY 10014
>
>
>
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>

Re: [PyMOL] Multiple origins possible?

[Tsjerk W. <ts...@gm...>]

Hi Jon,

It is also possible to use the origin command to set the origin to a
specified position or to use a selection for determining the origin (origin
selection). In that way you can get what you want by setting the origin for
each molecule before doing a rotation.

Cheers,

Tsjerk

On 2/20/06, Gr=E9gori Gerebtzoff <gre...@un...> wrote:
>
> Hi Jon,
>
> I don't know if this is possible, but Warren posted some weeks ago two
> scripts you can run on two PyMOL sessions, in order to synchronize the
> view
> on both visualization windows.
> Have a look at these two links:
> http://sourceforge.net/mailarchive/message.php?msg_id=3D14392630
> and
> http://sourceforge.net/mailarchive/message.php?msg_id=3D14394927
>
> It might do the trick for you.
>
> Cheers,
>
> Greg
>
>
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Jon Manning
> Sent: vendredi, 17. f=E9vrier 2006 19:59
> To: pym...@li...
> Subject: [PyMOL] Multiple origins possible?
>
> Hi all,
>
> I'm new new to PyMol, but have a question so would appreciate any
> pointers people have. I currently read in a molecule to pymol, 'copy'
> it, and color the two copies at different positions. I set a single
> origin, being the centre of gravity of the combined molecules. Ideally,
> I'd like to be able to set two origins, and have the molecules rotate
> synchronously side-by-side rather than as one object, so I can compare
> more easily. Is this possible with PyMol?
>
> Thanks,
>
> Jon
>
> --
>
> Smart Bomb: "Cogito Ergo Boom."
>
>
> ###########
>
> Jonathan Manning
> PhD Student
> Barton Group
> School of Life Sciences
> University of Dundee
> Scotland, UK
> Tel +44 1382 388707
>
>
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
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>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

RE: [PyMOL] Multiple origins possible?

[<gre...@un...>]

Hi Jon,

I don't know if this is possible, but Warren posted some weeks ago two
scripts you can run on two PyMOL sessions, in order to synchronize the =
view
on both visualization windows.
Have a look at these two links:
http://sourceforge.net/mailarchive/message.php?msg_id=3D14392630
and
http://sourceforge.net/mailarchive/message.php?msg_id=3D14394927

It might do the trick for you.

Cheers,

Greg


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Jon =
Manning
Sent: vendredi, 17. f=E9vrier 2006 19:59
To: pym...@li...
Subject: [PyMOL] Multiple origins possible?

Hi all,

I'm new new to PyMol, but have a question so would appreciate any=20
pointers people have. I currently read in a molecule to pymol, 'copy'=20
it, and color the two copies at different positions. I set a single=20
origin, being the centre of gravity of the combined molecules. Ideally,=20
I'd like to be able to set two origins, and have the molecules rotate=20
synchronously side-by-side rather than as one object, so I can compare=20
more easily. Is this possible with PyMol?

Thanks,

Jon

--=20

Smart Bomb: "Cogito Ergo Boom."


###########

Jonathan Manning
PhD Student
Barton Group
School of Life Sciences
University of Dundee
Scotland, UK
Tel +44 1382 388707

[PyMOL] 3D visualization on mac

[Wataru K. <wk...@jo...>]

Hi all,

I would like to provide feedback on 3D visualization on mac.  Both  
MacPyMOL and O is working nicely with the following combination:

	PowerMac G5 Quad with NVIDIA Quadro FX 4500 graphic card
	StereoGraphics E2 emitter and glasses
	Sony Multiscan CPD-G520 21" CRT monitor

The CRT monitor is set at 1344 x 1008 resolution and 120 Hz refresh  
rate.

I hope this is useful information to those considering mac.

Wataru Kagawa

#########################################

Wataru Kagawa, Ph. D.
Postdoctoral Researcher
Protein Research Group
RIKEN (Physical and Chemical Research Institute)

W221, West Research Bldg.
1-7-22 Suehiro-cho, Tsurumi-ku
Yokohama, Japan 230-0045

tel.    045-503-9206
fax.    045-503-9201

#########################################

[PyMOL] Re: electrostatic potential of nucleic acids possible in pyMOL?

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

Yes.  In fact I just added a description of how to do this in the PyMol
Wiki.

http://www.pymolwiki.org/index.php/APBS

The apbs plugin will work , but you should use pdb2pqr to generate the
nucleic acid pqr file externally, and then read it in.

Then it works the same as for proteins.

HTH,

Bill

>
> Hi,
> is there a possibility to calculate and display surface charge =
> distributions of RNA molecules in pyMOL? At present I only see an option =
> to do this for proteins. Or is there some kind of plugin that provides =
> such a function?
>
> All the best,
> Michael.
>

[PyMOL] Multiple origins possible?

[Jon M. <jr...@co...>]

Hi all,

I'm new new to PyMol, but have a question so would appreciate any 
pointers people have. I currently read in a molecule to pymol, 'copy' 
it, and color the two copies at different positions. I set a single 
origin, being the centre of gravity of the combined molecules. Ideally, 
I'd like to be able to set two origins, and have the molecules rotate 
synchronously side-by-side rather than as one object, so I can compare 
more easily. Is this possible with PyMol?

Thanks,

Jon

-- 

Smart Bomb: "Cogito Ergo Boom."


###########

Jonathan Manning
PhD Student
Barton Group
School of Life Sciences
University of Dundee
Scotland, UK
Tel +44 1382 388707

[PyMOL] surface display of electrostatic potential of nucleic acids possible in pyMOL?

[Michael W. <we...@st...>]

Hi,
is there a possibility to calculate and display surface charge =
distributions of RNA molecules in pyMOL? At present I only see an option =
to do this for proteins. Or is there some kind of plugin that provides =
such a function?

All the best,
Michael.

- - - - - - - - - -
Michael H.W. Weber
Chairman & Scientific Advisor of Rechenkraft.net e.V.

Rechenkraft.net e.V. - Verein zur F=F6rderung von Bildung, Forschung und =
Wissenschaft durch Einsatz vernetzter Computer
Am Richtsberg 88/208
D-35039 Marburg
Germany

email: in...@re...
http://www.rechenkraft.net - Germany's largest distributed computing =
community. We make those things possible that supercomputers don't.

- - - - - - - - - -
Proteins are nanomachines or nanomachine building blocks.
Examples: The ribosome and RNA polymerase holoenzyme.

RE: [PyMOL] thick c-alpha trace?

[<gre...@un...>]

Try the

set ribbon_width, 4.0=20

command=85

=20

Cherrs,


Greg

=20

=20

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Jose
Borreguero
Sent: jeudi, 16. f=E9vrier 2006 15:47
To: pymol mailing list
Subject: [PyMOL] thick c-alpha trace?

=20

I have a pdb with only CA entries. I did "set ribbon_trace,1" and "show
ribbon" to see the c-alpha trace, but is there a way to control the
thickness of the lines connecting the CA's ?

jose

RE: [PyMOL] movie of diffusion of atoms/molecules

[Warren D. <wa...@de...>]

Satya,

Hmm...for maximum performance, I'd recommend creating a fake PDB file
with a single HETATM entry for each protein/sphere. =20

You'll get much better load performance than with CGOs, you can stick a
radius value in the B or Q column if you need it, you can defer builds
(set defer_builds_mode,1) or if you have a nice graphics card you can
use "sphere_mode,5" for pixel-perfect spheres.

Cheers,
Warren

PS. No there isn't a CGO callback...just for PyOpenGL.

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Satya Arjunan
> Sent: Thursday, February 16, 2006 6:11 PM
> To: EPF (Esben Peter Friis); pym...@li...
> Subject: Re: [PyMOL] movie of diffusion of atoms/molecules
>=20
> Hi Esben and List,
>=20
> Thank you for your answering my questions. I realize now that=20
> it would be better to just represent a molecule as a sphere=20
> with diameter corresponding to the protein's diameter because=20
> like you said, with 4000 molecules, I don't need atomistic detail.
>=20
> Here is my situation: I now have a file with 100 frames, each=20
> frame has the 3D coordinates of 4000 spheres obtained from my=20
> simulator. Right now I have found a way to load the=20
> coordinates as cgo objects for each frame as shown in the=20
> script below. The problem is that Pymol needs to load all the=20
> frames before it can start playing the movie, which requires=20
> a lot of memory when considering 4000 spheres * 100 frames.=20
> Is there any callback function that is called when Pymol=20
> wants to move to the next frame? With such a function, I can=20
> clear the previous frames in the memory using cmd.delete and=20
> load a new frame from the file.
>=20
> I appreciate if there is any other solution for the above=20
> problem. Thanks!
>=20
> satya
>=20
>=20
>=20
>=20
> import string
> import random
> from pymol.cgo import *
> from pymol import cmd
>=20
> axes =3D [
>         LINEWIDTH, 3.0,
>         BEGIN, LINES,
>         COLOR, 0.2, 1.0, 0.2,
>=20
>         VERTEX, 0.0, 0.0, 0.0,
>         VERTEX, 100.0, 0.0, 0.0,
>=20
>         COLOR, 1.0, 0.2, 0.2,
>         VERTEX, 0.0, 0.0, 0.0,
>         VERTEX, 0.0, 100.0, 0.0,
>       =20
>         COLOR, 0.2, 0.2, 1.0, =20
>         VERTEX, 0.0, 0.0, 0.0,
>         VERTEX, 00, 0.0, 100.0,
>         END
>         ]
>=20
>=20
>=20
> c=3D0
> for a in xrange(0,100):
>     balls =3D []
>     for i in xrange(0,40):
>         balls.extend([COLOR,
>                       random.randrange(0,10,1)/10.0,
>                       random.randrange(0,10,1)/10.0,
>                       random.randrange(0,10,1)/10.0,
>                       SPHERE,
>                       random.randint(0,100),
>                       random.randint(0,100),
>                       random.randint(0,100),
>                       1,])
>     obj =3D axes + balls
>     cmd.load_cgo(obj,'cgo01',c)
>     c =3D c + 1
>=20
> pdb_list =3D [
>             "HETATM    1  X   UNK     1    %8.3f%8.3f%8.3f  1.00=20
> 10.00\n"%(3.2,0,0),
>             "HETATM    2  Y   UNK     2    %8.3f%8.3f%8.3f  1.00=20
> 10.00\n"%(0,3.2,0),
>             "HETATM    3  Z   UNK     3    %8.3f%8.3f%8.3f  1.00=20
> 10.00\n"%(0,0,3.2),
>             ]
> cmd.read_pdbstr(string.join(pdb_list,''),'lab2')
> cmd.hide('(lab2)')
> cmd.label('lab2','name')
> cmd.color('white','lab2')
> cmd.zoom('cgo01')
> cmd.clip('far',-5)
>=20
> >
> > Hi Satya
> >
> > You can use the command "translate" to move the individual=20
> objects in=20
> > pymol. Is takes a list of 3 floating points numbers as the=20
> > translational vector.
> >
> > I don't know how Pymol would handle 4000 objects, but an=20
> alternative=20
> > might be to load them as states within one object, and then use the=20
> > "show all states" command from the "Movie" menu. The "translate"
> > command can also move the individual states independently. (If you=20
> > also need to rotate the molecules, it gets more difficult :-)
> >
> > Another suggestion: If you have 4000 proteins, you may not=20
> need a very=20
> > high level of detail for each molecule. You could save a lot by=20
> > loading only the alpha carbon atoms and then increase their=20
> vdw-size=20
> > to make them "stick" together:
> >
> > pymol> alter my_object, vdw=3D3.0
> > pymol> show spheres, my_object
> > pymol> sort
> >
> >
> > Cheers,
> >
> > Esben
> >
> >
> > -----Original Message-----
> > From: pym...@li... on behalf of Satya=20
> > Arjunan
> > Sent: Sat 2006-02-11 03:56
> > To: pym...@li...
> > Subject: [PyMOL] movie of diffusion of atoms/molecules
> >
> > Hi all,
> >
> > I would like to use Pymol to visualize 3D simulation of=20
> lattice-based=20
> > diffusion of molecules. The simulator provides the 3D=20
> coordinates (or=20
> > the translational direction since they have fixed diffusion=20
> distance)=20
> > of the molecules at everytime step. At the end of the simulation, I=20
> > would like to feed the coordinates (or the translational=20
> direction) to=20
> > Pymol using a python script and make a movie of this.
> >
> > What is a good way of implementing this with Pymol with lowest=20
> > computational cost because there are about 4000 protein molecules=20
> > altogether? I have come across a sample script at=20
> > http://www.rubor.de/bioinf/tips_python.html#chempy which I=20
> think I can=20
> > use to place the atoms/molecules in pymol. I am wondering=20
> if there is=20
> > any other cost effective way of implementing this? Is it=20
> possible just=20
> > to provide the translational angle and distance for certain=20
> molecules=20
> > already in the model?
> >
> > Thanks in advance.
> > satya
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log=20
> > files for problems?  Stop!  Download the new AJAX search=20
> engine that=20
> > makes searching your log files as easy as surfing the  web.=20
>  DOWNLOAD=20
> > SPLUNK!
> >=20
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=3D=
1216
> > 42=20
> >=20
> =
<http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=3D=
121
> > 642> _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] movie of diffusion of atoms/molecules

[Satya A. <sa...@sf...>]

Hi Esben and List,

Thank you for your answering my questions. I realize now that it would 
be better to just represent a molecule as a sphere with diameter 
corresponding to the protein's diameter because like you said, with 4000 
molecules, I don't need atomistic detail.

Here is my situation: I now have a file with 100 frames, each frame has 
the 3D coordinates of 4000 spheres obtained from my simulator. Right now 
I have found a way to load the coordinates as cgo objects for each frame 
as shown in the script below. The problem is that Pymol needs to load 
all the frames before it can start playing the movie, which requires a 
lot of memory when considering 4000 spheres * 100 frames. Is there any 
callback function that is called when Pymol wants to move to the next 
frame? With such a function, I can clear the previous frames in the 
memory using cmd.delete and load a new frame from the file.

I appreciate if there is any other solution for the above problem. Thanks!

satya




import string
import random
from pymol.cgo import *
from pymol import cmd

axes = [
        LINEWIDTH, 3.0,
        BEGIN, LINES,
        COLOR, 0.2, 1.0, 0.2,

        VERTEX, 0.0, 0.0, 0.0,
        VERTEX, 100.0, 0.0, 0.0,

        COLOR, 1.0, 0.2, 0.2,
        VERTEX, 0.0, 0.0, 0.0,
        VERTEX, 0.0, 100.0, 0.0,
       
        COLOR, 0.2, 0.2, 1.0,  
        VERTEX, 0.0, 0.0, 0.0,
        VERTEX, 00, 0.0, 100.0,
        END
        ]



c=0
for a in xrange(0,100):
    balls = []
    for i in xrange(0,40):
        balls.extend([COLOR,
                      random.randrange(0,10,1)/10.0,
                      random.randrange(0,10,1)/10.0,
                      random.randrange(0,10,1)/10.0,
                      SPHERE,
                      random.randint(0,100),
                      random.randint(0,100),
                      random.randint(0,100),
                      1,])
    obj = axes + balls
    cmd.load_cgo(obj,'cgo01',c)
    c = c + 1

pdb_list = [
            "HETATM    1  X   UNK     1    %8.3f%8.3f%8.3f  1.00 
10.00\n"%(3.2,0,0),
            "HETATM    2  Y   UNK     2    %8.3f%8.3f%8.3f  1.00 
10.00\n"%(0,3.2,0),
            "HETATM    3  Z   UNK     3    %8.3f%8.3f%8.3f  1.00 
10.00\n"%(0,0,3.2),
            ]
cmd.read_pdbstr(string.join(pdb_list,''),'lab2')
cmd.hide('(lab2)')
cmd.label('lab2','name')
cmd.color('white','lab2')
cmd.zoom('cgo01')
cmd.clip('far',-5)

>
> Hi Satya
>
> You can use the command "translate" to move the individual objects in 
> pymol. Is takes a list of 3 floating points numbers as the 
> translational vector.
>
> I don't know how Pymol would handle 4000 objects, but an alternative 
> might be to load them as states within one object, and then use the 
> "show all states" command from the "Movie" menu. The "translate" 
> command can also move the individual states independently. (If you 
> also need to rotate the molecules, it gets more difficult :-)
>
> Another suggestion: If you have 4000 proteins, you may not need a very 
> high level of detail for each molecule. You could save a lot by 
> loading only the alpha carbon atoms and then increase their vdw-size 
> to make them "stick" together:
>
> pymol> alter my_object, vdw=3.0
> pymol> show spheres, my_object
> pymol> sort
>
>
> Cheers,
>
> Esben
>
>
> -----Original Message-----
> From: pym...@li... on behalf of Satya Arjunan
> Sent: Sat 2006-02-11 03:56
> To: pym...@li...
> Subject: [PyMOL] movie of diffusion of atoms/molecules
>
> Hi all,
>
> I would like to use Pymol to visualize 3D simulation of lattice-based
> diffusion of molecules. The simulator provides the 3D coordinates (or
> the translational direction since they have fixed diffusion distance) of
> the molecules at everytime step. At the end of the simulation, I would
> like to feed the coordinates (or the translational direction) to Pymol
> using a python script and make a movie of this.
>
> What is a good way of implementing this with Pymol with lowest
> computational cost because there are about 4000 protein molecules
> altogether? I have come across a sample script at
> http://www.rubor.de/bioinf/tips_python.html#chempy which I think I can
> use to place the atoms/molecules in pymol. I am wondering if there is
> any other cost effective way of implementing this? Is it possible just
> to provide the translational angle and distance for certain molecules
> already in the model?
>
> Thanks in advance.
> satya
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log 
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 
> <http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Re: [PyMOL] fofc map

[Sabuj P. <sab...@va...>]

try changing the name of the map to fofc.ccp4

load fofc.ccp4, fofc
isomesh fo1,fofc,3.0,(chain D),buffer=2.0,carve=2.8

S. Shanmuga Sundara Raj wrote:
> Hi,
> 
> I tried to show the fofc map by using the following lines:
> 
> load fofc.map, fofc
> isomesh fo1, fofc,3.0, (chain D), buffer=2.0
> 
> but it gives the error as, Isomesh: map or brick object "fofc" not found.
> 
> i would like to show at different  contour  levels.
> 
> Thanks in advance
> Raj
> 
> ------------------------------------------------------------------------
> 
> What are the most popular cars? Find out at Yahoo! Autos
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