pymol-users Mailing List for PyMOL Molecular Graphics System

Is it possible to make a 2D image in pymol that can be used with 3D
glasses, the kind you used to get with really bad movies? Or is there a
way to do this with standard images generated in pymol? I'd like to add
these kinds of images to a poster so that people normally uninterested
in structural biology will at least show a superficial interest - "look
at the pretty pictures!"


-- 
James Knight <kni...@gm...>

Shivesh,

try
show ribbon,
set ribbon_sampling, 10

-bob

Dear all,
  How can I get the thread like structure of the protein molecule as for superimposition,ribbon doesn't look good.Thread is smooth and looks beautiful.thanx 
  Shivesh


shivesh
 
---------------------------------
We have the perfect Group for you. Check out the handy changes to Yahoo! Groups.

> Don't pay too much attention to the menus.  They're really 
> just there so traditional Mac and Windows users [won't] get scared 
> when they start using PyMOL.  You will find that the command 
> line does everything quicker and easier.

That is not quite as true as it once was. 

While it absolutely correct that command scripts are the most effective way
of controlling PyMOL, the menus, when combined with the sequence viewer,
selection modification actions, and wizards, can be pretty powerful too.  

Cheers,

DeLano Scientific LLC
Email Support Services 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of an...@bi...
> Sent: Saturday, October 28, 2006 8:01 AM
> To: 'shivesh kumar'; pym...@li...
> Subject: Re: [PyMOL] color in pymol
> 
> Hey Shivesh,
> 
> you can get more color in your cartoons by coloring every 
> residue differently.
> 
> color red, i. 20
> color blue, i. 21
> color yellow, i. 22
> 
> Don't pay too much attention to the menus.  They're really 
> just there so traditional Mac and Windows users to get scared 
> when they start using PyMOL.  You will find that the command 
> line does everything quicker and easier.
> 
> 
> Andreas
> 
> 
> >> -----Original Message-----
> >> From: pym...@li...
> >> [mailto:pym...@li...] On Behalf Of 
> >> shivesh kumar
> >> Sent: Saturday, October 28, 2006 4:33 AM
> >> To: PyM...@li...
> >> Subject: [PyMOL] color in pymol
> >>
> >> Dear all,
> >> How can I use the color option in the Setting menu(Edit 
> all) to get 
> >> more color in the cartoon.Thanx.
> >> Shivesh
> >>
> >> shivesh
> >>
> 
> 
> 
> --------------------------------------------------------------
> -----------
> Using Tomcat but need to do more? Need to support web 
> services, security?
> Get stuff done quickly with pre-integrated technology to make 
> your job easier Download IBM WebSphere Application Server 
> v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&
dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

When the "-p" option is used, PyMOL creates a dedicated thread for reading
commands on standard input.  This thread uses the normal blocking IO calls
to read each line of input and then hands it off to the main thread via
'cmd.do(..)'.   Unless the "-K" is also used, that thread will message the
main thread to terminate via 'cmd.quit()' when standard input is closed.

For the actual code, see 'stdin_reader' in modules/pymol/parser.py.

Cheers,

DeLano Scientific LLC
Email Support Services 

> -----Original Message-----
> From: edw...@gm... 
> [mailto:edw...@gm...] On Behalf Of Edward d'Auvergne
> Sent: Sunday, October 29, 2006 10:26 PM
> To: DeLano Scientific
> Cc: pym...@li...
> Subject: Re: [PyMOL] Persistent PyMOL pipes? Preventing a 
> call to 'cmd.quit()'.
> 
> Thank you.  That option kept the PyMOL pipe alive.  As the 
> option is stored in the structure 
> 'options.keep_thread_alive', would this '-K'
> option cause a different behaviour of the program or is the 
> program simply run as a parent thread and this option keeps 
> the parent alive?
> 
> Cheers,
> 
> Edward
> 
> 
> On 10/30/06, DeLano Scientific <de...@de...> wrote:
> > Edward,
> >
> > Add a "K" keepalive option along with the -p:
> >
> > pymol -pK
> >
> > Cheers,
> >
> > DeLano Scientific LLC
> > Email Support Services
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On Behalf Of 
> > > Edward d'Auvergne
> > > Sent: Sunday, October 29, 2006 9:01 PM
> > > To: pym...@li...
> > > Subject: [PyMOL] Persistent PyMOL pipes? Preventing a call to 
> > > 'cmd.quit()'.
> > >
> > > Hi,
> > >
> > > I am the project administrator for the open source program relax 
> > > (http://nmr-relax.com or
> > > https://gna.org/projects/relax) and am interested in interfacing 
> > > relax with PyMOL.  relax is a program for studying the 
> dynamics of 
> > > proteins, RNA, or other organic molecules through the analysis of 
> > > NMR relaxation data and I would like to display the 
> dynamics results 
> > > superimposed onto molecular structures within PyMOL.  I have 
> > > attempted to open a PyMOL pipe using the '-p'
> > > flag however, when relax finishes and closes the pipe, PyMOL 
> > > terminates printing the message:
> > >
> > >   PyMOL: normal program termination.
> > >
> > > Is there a simple way to keep the PyMOL binary running after a 
> > > script terminates?  I've searched through the sources but 
> a solution 
> > > isn't immediately obvious.  I've tracked back from the file 
> > > 'layer5/main.c'
> > > where the 'printf()' statement is located back to the function 
> > > 'CmdQuit' in the file 'layer4/Cmd.c', but can't find what 
> is calling 
> > > the 'cmd.quit()' method.
> > >
> > > Thanks,
> > >
> > > Edward
> > >
> > > --------------------------------------------------------------
> > > -----------
> > > Using Tomcat but need to do more? Need to support web services, 
> > > security?
> > > Get stuff done quickly with pre-integrated technology to 
> make your 
> > > job easier Download IBM WebSphere Application Server
> > > v.1.0.1 based on Apache Geronimo
> > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&
> > dat=121642
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >
> >
> >
> >
> 

Thank you.  That option kept the PyMOL pipe alive.  As the option is
stored in the structure 'options.keep_thread_alive', would this '-K'
option cause a different behaviour of the program or is the program
simply run as a parent thread and this option keeps the parent alive?

Cheers,

Edward


On 10/30/06, DeLano Scientific <de...@de...> wrote:
> Edward,
>
> Add a "K" keepalive option along with the -p:
>
> pymol -pK
>
> Cheers,
>
> DeLano Scientific LLC
> Email Support Services
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf
> > Of Edward d'Auvergne
> > Sent: Sunday, October 29, 2006 9:01 PM
> > To: pym...@li...
> > Subject: [PyMOL] Persistent PyMOL pipes? Preventing a call to
> > 'cmd.quit()'.
> >
> > Hi,
> >
> > I am the project administrator for the open source program
> > relax (http://nmr-relax.com or
> > https://gna.org/projects/relax) and am interested in
> > interfacing relax with PyMOL.  relax is a program for
> > studying the dynamics of proteins, RNA, or other organic
> > molecules through the analysis of NMR relaxation data and I
> > would like to display the dynamics results superimposed onto
> > molecular structures within PyMOL.  I have attempted to open
> > a PyMOL pipe using the '-p'
> > flag however, when relax finishes and closes the pipe, PyMOL
> > terminates printing the message:
> >
> >   PyMOL: normal program termination.
> >
> > Is there a simple way to keep the PyMOL binary running after
> > a script terminates?  I've searched through the sources but a
> > solution isn't immediately obvious.  I've tracked back from
> > the file 'layer5/main.c'
> > where the 'printf()' statement is located back to the
> > function 'CmdQuit' in the file 'layer4/Cmd.c', but can't find
> > what is calling the 'cmd.quit()' method.
> >
> > Thanks,
> >
> > Edward
> >
> > --------------------------------------------------------------
> > -----------
> > Using Tomcat but need to do more? Need to support web
> > services, security?
> > Get stuff done quickly with pre-integrated technology to make
> > your job easier Download IBM WebSphere Application Server
> > v.1.0.1 based on Apache Geronimo
> > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&
> dat=121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
>
>

Edward,

Add a "K" keepalive option along with the -p:

pymol -pK

Cheers,

DeLano Scientific LLC
Email Support Services 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Edward d'Auvergne
> Sent: Sunday, October 29, 2006 9:01 PM
> To: pym...@li...
> Subject: [PyMOL] Persistent PyMOL pipes? Preventing a call to 
> 'cmd.quit()'.
> 
> Hi,
> 
> I am the project administrator for the open source program 
> relax (http://nmr-relax.com or 
> https://gna.org/projects/relax) and am interested in 
> interfacing relax with PyMOL.  relax is a program for 
> studying the dynamics of proteins, RNA, or other organic 
> molecules through the analysis of NMR relaxation data and I 
> would like to display the dynamics results superimposed onto 
> molecular structures within PyMOL.  I have attempted to open 
> a PyMOL pipe using the '-p'
> flag however, when relax finishes and closes the pipe, PyMOL 
> terminates printing the message:
> 
>   PyMOL: normal program termination.
> 
> Is there a simple way to keep the PyMOL binary running after 
> a script terminates?  I've searched through the sources but a 
> solution isn't immediately obvious.  I've tracked back from 
> the file 'layer5/main.c'
> where the 'printf()' statement is located back to the 
> function 'CmdQuit' in the file 'layer4/Cmd.c', but can't find 
> what is calling the 'cmd.quit()' method.
> 
> Thanks,
> 
> Edward
> 
> --------------------------------------------------------------
> -----------
> Using Tomcat but need to do more? Need to support web 
> services, security?
> Get stuff done quickly with pre-integrated technology to make 
> your job easier Download IBM WebSphere Application Server 
> v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&
dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hi,

I am the project administrator for the open source program relax
(http://nmr-relax.com or https://gna.org/projects/relax) and am
interested in interfacing relax with PyMOL.  relax is a program for
studying the dynamics of proteins, RNA, or other organic molecules
through the analysis of NMR relaxation data and I would like to
display the dynamics results superimposed onto molecular structures
within PyMOL.  I have attempted to open a PyMOL pipe using the '-p'
flag however, when relax finishes and closes the pipe, PyMOL
terminates printing the message:

  PyMOL: normal program termination.

Is there a simple way to keep the PyMOL binary running after a script
terminates?  I've searched through the sources but a solution isn't
immediately obvious.  I've tracked back from the file 'layer5/main.c'
where the 'printf()' statement is located back to the function
'CmdQuit' in the file 'layer4/Cmd.c', but can't find what is calling
the 'cmd.quit()' method.

Thanks,

Edward

Hi,
I have built two models from one protein molecule with the different 
nucleotides bound: one is ATP, one is ADP. Their overall structures 
are similar except that a few secondary structure domains shift. For 
example, alpha4 helix has move left for about 1.2=C5 and rotate about 
4=BA.
Could I use pymol to accurately measure the shift, not just give 
rough approximation?

Thanks!

Hey Shivesh,

you can get more color in your cartoons by coloring every residue
differently.

color red, i. 20
color blue, i. 21
color yellow, i. 22

Don't pay too much attention to the menus.  They're really just there so
traditional Mac and Windows users to get scared when they start using
PyMOL.  You will find that the command line does everything quicker and
easier.


Andreas


>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf
>> Of shivesh kumar
>> Sent: Saturday, October 28, 2006 4:33 AM
>> To: PyM...@li...
>> Subject: [PyMOL] color in pymol
>>
>> Dear all,
>> How can I use the color option in the Setting menu(Edit all)
>> to get more color in the cartoon.Thanx.
>> Shivesh
>>
>> shivesh
>>

> How can I use the color option in the Setting menu(Edit all) 
> to get more color in the cartoon.Thanx.

What do you mean by "more color in the cartoon"?  You set the cartoon color
independently using a command such as:

set cartoon_color, color-name

for example

set cartoon_color, red

Cheers,

DeLano Scientific LLC
Email Support Services 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of shivesh kumar
> Sent: Saturday, October 28, 2006 4:33 AM
> To: PyM...@li...
> Subject: [PyMOL] color in pymol
> 
> Dear all,
> How can I use the color option in the Setting menu(Edit all) 
> to get more color in the cartoon.Thanx.
> Shivesh
> 
> shivesh
> 
> 
> shivesh
> 
> ________________________________
> 
> Get your email and see which of your friends are online - 
> Right on the new Yahoo.com 
> <" rel="nofollow">http://us.rd.yahoo.com/evt=42973/*http://www.yahoo.com/preview>  
> 

Dear all,
How can I use the color option in the Setting
menu(Edit all) to get more color in the cartoon.Thanx.
Shivesh

shivesh


shivesh
 
---------------------------------
Get your email and see which of your friends are online - Right on the  new Yahoo.com

Oh, works like a charm.

(If you're a bit more descriptive about your problem, we can help you 
better.)


Andreas


surendra negi wrote:
> Is there any 32 bit version of pymol?  I am unable to install it  in XP
> 
> ----- Original Message ----
> 
> 
> 
> 

Is there any 32 bit version of pymol?  I am unable to install it  in XP=0A=
=0A----- Original Message ----=0A=0A=0A

Hi Martin,

> ...got the svn code compiled with -D VMD...

Great!=20

> CmdLoad: "/home/martin/workspace/testdata/ProtOut.pdb" loaded=20
> as "ProtOut".
> PyMOL>load /home/martin/workspace/testdata/topol.tpr
> CmdLoad: "/home/martin/workspace/testdata/topol.tpr" loaded=20
> as "topol.tpr".
> PyMOL>load /home/martin/workspace/testdata/ProteinTraj.xtc

Skip the tpr -- PYMOL can't read that at all. Try

load ProtOut.pdb, your-object-name
load ProteinTraj.xtc, your-object-name

where your-object-name is the same object.

Cheers,

DeLano Scientific LLC
Email Support Services=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Martin H=F6fling
> Sent: Friday, October 27, 2006 2:20 PM
> To: pym...@li...
> Subject: Re: [PyMOL] Support for gromacs trajectories and cube files
>=20
> ...got the svn code compiled with -D VMD...
> If i load a PDB, then load a topology and then try to load a=20
> trajectory via "load" loading the trajectory fails,=20
> complaining like this:
>=20
> CmdLoad: "/home/martin/workspace/testdata/ProtOut.pdb" loaded=20
> as "ProtOut".
> PyMOL>load /home/martin/workspace/testdata/topol.tpr
> CmdLoad: "/home/martin/workspace/testdata/topol.tpr" loaded=20
> as "topol.tpr".
> PyMOL>load /home/martin/workspace/testdata/ProteinTraj.xtc
>=20
> Best wishes,
> 	Martin
> --
> Meinungsfreiheit hei=DFt nicht, dass ich mir jeden Schei=DF anh=F6ren =
muss.
> (Tobias Erle in bln.misc)
>=20
> --------------------------------------------------------------
> -----------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier Download IBM WebSphere Application Server=20
> v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

=2E..got the svn code compiled with -D VMD...
If i load a PDB, then load a topology and then try to load a trajectory=20
via "load" loading the trajectory fails, complaining like this:

CmdLoad: "/home/martin/workspace/testdata/ProtOut.pdb" loaded as "ProtOut".
PyMOL>load /home/martin/workspace/testdata/topol.tpr
CmdLoad: "/home/martin/workspace/testdata/topol.tpr" loaded as "topol.tpr".
PyMOL>load /home/martin/workspace/testdata/ProteinTraj.xtc

Best wishes,
	Martin
=2D-=20
Meinungsfreiheit hei=DFt nicht, dass ich mir jeden Schei=DF anh=F6ren muss.
(Tobias Erle in bln.misc)

Hello:

Not exactly sure what you are asking here but if you want to calculate the
distance moved you could use the distance command:
distance atomx, atomy
to tell you how far atoms in the residues has moved.

you can also calculate dihedrals (ie/ X values) using the dihedral command
dihedral name_you_give, atomw, atomx, atomy, atomz
so you could compare the dihedral values for rotation of the residue.

but you are more likely to want rotation around axes or relative
movements, in which case using the actual coordinates of the atoms and
doing the math (ie. movements of centriods of the residues around a
central axis) is going to yield more meaningful results.  You can even get
the coords of an atom in pymol without looking at the pdb by turning on
the label wizard and selecting an atom.

Cheers,
JTM

"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."

Linus Pauling, Nobel Laureate 1954

"...everything that living things do can be understood in terms of the
jigglings and wigglings of atoms."

Richard Feynman, Nobel Laureate 1965

****************************************
Jason Thomas Maynes, MD/PhD
Department of Biochemistry and Molecular Biophysics
Resident in Anaesthesia and Paediatrics
Faculty of Medicine
Washington University in St. Louis
jm...@bi...
****************************************

> Hi,
>
> I am a new user of Pymol. I am currently working on mutant protein
> structures and I would like to compare the side chain shift between the
> mutant and wild-type structures. May I know how could I measure the side
> chain shift?
>
> Thanks a lot!
>
>
> Phoebe
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642_______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Anne,

Okay, the problem has been identified and fixed in the open-source code. =
 It
was an all-or-nothing failure to expand geometry in situations where the
sole target atoms are one or both last two atoms in the source object (a
rare scenario).

Cheers,

DeLano Scientific LLC
Email Support Services=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Anne M=F8lgaard
> Sent: Friday, October 27, 2006 4:43 AM
> To: pym...@li...
> Subject: [PyMOL] problems using "within" in selections
>=20
> I was trying to study the ligands in a structure, and then=20
> zoomed in on a Zn ion in molecule A:
> =20
> create ligands, 1q74 and het and not resn HOH
>=20
> (Selector: found 28 atoms.)
>=20
> create ZnA, ligands and chain A
>=20
> (Selector: found 1 atoms.)
>=20
> create nearZnA, 1q74 within 6 of ZnA=20
>=20
> (Selector: found 0 atoms.)
>=20
> =20
>=20
> Last night, this worked fine. This morning, I talked to a=20
> friend who could not make it work (same example), and then I=20
> typed in the commands in her session and it worked. Using the=20
> up arrow, we could not tell the difference between her=20
> command and mine. Now, I can't make it work on my computer.=20
> Why?? Should I be doing this in a smarter way? I am using=20
> version 0.99rc7 with Windows XP.=20
>=20
> =20
>=20
> Best regards,
>=20
> =20
>=20
> Anne M=F8lgaard
>=20
> =20
>=20
> =20
>=20
> =20
>=20
>=20
> --------------------------------------------------------------
> -----------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier Download IBM WebSphere Application Server=20
> v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Hi,=0A=0AI am a new user of Pymol. I am currently working on mutant protein=
 structures and I would like to compare the side chain shift between the mu=
tant and wild-type structures. May I know how could I measure the side chai=
n shift?=0A=0AThanks a lot!=0A=0A=0APhoebe=0A=0A

Anne,

There is definitely a problem with PyMOL here: that ZnA object is not
behaving correctly with respect to any of the distance-based selection
operators, and so for it is not yet clear why.  However,=20

create nearZnA, 1q74 within 6 of (ligands and chain A)=20

does work.

Cheers,

DeLano Scientific LLC
Email Support Services=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Anne M=F8lgaard
> Sent: Friday, October 27, 2006 4:43 AM
> To: pym...@li...
> Subject: [PyMOL] problems using "within" in selections
>=20
> I was trying to study the ligands in a structure, and then=20
> zoomed in on a Zn ion in molecule A:
> =20
> create ligands, 1q74 and het and not resn HOH
>=20
> (Selector: found 28 atoms.)
>=20
> create ZnA, ligands and chain A
>=20
> (Selector: found 1 atoms.)
>=20
> create nearZnA, 1q74 within 6 of ZnA=20
>=20
> (Selector: found 0 atoms.)
>=20
> =20
>=20
> Last night, this worked fine. This morning, I talked to a=20
> friend who could not make it work (same example), and then I=20
> typed in the commands in her session and it worked. Using the=20
> up arrow, we could not tell the difference between her=20
> command and mine. Now, I can't make it work on my computer.=20
> Why?? Should I be doing this in a smarter way? I am using=20
> version 0.99rc7 with Windows XP.=20
>=20
> =20
>=20
> Best regards,
>=20
> =20
>=20
> Anne M=F8lgaard
>=20
> =20
>=20
> =20
>=20
> =20
>=20
>=20
> --------------------------------------------------------------
> -----------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier Download IBM WebSphere Application Server=20
> v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

I was trying to study the ligands in a structure, and then zoomed in on =
a Zn ion in molecule A:
=20
create ligands, 1q74 and het and not resn HOH

(Selector: found 28 atoms.)

create ZnA, ligands and chain A

(Selector: found 1 atoms.)

create nearZnA, 1q74 within 6 of ZnA=20

(Selector: found 0 atoms.)

=20

Last night, this worked fine. This morning, I talked to a friend who =
could not make it work (same example), and then I typed in the commands =
in her session and it worked. Using the up arrow, we could not tell the =
difference between her command and mine. Now, I can't make it work on my =
computer. Why?? Should I be doing this in a smarter way? I am using =
version 0.99rc7 with Windows XP.=20

=20

Best regards,

=20

Anne M=F8lgaard

=20

=20

=20

Hi All=0A    A quick fix to the problem with the newest nVIDIA linux driver=
s and broken stereo is to install the nvidia-glx-legacy package if it is av=
ailable for your distribution. In Ubuntu this contains the 7184 driver whic=
h was the last to support  TNT, TNT2, TNT Ultra, GeForce, and GeForce2 chip=
sets. However, it also supports quadro 4 chipsets with working stereo, even=
 though the package description doesnt mention this.=0A    sudo apt-get ins=
tall nvidia-glx-legacy, close X, rmmod nvidia or restart, restart X. There =
might be a problem with the initrd image containing the wrong kernel-driver=
, so that rmmod nvidia have to be issued after the kernel have mounted root=
 and before X is started.=0A=0AAnother note: the new composite extension br=
eaks stereo support. =0Asudo nvidia-xconfig --no-composite fixes this on Ed=
gy Eft.=0A=0AEsben=0A=0A=0A----- Original Message ----=0AFrom: "pymol-users=
-re...@li..." <pym...@li...>=
=0ATo: pym...@li...=0ASent: Thursday, October 26, 2006=
 9:28:22 PM=0ASubject: PyMOL-users Digest, Vol 5, Issue 21=0A=0ASend PyMOL-=
users mailing list submissions to=0A    pym...@li...=
=0A=0ATo subscribe or unsubscribe via the World Wide Web, visit=0A    https=
://lists.sourceforge.net/lists/listinfo/pymol-users=0Aor, via email, send a=
 message with subject or body 'help' to=0A    pym...@li...=
rceforge.net=0A=0AYou can reach the person managing the list at=0A    pymol=
-use...@li...=0A=0AWhen replying, please edit your Sub=
ject line so it is more specific=0Athan "Re: Contents of PyMOL-users digest=
..."=0A=0A=0AToday's Topics:=0A=0A   1. Transparent cartoon disapearing wit=
h ray trace=0A      (Emeric Wasielewski)=0A   2. more color in pymol (shive=
sh kumar)=0A   3. Re: Transparent cartoon disapearing with ray trace=0A    =
  (Mat...@im...)=0A=0A=0A----------------------------------=
------------------------------------=0A=0AMessage: 1=0ADate: Wed, 25 Oct 20=
06 19:11:27 -0500=0AFrom: Emeric Wasielewski <Was...@ma...>=
=0ASubject: [PyMOL] Transparent cartoon disapearing with ray trace=0ATo: py=
mol...@li...=0AMessage-ID: <453...@ma...>=
=0AContent-Type: text/plain; charset=3DISO-8859-1; format=3Dflowed=0A=0AHel=
lo everybody,=0A=0AI wish to represent the backbone of my protein in cartoo=
n with a =0Atransparency of 0.6. Around it I show the surface with a transp=
arency of =0A0.4. (the aim is to highlight some specific residues by showin=
g their =0Aside chains in stick without transparency).=0AI can see the want=
ed result in OpenGL view. But when I raytrace the =0Apicture a kind of "Cop=
perfield" effect happens: the cartoon backbone =0Adisappears (NB: it happen=
s for any kind of combination of transparency =0Avalue for cartoon and surf=
ace).=0AIs anybody have an idea of what is happening ?=0A=0AThanks,=0A=0AEm=
eric=0A-- =0A+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=3D+=
=3D+=3D+=3D+=3D+=3D+=0AEmeric Wasielewski, Ph. D.=0ADepartment of Biochemis=
try and Molecular Biology=0A=0AMayo Clinic College of Medicine=0AGuggenheim=
 15-93=0A200, First Street SW=0ARochester, MN 55905, USA=0A=0AOffice: (507)=
 284 9189 Fax: (507) 284 1209=0Amailto: eme...@ma...=0A=0A=
=0A=0A------------------------------=0A=0AMessage: 2=0ADate: Wed, 25 Oct 20=
06 21:59:06 -0700 (PDT)=0AFrom: shivesh kumar <shi...@ya...>=0ASub=
ject: [PyMOL] more color in pymol=0ATo: pym...@li...=
=0AMessage-ID: <200...@we...>=0AConte=
nt-Type: text/plain; charset=3Diso-8859-1=0A=0ADear all,=0AHow can I use th=
e color option in the Setting=0Amenu(Edit all) to get more color in the car=
toon.Thanx.=0AShivesh=0A=0Ashivesh=0A=0A___________________________________=
_______________=0ADo You Yahoo!?=0ATired of spam?  Yahoo! Mail has the best=
 spam protection around =0Ahttp://mail.yahoo.com =0A=0A=0A=0A--------------=
----------------=0A=0AMessage: 3=0ADate: Thu, 26 Oct 2006 10:26:47 -0400=0A=
From: Mat...@im...=0ASubject: Re: [PyMOL] Transparent carto=
on disapearing with ray trace=0ATo: Emeric Wasielewski <Wasielewski.Emeric@=
mayo.edu>=0ACc: pym...@li...=0AMessage-ID:=0A    <OFDF=
434...@im...>=0A    =
=0AContent-Type: text/plain; charset=3DUS-ASCII=0A=0A=0A=0Apymol-users-boun=
ce...@li... wrote on 10/25/2006 08:11:27 PM:=0A=0A> Hello eve=
rybody,=0A>=0A> I wish to represent the backbone of my protein in cartoon w=
ith a=0A> transparency of 0.6. Around it I show the surface with a transpar=
ency of=0A> 0.4. (the aim is to highlight some specific residues by showing=
 their=0A> side chains in stick without transparency).=0A> I can see the wa=
nted result in OpenGL view. But when I raytrace the=0A> picture a kind of "=
Copperfield" effect happens: the cartoon backbone=0A> disappears (NB: it ha=
ppens for any kind of combination of transparency=0A> value for cartoon and=
 surface).=0A> Is anybody have an idea of what is happening ?=0A>=0A> Thank=
s,=0A>=0A> Emeric=0A=0AHi Emeric -=0A=0APymol has a few different ways of h=
andling multiple nested transparent=0Asurfaces.  The default is to just sho=
w the one closest to the viewer=0A(uni-layer transparency).  This gives pre=
ttier pictures with a single=0Asurface, since you don't see the backside of=
 the protein or any pockets in=0Athe surface.  However, for your purposes, =
you want multi-layer=0Atransparency.  To select this, choose "Setting->Tran=
sparency->Multi-layer".=0A=0AI just confirmed that this works.  I find the =
results a bit busy, unless=0Ayou're looking at just a small part of the pro=
tein.  You may need to hide=0Abackground details with the clipping planes.=
=0A=0A- Matt=0A=0A=0A--=0AMatthew Franklin , Ph.D.=0ASenior Scientist, ImCl=
one Systems=0A180 Varick Street, 6th floor=0ANew York, NY 10014=0Aphone:(91=
7)606-4116   fax:(212)645-2054=0A=0A=0AConfidentiality Note:  This e-mail, =
and any attachment to it, contains=0Aprivileged and confidential informatio=
n intended only for the use of the=0Aindividual(s) or entity named on the e=
-mail.  If the reader of this e-mail=0Ais not the intended recipient, or th=
e employee or agent responsible for=0Adelivering it to the intended recipie=
nt, you are hereby notified that=0Areading it is strictly prohibited.  If y=
ou have received this e-mail in=0Aerror, please immediately return it to th=
e sender and delete it from your=0Asystem.  Thank you.=0A=0A=0A=0A=0A------=
------------------------=0A=0A---------------------------------------------=
----------------------------=0AUsing Tomcat but need to do more? Need to su=
pport web services, security?=0AGet stuff done quickly with pre-integrated =
technology to make your job easier=0ADownload IBM WebSphere Application Ser=
ver v.1.0.1 based on Apache Geronimo=0Ahttp://sel.as-us.falkag.net/sel?cmd=
=3Dlnk&kid=3D120709&bid=3D263057&dat=3D121642=0A=0A------------------------=
------=0A=0A_______________________________________________=0APyMOL-users m=
ailing lis...@li...=0Ahttps://lists.sourceforge=
.net/lists/listinfo/pymol-users=0A=0A=0AEnd of PyMOL-users Digest, Vol 5, I=
ssue 21=0A******************************************=0A=0A=0A=0A=0A

pym...@li... wrote on 10/25/2006 08:11:27 PM:

> Hello everybody,
>
> I wish to represent the backbone of my protein in cartoon with a
> transparency of 0.6. Around it I show the surface with a transparency of
> 0.4. (the aim is to highlight some specific residues by showing their
> side chains in stick without transparency).
> I can see the wanted result in OpenGL view. But when I raytrace the
> picture a kind of "Copperfield" effect happens: the cartoon backbone
> disappears (NB: it happens for any kind of combination of transparency
> value for cartoon and surface).
> Is anybody have an idea of what is happening ?
>
> Thanks,
>
> Emeric

Hi Emeric -

Pymol has a few different ways of handling multiple nested transparent
surfaces.  The default is to just show the one closest to the viewer
(uni-layer transparency).  This gives prettier pictures with a single
surface, since you don't see the backside of the protein or any pockets in
the surface.  However, for your purposes, you want multi-layer
transparency.  To select this, choose "Setting->Transparency->Multi-layer".

I just confirmed that this works.  I find the results a bit busy, unless
you're looking at just a small part of the protein.  You may need to hide
background details with the clipping planes.

- Matt


--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

Dear all,
How can I use the color option in the Setting
menu(Edit all) to get more color in the cartoon.Thanx.
Shivesh

shivesh

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

Hello everybody,

I wish to represent the backbone of my protein in cartoon with a 
transparency of 0.6. Around it I show the surface with a transparency of 
0.4. (the aim is to highlight some specific residues by showing their 
side chains in stick without transparency).
I can see the wanted result in OpenGL view. But when I raytrace the 
picture a kind of "Copperfield" effect happens: the cartoon backbone 
disappears (NB: it happens for any kind of combination of transparency 
value for cartoon and surface).
Is anybody have an idea of what is happening ?

Thanks,

Emeric
-- 
+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+
Emeric Wasielewski, Ph. D.
Department of Biochemistry and Molecular Biology

Mayo Clinic College of Medicine
Guggenheim 15-93
200, First Street SW
Rochester, MN 55905, USA

Office: (507) 284 9189 Fax: (507) 284 1209
mailto: eme...@ma...