pymol-users Mailing List for PyMOL Molecular Graphics System

Hi,
I want to generate a figure that shows clearly the conformation change 
upon ligand-binding in 3tga(unbound) and 1mtw (ligand bound).
The ligand-binding site is a small pocket in the 3tga and is bigger 
pocket in bound structure. The loops of resi 190-195 strech to allow 
ligand binds.
I want a figure that can show the conformation change of the loops of 
resi 190-195 and also the change of the pocket.
Can anyone  give me a hint?

Thanks

Bingding

Hi Stuart,

Well, 20,000 =A3 (ex VAT) for a 20" UXGA is probably not something a lab=20=

can afford as easily as a CRT + graphic board... unless you would like=20=

to ship some free for advertisement (-;

Best regards,
Philippe

Le 31 janv. 06, =E0 14:25, Stuart McKay a =E9crit :

> Anastassis,
> =A0
> Interesting to read about the demise of the CRT and your problems with=20=

> flickering screens.
> =A0
> You (and the other BB members) may be interested to learn of an=20
> alternative technology from IRIS-3D in the UK.=A0Historically=20
> targeted=A0at the=A0Oil and Gas Sector for subsurface imaging,=A0it is =
now=20
> being evaluated in the Life Sciences. This product does not suffer=20
> from the flickering issues mentioned in this thread, being based=20
> around dual projection LCD technology and not requiring special=20
> glasses to view:
> =A0
> The IRIS=A0solution is a glasses-free 3D display system that enables =
you=20
> to work at up to UXGA resolution in stereo mode, is 2D/3D compatible,=20=

> can be used in a normal office environment,=A0does not suffer from=20
> stereo cross-talk (this means no more ghosting, eye-strain or=20
> headaches - enabling you=A0to concentrate on your data=A0rather than =
be=20
> distracted by the display technology) and is compatible with all=20
> stereo enabled software on a wide range of=A0SW/HW platforms.
> =A0
> More information is available from the company website or by=20
> contacting me directly.
> =A0
> Regards,
> =A0
> Stuart
> ...........................
> Stuart McKay, PhD
> CEO
> IRIS-3D Ltd
> James Weir Building
> 75 Montrose St
> Glasgow G1 1XJ
> Scotland, UK
> =A0
> (T) +44-141-548-2423
> (F) +44-141-552-5105
> (M) +44 7786 073663
> =A0
> http://www.iris3d.com
> =A0
> =A0
>> ----- Original Message -----
>> From: Anastassis Perrakis
>> To: Warren DeLano
>> Cc: pym...@li... ; CCP4 Board ; ono ; Albert =
Pauw
>> Sent: Tuesday, January 31, 2006 11:08 AM
>> Subject: Re: [ccp4bb]: Current Stereo 3D Display Info
>>
>> Hi all -
>>
>> While on the subject and after thanking Warren for providing the=20
>> excellent resource ...:
>>
>> We have some nice 3D monitors and Nvidia cards in Linux PC's we do=20
>> stereo with.
>>
>> Warren correctly points out that you need:
>>
>> =A0 =A01280x960=A0 @ 120 Hz requires H-sync of 123 kHz=A0
>> =A0 =A0 =A0 1344x1008 @ 120 Hz requires H-sync of 130 kHz=A0
>> =A0 =A0 =A0 1400x1050 @ 120 Hz requires H-sync of 136 kHz =A0
>>
>> (In fact you need your monitor to switch to these refresh rates 

>> when in stereo, but thats a detail)
>>
>> However, I am totally unable to convince the NVidia drivers we have=20=

>> for Linux to
>> operate at the sync rates I want them to and Warren advices! Thus, we=20=

>> have noticeable flicker at stereo
>> mode (in the non-stereo windows only) which is a shame, given our=20
>> excellent monitors.
>> Is that expected or can be corrected ?
>>
>> Could anyone please advice me how to set the Nvidia Linux drivers to=20=

>> operate at the proper sync rates then ?
>>
>> Tassos
>>
>> PS=A0- Iiyama Vision Master Pro 514 / HM204DT (H-sync: 142 kHz) is=20
>> still available by some European vendors new and is great, we have=20
>> two, plus an old trusty EIZO T966 which is also cool. (Warren, I=20
>> could not find that on your list,its a good machine, does 136 and you=20=

>> might be able to find one still)
>>
>>
>> On Jan 28, 2006, at 20:59, Warren DeLano wrote:
>>
>>> ***=A0 For details on how to be removed from this list visit the=A0 =
***
>>> ***=A0 =A0 =A0 =A0 =A0 CCP4 home page http://www.ccp4.ac.uk =A0 =A0 =
=A0 =A0 ***
>>>
>>>
>>> Folks,
>>>
>>> Whether you favor Macintosh, Linux, or Windows for stereo 3D
>>> visualization, you're going to need some specific (and increasingly
>>> rare) hardware. =A0
>>>
>>> To help you find it, we've just updated our information page on
>>> stereo-3D-capable displays, cards, emitters, and glasses:
>>>
>>> http://pymol.sf.net/stereo3d.html
>>>
>>> Remarkably, we can now only find one company selling a brand new CRT
>>> monitor suitable for stereo 3D.=A0 If you find any others, please do=20=

>>> let
>>> us know!
>>>
>>> Cheers,
>>> Warren
>>>
>>> --
>>> Warren L. DeLano, Ph.D.=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
>>> Principal Scientist
>>>
>>> . DeLano Scientific LLC =A0
>>> . 400 Oyster Point Blvd., Suite 213=A0 =A0 =A0 =A0 =A0 =A0
>>> . South San Francisco, CA 94080 USA=A0 =A0
>>> . Biz:(650)-872-0942=A0 Tech:(650)-872-0834=A0 =A0 =A0
>>> . Fax:(650)-872-0273=A0 Cell:(650)-346-1154
>>> . mailto:wa...@de... =A0 =A0 =A0
>>>
>>>

Hi there,

Most modern monitors are very clever and tell the X server their
preferred sync rates (which never exceed 85 Hz).  You can override
this functionality by adding
    Option    "UseEdidFreqs"    "0"
to the "Device" section of your Xorg (or XFree86) config file.

You will also need to specify your own Modeline to control the monitor
timings.  The program 'gtf', which should come standard in most linux
distros, will help you do this.  Typing 'gtf' without args will give
you a short blurb on how to use the program.  Shove the modeline
output by gtf into the "Monitor" section of your Xorg config file, set
this new modeline as the default timing in the "Screen" section of the
config file, and you should be in business.

HTH,

Stephen

P.S. See http://o-info.bioxray.dk/pipermail/o-info/2003-April/006676.html
for more details.

On 1/31/06, Anastassis Perrakis <a.p...@nk...> wrote:
> Hi all -
>
> While on the subject and after thanking Warren for providing the excellen=
t
> resource ...:
>
> We have some nice 3D monitors and Nvidia cards in Linux PC's we do stereo
> with.
>
> Warren correctly points out that you need:
>
>     1280x960  @ 120 Hz requires H-sync of 123 kHz
>       1344x1008 @ 120 Hz requires H-sync of 130 kHz
>       1400x1050 @ 120 Hz requires H-sync of 136 kHz
> (In fact you need your monitor to switch to these refresh rates only when=
 in
> stereo, but thats a detail)
>
> However, I am totally unable to convince the NVidia drivers we have for
> Linux to
> operate at the sync rates I want them to and Warren advices! Thus, we hav=
e
> noticeable flicker at stereo
> mode (in the non-stereo windows only) which is a shame, given our excelle=
nt
> monitors.
> Is that expected or can be corrected ?
>
> Could anyone please advice me how to set the Nvidia Linux drivers to oper=
ate
> at the proper sync rates then ?
>
>  Tassos
>
> PS - Iiyama Vision Master Pro 514 / HM204DT (H-sync: 142 kHz) is still
> available by some European vendors new and is great, we have two, plus an
> old trusty EIZO T966 which is also cool. (Warren, I could not find that o=
n
> your list,its a good machine, does 136 and you might be able to find one
> still)
>
>
>
>
> On Jan 28, 2006, at 20:59, Warren DeLano wrote:
>
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
> Folks,
>
> Whether you favor Macintosh, Linux, or Windows for stereo 3D
> visualization, you're going to need some specific (and increasingly
> rare) hardware.
>
> To help you find it, we've just updated our information page on
> stereo-3D-capable displays, cards, emitters, and glasses:
>
> http://pymol.sf.net/stereo3d.html
>
> Remarkably, we can now only find one company selling a brand new CRT
> monitor suitable for stereo 3D.  If you find any others, please do let
> us know!
>
> 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...
>
>
>
>


--
Stephen Graham
Crystallography Group
School of Molecular and Microbial Biosciences
University of Sydney

Hi all -

While on the subject and after thanking Warren for providing the  
excellent resource ...:

We have some nice 3D monitors and Nvidia cards in Linux PC's we do  
stereo with.

Warren correctly points out that you need:

	   1280x960  @ 120 Hz requires H-sync of 123 kHz
       1344x1008 @ 120 Hz requires H-sync of 130 kHz
       1400x1050 @ 120 Hz requires H-sync of 136 kHz

(In fact you need your monitor to switch to these refresh rates only  
when in stereo, but thats a detail)

However, I am totally unable to convince the NVidia drivers we have  
for Linux to
operate at the sync rates I want them to and Warren advices! Thus, we  
have noticeable flicker at stereo
mode (in the non-stereo windows only) which is a shame, given our  
excellent monitors.
Is that expected or can be corrected ?

Could anyone please advice me how to set the Nvidia Linux drivers to  
operate at the proper sync rates then ?

	Tassos

PS - Iiyama Vision Master Pro 514 / HM204DT (H-sync: 142 kHz) is  
still available by some European vendors new and is great, we have  
two, plus an old trusty EIZO T966 which is also cool. (Warren, I  
could not find that on your list,its a good machine, does 136 and you  
might be able to find one still)


On Jan 28, 2006, at 20:59, Warren DeLano wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
> Folks,
>
> Whether you favor Macintosh, Linux, or Windows for stereo 3D
> visualization, you're going to need some specific (and increasingly
> rare) hardware.
>
> To help you find it, we've just updated our information page on
> stereo-3D-capable displays, cards, emitters, and glasses:
>
> http://pymol.sf.net/stereo3d.html
>
> Remarkably, we can now only find one company selling a brand new CRT
> monitor suitable for stereo 3D.  If you find any others, please do let
> us know!
>
> 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...
>
>

I believe that even the large Phillips (22") that you list is no longer
being made and that what is in stock at places is just old inventory (could
be wrong though).  It is hard to believe, but these monitors just aren't
being made anymore.  We literally have people in our modeling group hording
these displays for a rainy day.  I've just given up on stereo and switched
to using higher-end LCD displays.  Less energy, less heat, and less eye
fatigue for me.

Steve

-----Original Message-----
From: own...@dl... [mailto:own...@dl...] On Behalf Of
Warren DeLano
Sent: Saturday, January 28, 2006 2:59 PM
To: pym...@li...
Cc: cc...@dl...; vm...@ks...; pd...@sd...;
o-...@o-...; CCL Subscribers
Subject: [ccp4bb]: Current Stereo 3D Display Info


***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


Folks,

Whether you favor Macintosh, Linux, or Windows for stereo 3D
visualization, you're going to need some specific (and increasingly
rare) hardware.  

To help you find it, we've just updated our information page on
stereo-3D-capable displays, cards, emitters, and glasses:

http://pymol.sf.net/stereo3d.html

Remarkably, we can now only find one company selling a brand new CRT
monitor suitable for stereo 3D.  If you find any others, please do let
us know!

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...      




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Matthew,

Could you be thinking of the "-j" launch option?  This can also be
accessed with

stereo on
set stereo_mode, 4

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
> Matthew Bowler
> Sent: Thursday, January 26, 2006 5:04 AM
> To: pym...@li...
> Subject: [PyMOL] Menu Bar viewed in stereo on Geowall
>=20
> Dear All,
> 	I am sure that around 3 months ago I found a command=20
> that would allow the menu bar in pymol to be seen and used=20
> while viewing a session in stereo on a geowall.  However, try=20
> as I might I cannot find the command now, any ideas?  Many=20
> thanks in advance, Matt.
>=20
>=20
>=20
> Matthew Bowler
> MRC Dunn Human Nutrition Unit
> Wellcome Trust / MRC Building
> Hills Road
> Cambridge CB2 2XY
> Tel: 0044 (0) 1223 252826
> Fax: 0044 (0) 1223 252825
>=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
> 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

Stephen,

set ray_interior_color, color-name
ray

or

set ray_interior_color, -5
ray

to get an an effect like in that figure where the interiors are
different colors (on a per-object basis, or simply recolor afterwards in
Photoshop).

Note that the entire interior needs to be within the clip slab in order
for this to work.

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
> Stephen Graham
> Sent: Friday, January 27, 2006 5:32 AM
> To: pym...@li...
> Subject: [PyMOL] Cutaway surface
>=20
> Hi all,
>=20
> Is there any way good way in pymol of displaying a slice=20
> through a surface and block colouring the 'inner' face of the=20
> surface.=20
> Basically, I would like to generate a figure that looks like=20
> part (b) of=20
> http://www.nature.com/nature/journal/v432/n7014/fig_tab/nature
> 02988_F3.html
> using pymol.  I have tried playing with the lighting models=20
> and backpace culling (a-la set ambient=3D0; set direct=3D0.7; set=20
> reflect=3D0.0; set backface_cull=3D0) but they are not quite what=20
> I am after.
>=20
> Can anyone recommend a good way to achieve this effect?
>=20
> Thanks,
>=20
> Stephen
>=20
> --
> Stephen Graham
> Crystallography Group
> School of Molecular and Microbial Biosciences University of Sydney
>=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=3Dk&kid=103432&bid#0486&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

I recently got a color 3D printer that only accepts color
output from vrml files.

Attached is a patch for current CVS that does the following:

1) When a surface display is shown, it dumps the surface to a
VRML 2.0 file in /tmp/pymol.wrl

2) everytime the color scheme of the surface is changed, it
rewrites that wrl file.

I know this isn't a very elegant way to add a feature like this
(should have GUI elements, etc), but it was the quickest way
to get the job done for me, with my very limited knowledge of
the source code.

Here's some pics involving the demo file 1tii.pdb file, using
the "chainbow" coloring scheme:

http://bebop.cns.ualberta.ca/~cwant/pymol_wrl/pymol_1tii.jpg
http://bebop.cns.ualberta.ca/~cwant/pymol_wrl/pymol_1tii_print.jpg

Anyways, maybe somebody else will find the patch useful ...

Regards,
Chris


-- 
  ____________________________________________________________________
( Chris Want                                                         )
( Research Computing Support                                         )
( Academic Information and Communication Technologies (AICT)         )
( University of Alberta                                              )
( Tel: 1-780-492-9418                                                )
  --------------------------------------------------------------------

Hi all,

Is there any way good way in pymol of displaying a slice through a
surface and block colouring the 'inner' face of the surface.=20
Basically, I would like to generate a figure that looks like part (b)
of http://www.nature.com/nature/journal/v432/n7014/fig_tab/nature02988_F3.h=
tml
using pymol.  I have tried playing with the lighting models and
backpace culling (a-la set ambient=3D0; set direct=3D0.7; set reflect=3D0.0=
;
set backface_cull=3D0) but they are not quite what I am after.

Can anyone recommend a good way to achieve this effect?

Thanks,

Stephen

--
Stephen Graham
Crystallography Group
School of Molecular and Microbial Biosciences
University of Sydney

 hii,=0A=0AIam trying to run the script "show NMR constraints" after loadin=
g pdb on the pymol screen. but iam not getting any output. i have tried to =
put 'fname'for upl both within the script and also in the command line. Is =
there any specific format for Upl too that it will read.please guide me how=
 to run this script.=0AThanks in advance=0Abest regards=0Aanjali=0A=0A

 hii,=0A=0AIam trying to run the script "show NMR constraints" after loadin=
g pdb on the pymol screen. but iam not getting any output. i have tried to =
put 'fname'for upl both within the script and also in the command line. Is =
there any specific format for Upl too that it will read.please guide me how=
 to run this script.=0AThanks in advance=0Abest regards=0Aanjali=0A=0A

Dear All,
	I am sure that around 3 months ago I found a command that would  
allow the menu bar in pymol to be seen and used while viewing a  
session in stereo on a geowall.  However, try as I might I cannot  
find the command now, any ideas?  Many thanks in advance, Matt.



Matthew Bowler
MRC Dunn Human Nutrition Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge CB2 2XY
Tel: 0044 (0) 1223 252826
Fax: 0044 (0) 1223 252825

Hi Balaji,

In addition you can try the strategy I proposed earlier. Split your scene
into separate objects and exdport them to povray one at a time (by turning
all other objects off). In this way, you'll keep pymol from rendering the
whole scene at once, which can lead to memory problems. Subsequently, you
take one of the output .pov files and add an #include statement for each
.inc file generated, thus combining them to a single povray scene. And then
you pray that povray will be able to manage. With 1 or 2 Gb of ram and a
good cpu you might get away with a large scene, though it may still take a
while to render.

Tsjerk

On 1/25/06, Warren DeLano <wa...@de...> wrote:
>
> Balaji,
>
> One thing you might try is reducing "hash_max" to a smaller number -- 80
> or even 50.  This will use less RAM but cause rendering to take much
> much longer.
>
> 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
> > Bhyravbhatla, Balaji
> > Sent: Wednesday, January 25, 2006 9:50 AM
> > To: Tsjerk Wassenaar
> > Cc: pym...@li...
> > Subject: RE: [PyMOL] getting pov-ray temp files
> >
> > Thanks Tsjerk,
> >
> > I still have the same issue of PyMOL aborting on me:
> >
> >
> >
> > RayRenderPovRay: processed 2956434 graphics primitives.
> >
> > VLAExpand-ERR: realloc failed.
> >
> > ****EEK! PyMOL just ran out of memory and crashed
> >
> >
> >
> > /usr/local/pymol/pymol.com: line 14: 3812 Aborted
> >
> >
> >
> >
> >
> > So I guess I really need to look for larger resources
> > (hardware) meanwhile is it possible to use PyMOL on a command
> > line and have it write out the output files? What I had in
> > mind was to install PyMOL on our cluster (Opteron based) that
> > has 8GB RAM on the node and submit it without the invocation
> > of the GUI? The cluster does only computations and no
> > graphics as most clusters are. Will it work?
> >
> >
> >
> > Thanks
> >
> >
> >
> > Balaji
> >
> >
> >
> > ________________________________
> >
> > From: Tsjerk Wassenaar [mailto:ts...@gm...]
> > Sent: Tuesday, January 24, 2006 3:41 PM
> > To: Bhyravbhatla, Balaji
> > Cc: pym...@li...
> > Subject: Re: [PyMOL] getting pov-ray temp files
> >
> >
> >
> >
> > Hi Balaji,
> >
> > The temporary povray file is written to the working
> > directory. However, you may want to use the attached script
> > instead. This will write your scene in two parts, a .pov file
> > containing all meta data, such as the lights, camera and
> > #defaults, and an include file (.inc) which contains the
> > structure. In this way you have maximum control over your
> > scene without having to edit a huge povray file. You may even
> > want to consider splitting your scene up in separate parts
> > (taken from the same perspective), which you combine in a
> > global .pov file using #include statements. This will give
> > even more control with regards to modifications to the scene.
> >
> > The magic word in pymol (after run make_pov.py) is make_pov
> >
> > NB. the .pov file contains a commented statement with regards
> > to a povray script, which allows transforming scenes and
> > objects from model space to camera space and vice versa. If
> > you want, you can get a copy of that script.
> >
> > Good luck!
> >
> > Tsjerk
> >
> > On 1/24/06, Bhyravbhatla, Balaji
> > <Bal...@um... > wrote:
> >
> > Hello All,
> > I am trying to render a large mega Dalton complex and can get
> > it up on the screen but rendering it causes a crash because
> > of memory issues (I have 1Gb on the system and tried on a 2Gb
> > system also). So what I would like is to get the temp pov ray
> > files that Pymol is writing out and use those with PoVRAY.
> > I am unable to find the location of those files. Can you
> > please point me to where they are written?
> >
> > If anyone also has ideas on how to get a decent publication
> > quality output for a complex (think in terms of viruses) that
> > would be helpful.
> > I do have a session file saved with my views.
> >
> > Thanks
> >
> > Balaji
> >
> >
> >
> > -------------------------------------------------------
> > 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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> > 42
> > <" rel="nofollow">http://sel.as-us.falkag.net/sel?cmdlnk&kid%103432&bid#0486&dat=121642>
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> >
> > --
> >
> > 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
> >
> >
>



--

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

HI everyone
I have been able to show electrostatics from APBS by loading the .dx map
using a pml script. However, I would really like to display it on the
surface similar to the apbs plugin option which says "color by potential
on solvent accessible surface" in the visualization menu. Does anyone
know how to do this using a pml script?
Actually, when I use this the potentials on the surface look a lot
smoother. I was also wondering, which representation is best.
Thanks
MIke
--=20
Mike Osborne
Universit=C3=A9 de Montr=C3=A9al
Montreal, Quebec, H3T 1J4

Hi,

I came across a possible (and maybe debatable) problem
with RNA cartoons:

With default settings (i.e. cartoon_nucleic_acid_mode
= 0, so the ribbon goes through P's), the "rungs" or
sticks in the ladder representation don't always
intersect with the backbone ribbon. In other words,
sometimes the ladder sticks are floating in space.
This is exacerbated in highly kinked areas of the
backbone and fixed with cartoon_nucleic_acid_mode = 1
(ribbon through C3').

To be correct, I imagine the algorithm for drawing the
ladder should be different for each mode. Is there an
easy fix (keeping cartoon_nucleic_acid_mode = 0)? 

By the way, I'm using the latest Linux beta build
(0.99-37).

Thanks much,

Leven


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

Thanks Tsjerk,

I still have the same issue of PyMOL aborting on me:

=20

RayRenderPovRay: processed 2956434 graphics primitives.

VLAExpand-ERR: realloc failed.

****EEK! PyMOL just ran out of memory and crashed

=20

/usr/local/pymol/pymol.com: line 14: 3812 Aborted

=20

=20

So I guess I really need to look for larger resources (hardware)
meanwhile is it possible to use PyMOL on a command line and have it
write out the output files? What I had in mind was to install PyMOL on
our cluster (Opteron based) that has 8GB RAM on the node and submit it
without the invocation of the GUI? The cluster does only computations
and no graphics as most clusters are. Will it work?

=20

Thanks

=20

Balaji

=20

________________________________

From: Tsjerk Wassenaar [mailto:ts...@gm...]=20
Sent: Tuesday, January 24, 2006 3:41 PM
To: Bhyravbhatla, Balaji
Cc: pym...@li...
Subject: Re: [PyMOL] getting pov-ray temp files

=20


Hi Balaji,

The temporary povray file is written to the working directory. However,
you may want to use the attached script instead. This will write your
scene in two parts, a .pov file containing all meta data, such as the
lights, camera and #defaults, and an include file (.inc) which contains
the structure. In this way you have maximum control over your scene
without having to edit a huge povray file. You may even want to consider
splitting your scene up in separate parts (taken from the same
perspective), which you combine in a global .pov file using #include
statements. This will give even more control with regards to
modifications to the scene.=20

The magic word in pymol (after run make_pov.py) is make_pov

NB. the .pov file contains a commented statement with regards to a
povray script, which allows transforming scenes and objects from model
space to camera space and vice versa. If you want, you can get a copy of
that script.=20

Good luck!

Tsjerk

On 1/24/06, Bhyravbhatla, Balaji <Bal...@um... >
wrote:

Hello All,
I am trying to render a large mega Dalton complex and can get it up on=20
the screen but rendering it causes a crash because of memory issues (I
have 1Gb on the system and tried on a 2Gb system also). So what I would
like is to get the temp pov ray files that Pymol is writing out and use=20
those with PoVRAY.
I am unable to find the location of those files. Can you please point me
to where they are written?

If anyone also has ideas on how to get a decent publication quality
output for a complex (think in terms of viruses) that would be helpful.=20
I do have a session file saved with my views.

Thanks

Balaji



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--=20

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

# make_pov.py                                                                                       
# Do "run make_pov.py" from within pymol and then execute the script                                
# with "make_pov('povray.inp')" to create the povray.inp file.                                      
#                                                                                                   

from pymol import cmd

def make_pov(file, meta=True):
	f1, f2 = file, file[:-4] + '.inc'

        (header,data) = cmd.get_povray()
        povfile = open(f1,'w')
	if meta: povfile.write(header)
	povview = cmd.get_view()

	povfile.write("""\n
// Uncomment the following lines if you have the pymolmacro.inc include file and want to use it.
/*
#include \"pymolmacro.inc\"
PYMOL_VIEW( %10.5f, %10.5f, %10.5f,
            %10.5f, %10.5f, %10.5f,
	    %10.5f, %10.5f, %10.5f,
	    %10.5f, %10.5f, %10.5f,
	    %10.5f, %10.5f, %10.5f,
	    %10.5f, %10.5f, %10.5f )
*/

""" % povview)
	povfile.write('#include "%s"\n\n' % f2)
	povfile.close()
	povfile = open(f2,'w')
        povfile.write(data)
        povfile.close()

cmd.extend('make_pov',make_pov)

Hello All,
I am trying to render a large mega Dalton complex and can get it up on
the screen but rendering it causes a crash because of memory issues (I
have 1Gb on the system and tried on a 2Gb system also). So what I would
like is to get the temp pov ray files that Pymol is writing out and use
those with PoVRAY.
I am unable to find the location of those files. Can you please point me
to where they are written?

If anyone also has ideas on how to get a decent publication quality
output for a complex (think in terms of viruses) that would be helpful.
I do have a session file saved with my views.

Thanks

Balaji

I think I have found two problems with pyMOl that might require a fix:

1) I experience sporadic crashes of pyMOL on two Windows XP Pro machines =
(more I have not tested): AMD Athlon-A 1.1 GHz (TBird), ASUS A7V =
mainboard, Leadtek A280 graphics board (Geforce 4), 768 MB RAM and on my =
Fujitsu-Siemens Notebook Amilo A series, AMD Athlon-64 3000+ =
(Clawhammer), ATI Radeon 9700+, 512 MB RAM. The program sometimes simply =
shuts down after loading a PDB file or after some manipulations of =
files. I do not see any reason for that. I previously also had the same =
problem on the same machines with the stable release client pyMOL 0.98.

2) Another problem that seems new with version 0.99beta31 is that =
selections disappear as soon as the measurement wizard is activated. I =
mean, the selection is no longer seen in the right-hand-side window =
while the corresponding atoms remain unchanged incl. all settings =
applied to them.

I do not know whether this is important. Although sometimes a bit =
annoying, I can live with this. ;-)

Michael.

- - - - - - - - - -
Michael H.W. Weber
Philipps-Universit=E4t Marburg
Germany

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

- - - - - - - - - -
This e-mail was scanned for potential virus contamination.

Paul,

PyMOL generally shows all sides of an exposed atom, but perhaps you
could load both the GOLD output and the original structure.

You could then only show the surface on the atoms in the original
structure with corresponding atoms in the gold output as follows:

load orig.pdb
load gold.pdb

then=20

show surface, orig in gold

or

show surface, orig like gold

That might produce something close to what you want.  Note that:

"in" matches chains, segments, residue names, residue ids, and atom
names.

"like" just matches residue ids and atom names.

You can use

alter all, segi=3D''
alter all, chain=3D''

to clear out the segment and/or chain IDs before using "in" to
selectively reduce its stringency.

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
> Paul Wilhelm Elsinghorst
> Sent: Friday, January 20, 2006 11:33 PM
> To: pym...@li...
> Subject: [PyMOL] Surface of cavity
>=20
> Hi,
>=20
>=20
> a little question regarding cavity surfaces :-)
>=20
>=20
> I have a set of active atoms (GOLD output) that surround a=20
> cavity. Now I want to dipslay the surface only for the cavity=20
> wall, not on the outside.
>=20
>=20
> Any ideas?
>=20
>=20
> Paul=20
>=20

Hi Paul,

> I have a set of active atoms (GOLD output) that surround a cavity. Now I
> want to dipslay the surface only for the cavity wall, not on the
> outside.

try this: show surface for the whole protein and then hide surface for 
"not the active residues" - something like this:

####
from pymol import cmd
from pymol import stored

# load your protein and the active atoms as GOLD output
cmd.load("protein.pdb", "prot")
cmd.load("active_atoms.pdb", "act_res")

# create a list of the activ residue-id's stored.act_res=[]
cmd.iterate("act_res", "stored.act_res.append(resi)")

# create selection of the actives
cmd.select("act_res","resi %s" %stored.act_res[0])
for i in stored.act_res:
	cmd.select("act_res","act_res or resi %s" %i)

# create selection of the "non-actives"
cmd.select("not_act_res", "prot and not act_res")

# show surface
cmd.show("surface", "prot")
cmd.hide("surface", "not_act_res" )

cmd.delete("not_act_res")
####



Cheers,
Betty

Hi,
you may try to use caver:

http://viper.chemi.muni.cz/caver/concept.php

or castp

http://cast.engr.uic.edu/cast/oldindex.php

regards

andrea

2006/1/21, Paul Wilhelm Elsinghorst <pa...@un...>:
>  Hi,
>
>
>  a little question regarding cavity surfaces :-)
>
>
>  I have a set of active atoms (GOLD output) that surround a cavity. Now I
> want to dipslay the surface only for the cavity wall, not on the outside.
>
>
>  Any ideas?
>
>
>  Paul
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.0 (GNU/Linux)
>
> iD8DBQBD0eKigFneuXxhreARAnFLAJ9Z3o6zMiphEzzKpVzMXtdXxh6dBwCeMp9u
> ZIoavXwL2DE+hMObJhTiD8o=3D
> =3DuZkv
> -----END PGP SIGNATURE-----
>
>
>


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

Hi,


a little question regarding cavity surfaces :-)


I have a set of active atoms (GOLD output) that surround a cavity. Now I
want to dipslay the surface only for the cavity wall, not on the
outside.


Any ideas?


Paul

Hi-
I'd second this; my brain doesn't do well keeping track of whether I'm,
for example, in maximum or reasonable performance mode.=20
David

-----------------------------=20
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016=20
Tel: 336 713-4194
Fax: 336 716-7671=20
email:  dh...@wf...
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Mark A
Saper
Sent: Friday, January 20, 2006 3:01 PM
To: Pymol
Subject: [PyMOL] GUI

Hi Warren,

Why can't we have little check marks in the main menu that indicate the
current setting?
For example, Setting>Rendering>Antialias   gets a check, but =20
selecting Setting>Rendering>Shadows>None doesn't give a check (as do any
of the other rendering options).

Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry Biophysics Research
Division, University of Michigan Chemistry Building Room 3040 930 N
University Ave Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html




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121642
_______________________________________________
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Hi Warren,

Why can't we have little check marks in the main menu that indicate  
the current setting?
For example, Setting>Rendering>Antialias   gets a check, but  
selecting Setting>Rendering>Shadows>None doesn't give a check (as do  
any of the other rendering options).

Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html