pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] pymol on amd64?

[Andrea S. <and...@gm...>]

Hi,
few weeks ago I had a problem with pymol-32bit on my laptop 64bit using sla=
md
Warren built a pymol for 64bit and you can download it from here:
http://delsci.com/beta/

In my case it worked.
Regards

andrea



2006/4/11, Florian Haberl <Flo...@ch...>:
> hi,
>
> On Tuesday 11 April 2006 19:59, Praedor Atrebates wrote:
> > Is anyone running pymol on an AMD64 system?  If so, did you find a preb=
uilt
> > binary or did you build it yourself?  If you built it yourself...HOW DI=
D
> > YOU DO IT?  I'd greatly appreciate help in this regard.
>
> also the normal 32 bit standalone executebale works for me on em64t cpu. =
You
> can find it at
>
> http://delsci.com/rel/099/
>
> don`t know if a special 64bit version is necessary if 32 bit version is
> running without problems.
> Os is Suse 10 for x86_64.
>
>
> >
> > Thank you,
> >
> > praedor
>
> Greetings,
>
> Florian
>
> --
> -------------------------------------------------------------------------=
------
>  Florian Haberl
>  Computer-Chemie-Centrum
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
> -------------------------------------------------------------------------=
------
>
>
>


--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

[PyMOL] PyMol & AMD64

[Jason V. <jav...@ut...>]

I use PyMol from CVS/SVN -- thus from source.  I build and install them by=
=20
hand (which is 3 easy commands).  Details on the wiki=20
(http://www.pymolwiki.org/index.php/Linux_Install#64-bit_.28x86_64.29).

I have two AMD64 machines, both SMP -- PyMol works great on both.

=2D- Jason

On Tuesday 11 April 2006 13:31, pym...@li...=20
wrote:
> Is anyone running pymol on an AMD64 system? =C2=A0If so, did you find a
> prebuilt=3D =3D20
> binary or did you build it yourself? =C2=A0If you built it yourself...HOW=
 DID
> YO=3D U=3D20
> DO IT? =C2=A0I'd greatly appreciate help in this regard.
>
> Thank you,
>
> praedor

=2D-=20
Jason Vertrees
BSCB Graduate Student @ UTMB, Galveston
jav...@ut... :: http://www.bscb.utmb.edu
PyMol Wiki        :: http://www.pymolwiki.org
Vertrees dot Org  :: http://www.vertrees.org

[PyMOL] pqr file

[Chun T. <tcs...@gm...>]

Hi there,

When one uses the APBS plugin of pymol to generate a pqr file, how
dose it assign the partial charges to the atoms, what force field is
it based on? Thank you.

Chun

Re: [PyMOL] pymol on amd64?

[Florian H. <Flo...@ch...>]

hi,

On Tuesday 11 April 2006 19:59, Praedor Atrebates wrote:
> Is anyone running pymol on an AMD64 system?  If so, did you find a prebui=
lt
> binary or did you build it yourself?  If you built it yourself...HOW DID
> YOU DO IT?  I'd greatly appreciate help in this regard.

also the normal 32 bit standalone executebale works for me on em64t cpu. Yo=
u=20
can find it at

http://delsci.com/rel/099/

don`t know if a special 64bit version is necessary if 32 bit version is=20
running without problems.
Os is Suse 10 for x86_64.


>
> Thank you,
>
> praedor

Greetings,

=46lorian

=2D-=20
=2D------------------------------------------------------------------------=
=2D-----
 Florian Haberl                       =20
 Computer-Chemie-Centrum  =20
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
=2D------------------------------------------------------------------------=
=2D-----

Re: [PyMOL] pymol on amd64?

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

I use gentoo linux's portage to do all the compile work (emerge pymol).
From the ebuild it looks like you need these prerequisites:

python, pmw (python library), numeric (python library), tk, libpng,
zlib, and glut .



Praedor Atrebates wrote:
> Is anyone running pymol on an AMD64 system?  If so, did you find a prebuilt 
> binary or did you build it yourself?  If you built it yourself...HOW DID YOU 
> DO IT?  I'd greatly appreciate help in this regard.
> 
> Thank you,
> 
> praedor

[PyMOL] pymol on amd64?

[Praedor A. <pr...@ya...>]

Is anyone running pymol on an AMD64 system?  If so, did you find a prebuilt=
=20
binary or did you build it yourself?  If you built it yourself...HOW DID YO=
U=20
DO IT?  I'd greatly appreciate help in this regard.

Thank you,

praedor
=2D-=20
The Reichstag fire is to Hitler as 9/11 is to Bush

Re: [PyMOL] PymOl INstallation PRoblems

[Noinaj <no...@uk...>]

My dear PyFriends,

OKay, I was able to successfully get Pymol up and running on Sony Vaio, =
thanks to my new friend Chris Yip!  Thanks a million!  Hip-Hip Hurray!

The cure you ask?  Well, as Chris mentioned in his suggestions, I simply =
went to the Sony website and downloaded the update driver for the =
graphics controller.  The funny thing was that, it wasn't nVidia, it was =
ATI.  So apparently, this driver issue may not be primarily an nVidia =
issue.  But after I installed updated driver and restarted, Pymol ran =
beautifully.  Now, I assume we may still run across some bugs in the =
future, but for today, we feast on victory!

Thanks again Chris and I hope this helps someone else in the future! =20



Cheers,
Nick




Couple of things that people tried - one was to go to an older PyMol =
version (and the corollary - go to the latest beta version).


we did try some drivers from the various vendors but that was also hit =
and miss...


There didn't seem to be a consistent fix


Chris




On Apr 10, 2006, at 4:47 PM, Noinaj wrote:


  Thanks Chris for your help.  As you have noted and as I have read =
online, there seems to be a problem with the graphics drivers, is this =
correct?  Do you know if updating the drivers remedied the problem?  If =
not, were you able to work around the problem?  Thanks again for your =
help!


  Cheers,
  Nick



    ----- Original Message -----
    From: Christopher Yip
    To: Noinaj
    Sent: Monday, April 10, 2006 4:31 PM
    Subject: Re: [PyMOL] PymOl INstallation PRoblems


    A lot of my students ran into the same problem this past fall - =
there are a bunch of notes on the list regarding nVidia graphics drivers =
that seem to be at the root cause of the problem - you might want to try =
a search under WinXP and Pymol...     =20


    http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4368.html=20


    here are some of the links that I found were of use, and posted to =
my class list


    Check here for some info and suggestions:


    http://delsci.com/beta/


    Specifically..


    Take a look here:
    http://sourceforge.net/mailarchive/message.php?msg_id=3D11962703
    ++++++


    If anyone else is experiencing a non-functional PyMOL with =
late-model nVidia
    drivers on Windows XP or similar, pymol-0_99beta96 contains a =
workaround
    that has been reported to eliminate the problem.


    http://delsci.com/beta


    Hopefully the next driver release for Windows will fix this problem =
just
    like it did on Linux...
    +++++


    Some may find this useful too - a Wiki with hints:


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


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


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






    On Apr 10, 2006, at 4:23 PM, Noinaj wrote:


      Hi PyWorld,


      I have been trying to help a friend install PyMol on her laptop =
(Sony Vaio) that has Windows XP Home Edition.  The installation runs =
smooth with no problem at all.  But once we try to open the program, its =
seems to stall, then crashes, and Windows XP asks if we would like to =
send a error report???

      I have searched the archives and online for answers, but with no =
luck.  Therefore, I present to you, my PyFriends, our dilemma and seek a =
remedy to our problem.  I give you my word, my good friends, that upon =
finding the solution, I will not take all the credit for solving this =
mystery....just kidding, credit will be duly noted.

      Thanks in advance for any and all help!


      Cheers,
      Nick







    Christopher M. Yip, Ph.D., P.Eng.
    Associate Professor - Canada Research Chair in Molecular Imaging
    Department of Chemical Engineering and Applied Chemistry
    Department of Biochemistry
    Institute of Biomaterials and Biomedical Engineering
    The Terrence Donnelly Centre for Cellular and Biomolecular Research
    University of Toronto
    Room 404 160 College St.
    Toronto, ON, CANADA M5S 3E1
    (416) 978-7853
    (416) 978-4317 (fax)
    chr...@ut...
    http://bigten.med.utoronto.ca








Christopher M. Yip, Ph.D., P.Eng.

Associate Professor - Canada Research Chair in Molecular Imaging

Department of Chemical Engineering and Applied Chemistry

Department of Biochemistry

Institute of Biomaterials and Biomedical Engineering

The Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

Room 404 160 College St.
Toronto, ON, CANADA M5S 3E1
(416) 978-7853

(416) 978-4317 (fax)

chr...@ut...

http://bigten.med.utoronto.ca

Re: [PyMOL] PymOl INstallation PRoblems

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

Hi Nick,

This sounds vaguely similar to the msvcr71.dll issues that were recently
discussed on the list (searching the list archives will give you more info
on this, but the quick fix is to search the hd for msvcr71.dll and copy it
to the pymol install directory).

If that doesn't resolve the problem, then some more details might be
useful.  Which version of pymol are you running (I'm assuming one of the
recent win32 binary distributions)?  Are there any error messages, and if
so what do they say?  Are you starting-up pymol by clicking the start menu
icon (if so, try opening a dos window, going to the pymol directory, and
starting from the dos prompt...this probably won't fix the problem, but
will probably give more detailed error messages)?

The quickest resolution (assuming msvcr71.dll isn't the problem) might be
to install a slightly older version.

Hope this helps,

Pete

> Hi PyWorld,
>
>
> I have been trying to help a friend install PyMol on her laptop (Sony
Vaio) that has Windows XP Home Edition.  The installation runs smooth
with
> no problem at all.  But once we try to open the program, its seems to
stall, then crashes, and Windows XP asks if we would like to send a
error
> report???
>
> I have searched the archives and online for answers, but with no luck. 
Therefore, I present to you, my PyFriends, our dilemma and seek a remedy
to our problem.  I give you my word, my good friends, that upon finding
the solution, I will not take all the credit for solving this
> mystery....just kidding, credit will be duly noted.
>
> Thanks in advance for any and all help!
>
>
> Cheers,
> Nick
>
>
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] PymOl INstallation PRoblems

[Noinaj <no...@uk...>]

Hi PyWorld,


I have been trying to help a friend install PyMol on her laptop (Sony =
Vaio) that has Windows XP Home Edition.  The installation runs smooth =
with no problem at all.  But once we try to open the program, its seems =
to stall, then crashes, and Windows XP asks if we would like to send a =
error report???

I have searched the archives and online for answers, but with no luck.  =
Therefore, I present to you, my PyFriends, our dilemma and seek a remedy =
to our problem.  I give you my word, my good friends, that upon finding =
the solution, I will not take all the credit for solving this =
mystery....just kidding, credit will be duly noted.

Thanks in advance for any and all help!


Cheers,
Nick

Re: [PyMOL] Protein representation

[Virgile A. <vir...@es...>]

Dear Noa,
you probably mean the backbone ribbons representation like here :
http://www.ccp4.ac.uk/newsletters/newsletter40/11_del2H.jpg or here :
http://pymol.sourceforge.net/newman/user/S0260tube.jpeg
You can obtain such representations by trying the commands "show ribbon" or
"cartoon tube"

cheers,

Virgile


Quoting Noa Godin <noa...@gm...>:

> Hello.
> I want to represent my protein in alpha carbon format but with rounded
> 'corners' and with no secondary structures.
> Is there a way to do this? what commands should I use?
> If not, what is the closest representation and matcing commands that
> I should use?
> 
> --
> Thanks in advance,
> 
> 
> 
> 
>     Noa
> 
> Everything happens to everybody sooner or later if there is time enough.
>   {George Bernard Shaw}
> 


Virgile Adam (vir...@es...)
European Synchrotron Radiation Facility
Office 18.1.07 - Sector 18
6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex 9 France
Tel: +33 (0)4 76 88 27 72  /  Fax: +33 (0)4 76 88 26 24
***There are 10 kinds of people: those who can count in binary and the others***

-------------------------------------------------
This mail sent through IMP: http://horde.org/imp/

[PyMOL] Protein representation

[Noa G. <noa...@gm...>]

Hello.
I want to represent my protein in alpha carbon format but with rounded
'corners' and with no secondary structures.
Is there a way to do this? what commands should I use?
If not, what is the closest representation and matcing commands that
I should use?

--
Thanks in advance,




    Noa

Everything happens to everybody sooner or later if there is time enough.
  {George Bernard Shaw}

[PyMOL] About the delsci.com site

[Feng X. <xu...@gm...>]

Hi All,
  I couldn't access the website of delsci.com for downloading the newest
pymol version 0.99rc6 recently. Is it down? Would anybody supply one mirror
site or attach the windows and linux static version in reply mail.
Thanks a lot in advance.

Cheers
F3ng

RE: [PyMOL] libnvidia-tls.so.1: cannot handle TLS data

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

Hi Warren:

Thanks.

glxgears for example works.

Bill



On Fri, 7 Apr 2006, Warren DeLano wrote:

> Bill,
>
> My initial suggestion would be to try some other OpenGL software to see whether the problem is PyMOL specific or not.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> William Scott
>> Sent: Friday, April 07, 2006 11:52 AM
>> To: pym...@li...
>> Subject: [PyMOL] libnvidia-tls.so.1: cannot handle TLS data
>>
>> Hi:
>>
>> I'm running pymol on Ubuntu with ubuntu's nvidia driver.
>>
>> I get the error
>>
>> libnvidia-tls.so.1: cannot handle TLS data
>>
>> upon startup.
>>
>> If I move the directory /usr/lib/tls
>>
>> out of the way, pymol works, but then upon reboot, my display
>> is blank.
>>
>> Any suggestions?
>>
>> Bill
>>
>> PS:  I just noticed that nvidia released new linux drivers today.
>> Can I do irreparable harm by installing it?
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by xPML, a groundbreaking
>> scripting language that extends applications into web and
>> mobile media. Attend the live webcast and join the prime
>> developer group breaking into this new coding territory!
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&
>> dat=121642
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>

RE: [PyMOL] libnvidia-tls.so.1: cannot handle TLS data

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

Bill,

My initial suggestion would be to try some other OpenGL software to see =
whether the problem is PyMOL specific or not. =20

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
> William Scott
> Sent: Friday, April 07, 2006 11:52 AM
> To: pym...@li...
> Subject: [PyMOL] libnvidia-tls.so.1: cannot handle TLS data
>=20
> Hi:
>=20
> I'm running pymol on Ubuntu with ubuntu's nvidia driver.
>=20
> I get the error
>=20
> libnvidia-tls.so.1: cannot handle TLS data
>=20
> upon startup.
>=20
> If I move the directory /usr/lib/tls
>=20
> out of the way, pymol works, but then upon reboot, my display=20
> is blank.
>=20
> Any suggestions?
>=20
> Bill
>=20
> PS:  I just noticed that nvidia released new linux drivers today.  =20
> Can I do irreparable harm by installing it?
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] libnvidia-tls.so.1: cannot handle TLS data

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

Hi:

I'm running pymol on Ubuntu with ubuntu's nvidia driver.

I get the error

libnvidia-tls.so.1: cannot handle TLS data

upon startup.

If I move the directory /usr/lib/tls

out of the way, pymol works, but then upon reboot, my display is blank.

Any suggestions?

Bill

PS:  I just noticed that nvidia released new linux drivers today.   
Can I do irreparable harm by installing it?

[PyMOL] RE:Ray-tracing inner surface backside

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

Paul (& Bob),

Have you tried

set two_sided_lighting, 1

Cheers,
seth

[PyMOL] RE: labels not displaying

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

Marilyn,
We saw this between unix and PC and one user figured out that
label_font_id's were different. Thus older versions didn't recognize as man=
y
fonts as newer ones. I'm thinking this matches your description if the
binaries on the two machines are in fact different versions.

Try:

set label_font_id, 1
and the missing labels should show up.

There are other fonts... 2, 3, 4, 5, etc.?
I don't know how high they go, but I think by #5 labels will vanish in some
older versions but still display in newer ones.

-Seth

[PyMOL] Last chance for Como !

[Anastassis P. <a.p...@nk...>]

Dear all,

11 April is the closing date for registering for the Como School if  
you want your abstract to be considered for an oral presentation !

http://www.crystallographyschool.org/

There's only a few places left ...!
We are looking forward to see you all there for what we hope it will  
be a great meeting.

Tassos, Andrea, Stefania, Marjolein and Derek.

[PyMOL] molecule translation & dynamic measurement changes

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

Hi all,
I am trying to arrange two (RNA) molecules relative to each other such =
that a number of selected residues are getting close enough to form =
contacts via H-bonds. To me it seems quite difficult to use pyMol to =
precisely arrange molecules in space (I use the translate and rotate =
commands or move the molecules around free-handed). Is there an option =
to at least display a coordinate system?
Furthermore, I have used the measurement wizard to define distances =
between interacting residues. I was hoping that these displayed =
distances would dynamically change as I change the molecules position =
such that I can monitor appropriate arrangement more easily, but this =
does not seem to happen. Is something like this possible at all in =
pyMOL? Or can anyone describe a reasonable pyMOL method of how to match =
two (RNA) molecules to interact. I know a docking program would be best, =
but I fear the molecules I work with are much too complicated for this.

Thanks for your help,
Michael.

Re: [PyMOL] Producing publication quality images

[Praedor A. <pr...@ya...>]

On Wednesday 22 March 2006 09:05 am, Joao Renato Carvalho Muniz wrote:
> Or using Gimp (on Linux and window$).

> Mark A Saper wrote:
> > You can easily change the resolution (dpi) of an image without
> > changing the number of pixels, by editing the file in Photoshop (in
> > Image Size, change resolution without rescaling) or in
> > GraphicConverter (on Mac).

I use gimp on linux.  I simply raytrace the image I want to use at a=20
resolution above what I will be aiming for in publication, render it, then=
=20
scale the image down to the appropriate size for submission.  Never ever=20
scale up.

praedor
=2D-=20
The Reichstag fire is to Hitler as 9/11 is to Bush

RE: [PyMOL] manual vs. more features

[Fischmann, T. <thi...@sp...>]

=20

The point that some have made about Pymol having reasonable
documentation is well-taken. But new features do not get used much - or
at least not to their full potential - if they are not documented. Hence
there is little point adding more and more features without keeping the
manual current.

By far, the best approach is to write the documentation as new features
get added.

Thierry


*********************************************************************
This message and any attachments are solely for the intended recipient. If =
you are not the intended recipient, disclosure, copying, use or distributio=
n of the information included in this message is prohibited -- Please immed=
iately and permanently delete.

[PyMOL] labels not displaying

[Yoder, M. <Yo...@um...>]

This is an unusual and annoying problem.
=20
I'm running the latest version of Pymol on two PC machines, one in my
office and one at home.  I cart my session file on a jump drive back and
forth.  On my PC at home, the session file displays the labels just fine
and dandy.  But using the same session file, the labels are not
displayed on my PC in my office.  Same session file, recurring problem
over several days.  Even when using the distance wizard, the dashed
lines display for the distance, but the text (residue number and the
distance) does not display in my office. =20
=20
Furthermore, this is not a problem with the machine, but with this
session file.  I can load a different session file on my office PC and
the labels display just like they always have and should.
=20
Why, if I'm using the same session file on two different machines, will
one display labels and the other machine does not?  Is there a setting
parameter that I'm not aware of?
=20
Thanks,
Marilyn
=20
Marilyn D. Yoder
Division of Cell Biology and Biophysics
University of Missouri-Kansas City
5007 Rockhill Rd.
Kansas City, MO  64110-2499
phone: 816-235-1986
fax: 816-235-1503
=20

[PyMOL] Re: Ray-tracing inner surface backside

[Paul W. E. <pa...@un...>]

So,


I tried rendering using transparency_mode = 1 or 0 and got this result:


http://pwe.no-ip.org/other/Pymol2.png


Is there a way to get rid of the transparency that darkens some parts of
the surface where something lies behind?


I also tried povray to render the surface and it gives me a texture on
the inner surface back, but there's again the "problem" with the double
transparency darkening some parts.


Thanks for Your help guys,


Paul

RE: [PyMOL] drawing walls

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

Dear Liu Shiyong,

Please have a look to the nice page of Gareth Stockwell,
http://www.ebi.ac.uk/~gareth/, you will find under the section -pymol- =
some
nice pymol scripts, and in particular wall.py
The script is commented so have a look inside to find how you shall use
it... You might also change the script to include transparency and other
colors.

Regards,

Gr=E9gori




-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Liu =
Shiyong
Sent: mardi, 4. avril 2006 11:44
To: pym...@li...
Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #1176 - 1 msg


http://www.ebi.ac.uk/~gareth/pymol/images/walls.png

how to draw this walls.png ?

Re: [PyMOL] Ray-tracing inner surface backside

[Robert I. <imm...@gm...>]

Paul,

I'm actually quite interested in an answer to this question as well.=20
An example of what I have been able to do is this:

http://kinemage.biochem.duke.edu/~immormino/neca_new.png

I like using this type of rendering to look at a protein cavity from
inside the protein.  For me it has been helpful in presenting the VDWs
interaction of ligands in the pocket.

To render this picture:

set surface_color, slate
set ray_interior_color, grey
set transparency, .3
set transparency_mode, 0
ray

The one thing that kinda bothers me with this approach is that
transparency_mode=3D0 is called fast and ugly in the GUI.  But this is
the only way that i have found to get this effect. Other ( better )
suggestions would be appreciated.

-bob





On 4/4/06, Paul Wilhelm Elsinghorst <pa...@un...> wrote:
>  Hi folks,
>
>
>  what I did for now is that I selected a subset of residues that sit arou=
nd
> a cavity. Then I showed the surface of the original protein inside the
> selection to get only the inside surface of the cavity. Now it looks sort=
 of
> like a hose with inside and outside just as I wanted.
>
>
>  Now I'd like to raytrace this and I find no texture on the outside surfa=
ce,
> which is actually just the back of the inside. I put a picture on
> http://pwe.no-ip.org/other/Pymol.png to illustrate my
> problem. See how the inner surface has texture and its back doesn't!
>
>
>  How can I get this fixed? Any ideas?
>
>
>  Paul