pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] disulfide bonds

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

Hi,
=20
I apologize because I suspect this question has been asked before, but I
don't see it in the FAQ, Wiki, and can't figure how to efficiently
search the maillist archive.
=20
How does one draw a disulfide bond?  My preference is the classical
'thunderbolt', from CA-S-S-CA atoms.
=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] labeling using PyMOL

[Isabel Garcia-S. <isa...@ib...>]

Hello,
	After being able to create labels in stereo  (thanks a lot, =
Warren,=20
for your quick answer!) I have another problem now: I would like to=20
know if it is possible to label using  "symbol" as a font (e.g. to=20
indicate helices with an "alpha" and beta-strands with a "beta").

Thanks to everyone,

Isabel


Isabel Garcia-Saez     PhD
Institut de Biologie Structurale Jean-Pierre Ebel
Laboratoire de Moteurs Mol=E9culaires
41, rue Jules Horowitz
F-38027 Grenoble CEDEX 1
France
tel.: 00-33-438 789262
FAX:  00-33-438 785494
e-mail: isa...@ib...
www.ibs.fr

[PyMOL] Re: building peptides (gilleain torrance)

[Alan <ala...@gm...>]

Thx Gilleain!

Cheers,
Alan

> Message: 1
> Date: Wed, 15 Mar 2006 09:37:55 +0000
> From: "gilleain torrance" <gil...@gm...>
> To: Pymol <pym...@li...>
> Subject: [PyMOL] Re: building peptides
>
> Hi,
>
> The wiki has a page on this:
>
> http://www.pymolwiki.org/index.php/Peptide_Sequence
>
> except it doesn't mention the zwitterion details. There's a link to
> Robert Campbell's scripts to do this sort of thing, so maybe the
> answer is there.
>
> As for for loops, this is best in a full python script (run with
> "run"). In fact, your pseudocode is almost valid python. More like:
>
> residues =3D3D ("A", "C", "D", "E", "F", "G", "H"  etc)
>
> for residue in residues:
>      for i in range(3):
>         cmd._alt(residue.lower())
>      cmd.set_geometry ??
>
> cmd.save(aa.pdb, "all")
>
> Unfortunately, I'm not sure the set_geometry command is right.
>
> gilleain torrance
>
--
Alan Wilter S. da Silva, D.Sc. - Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

Re: : [PyMOL] Surface Vertex Coordinates

[Tim F. <fe...@st...>]

On Wed, Mar 15, 2006 at 09:01:19AM -0800, Benjamin Hitz wrote:
> >
> >I am interested in the coordinates of the vertices of the mesh
> >representation of the molecular surface. Is there any method to read
> >them out?
> >
> >Thanks
> >
> 
> Me too.  With coloring and/or other "property" information as well.
> 

povscript+ will do all of this, in a somewhat-standardized GTS
(gts.sf.net) format that is easy to port to a number of other
programs.

It will also dump surfaces as vertex2 objects in povray.

HTH,
Tim

-- 
---------------------------------------------------------

        Tim Fenn
        fe...@st...
        Stanford University, School of Medicine
        James H. Clark Center
        318 Campus Drive, Room E300
        Stanford, CA  94305-5432
        Phone:  (650) 736-1714
        FAX:  (650) 736-1961

---------------------------------------------------------

Re: : [PyMOL] Surface Vertex Coordinates

[Laurence P. <Lau...@ic...>]

The Povray intermediate file generated when you do 'ray renderer = 1'  
contains all vertices, normals and colouring information for cartoon  
and surface object types. However you do need to produce a parsing  
script to extract these in to a useful form for importing into other  
programs. Have a look at the front cover of Mol Cell vol 20(4) - I  
generated a cartoon of the protein in PyMol, output it as a povray  
file, and then converted it to VRML using a jiffy produced by Chris  
Richardson, and then used it as an object in the Blender 3D modelling   
package to generate the picture.

Of course it would be a whole lot easier if PyMol output VRML directly   
..... Warren ?????

Laurence Pearl


On 15 Mar 2006, at 17:01, Benjamin Hitz wrote:

>>
>> I am interested in the coordinates of the vertices of the mesh
>> representation of the molecular surface. Is there any method to read
>> them out?
>>
>> Thanks
>>
>
> Me too.  With coloring and/or other "property" information as well.
>
>
>
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
> Consortium
> Stanford University ** hi...@ge...
>
>
>
>
>
> -------------------------------------------------------
> 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
>
------------------------------------------------------------------------ 
--
   Laurence H. Pearl

   Section of Structural Biology, Institute of Cancer Research
   Chester Beatty Laboratories,  237 Fulham Road, London SW3 6JB, UK

   Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443
   FAX   +44-(0)20 7153 5457 : E-Mail Lau...@ic...
------------------------------------------------------------------------ 
--
   " Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin
------------------------------------------------------------------------ 
--

[PyMOL] RE: [ccp4bb]: off-topic: labelling stereo with PyMOL

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

Isabel,

There is a PyMOL-Users mailing list for such questions at =
<http://lists.sourceforge.net/lists/listinfo/pymol-users>

As for making stereo labels, the latest PyMOL release 0.99rc6 =
<http://delsci.com/rel/099> has variable-size, stereo 3D labels that can =
be positioning using the mouse (when in editing mode).

there are 9 different scalable fonts:

   set label_font_id, number

where number is 5 through 14.

The font size can be adjusted

   set label_size, number

where number is the point size (or -number for Angstroms)

The color can be edited

   set label_color, color-name

And to set labels:

   label selection, expression
 =20
e.g.

  label all, name
  label resi 10 , b

or

   label 15/CA, "A Custom Label"

To position labels:

   edit_mode

then ctrl-middle-click-and-drag to position the label in space.

   stereo walleye

and

   ray

to generate a ray-traced stereo pair for publication.

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: own...@dl... [mailto:own...@dl...] On=20
> Behalf Of Isabel Garcia-Saez
> Sent: Wednesday, March 15, 2006 9:11 AM
> To: cc...@dl...
> Subject: [ccp4bb]: off-topic: labelling stereo with PyMOL
>=20
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>=20
>=20
> Hi everyone:
> Sorry for the off-topic subject.
> My problem: I need stereo labels in an stereo figure=20
> generated with PyMOL.
> My question: Is there a way to do that in PyMOL?
>=20
> Thanks,
>=20
> Isabel
>=20
>=20
>=20
> Isabel Garcia-Saez     PhD
> Institut de Biologie Structurale Jean-Pierre Ebel Laboratoire=20
> de Moteurs Mol=E9culaires 41, rue Jules Horowitz
> F-38027 Grenoble CEDEX 1
> France
> tel.: 00-33-438 789262
> FAX:  00-33-438 785494
> e-mail: isa...@ib...
> www.ibs.fr
>=20
>=20
>=20
>=20
>=20
>=20

RE:: [PyMOL] Surface Vertex Coordinates

[Benjamin H. <hi...@ge...>]

>
> I am interested in the coordinates of the vertices of the mesh
> representation of the molecular surface. Is there any method to read
> them out?
>
> Thanks
>

Me too.  With coloring and/or other "property" information as well.



--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hi...@ge...

[PyMOL] Re: building peptides

[gilleain t. <gil...@gm...>]

Hi,

The wiki has a page on this:

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

except it doesn't mention the zwitterion details. There's a link to
Robert Campbell's scripts to do this sort of thing, so maybe the
answer is there.

As for for loops, this is best in a full python script (run with
"run"). In fact, your pseudocode is almost valid python. More like:

residues =3D ("A", "C", "D", "E", "F", "G", "H"  etc)

for residue in residues:
     for i in range(3):
        cmd._alt(residue.lower())
     cmd.set_geometry ??

cmd.save(aa.pdb, "all")

Unfortunately, I'm not sure the set_geometry command is right.

gilleain torrance

On 3/14/06, Alan <ala...@gm...> wrote:
> Hello List,
>
> I would like to have any help.
>
> I want to build several 3-peptides, like AAA, FFF, KKK etc. I also
> would like to make them zwitterionics, add chain and save as a PDB
> file.
>
> I know how to do that using the graphic interface, but I what I am
> looking for is a way to do it via pymol script.
>
> Is is possible? May anyone give a idea of how create the 3-peptides
> and put right N- and C- terminals?
>
> BTW, a loop with "for" is possible in pymol scripting?
>
> Summarising, I am trying a script like this:
>
> -----------------------
> residue =3D ( ALA, ARG, etc)
>
> for res in residue:
>   'create peptide res-res-res'
>   'set NH3 in res 1 and COO- in res 3'
>
> save aa.pdb, all
> -----------------------
>
> Thanks a lot for any help.
>
> Cheers,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live webc=
ast
> and join the prime developer group breaking into this new coding territor=
y!
> http://sel.as-us.falkag.net/sel?cmdlnk&kid=110944&bid$1720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

RE: [PyMOL] PyMOL in CAVE

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

Just as an FYI:

DeLano Scientific LLC has no plans to support a CAVE-enabled version of
PyMOL.  However, a 3rd-party could perhaps create one using the
open-source code.

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
> Tsjerk Wassenaar
> Sent: Tuesday, March 14, 2006 7:09 AM
> To: Joe Zhou
> Cc: pym...@li...
> Subject: Re: [PyMOL] PyMOL in CAVE
>=20
>=20
> Hi Joe Zhou,
>=20
> Wow, four times CAVE in four lines of text :) I'm not=20
> completely sure, but I thought we had (have) a CAVEable=20
> version of Pymol here. You could contact Frans van Hoesel (=20
> F.H.J.van.Hoesel removing-the-usual-junk at rug.nl ). He will=20
> surely know.
>=20
> Cheers,
>=20
> Tsjerk
>=20
> On 3/13/06, Joe Zhou <jz...@de...> wrote:
> > Dear PyMOLers,
> >=20
> > Does anybody work on porting PyMOL to CAVE? Any plan or=20
> status for that?
> > VMD has a CAVE-enabled version, our clients would love to=20
> run PyMOL in=20
> > our CAVE. I am willing to do some porting and testing in the CAVE.
> >=20
> > Best regards,
> >=20
> > Joe Zhou
> >=20
> > Delta Search Labs
> > 400 Technology Square,
> > Cambridge, MA 02139
> > http://www.deltasearchlabs.com/
> >=20

[PyMOL] building peptides

[Alan <ala...@gm...>]

Hello List,

I would like to have any help.

I want to build several 3-peptides, like AAA, FFF, KKK etc. I also
would like to make them zwitterionics, add chain and save as a PDB
file.

I know how to do that using the graphic interface, but I what I am
looking for is a way to do it via pymol script.

Is is possible? May anyone give a idea of how create the 3-peptides
and put right N- and C- terminals?

BTW, a loop with "for" is possible in pymol scripting?

Summarising, I am trying a script like this:

-----------------------
residue =3D ( ALA, ARG, etc)

for res in residue:
  'create peptide res-res-res'
  'set NH3 in res 1 and COO- in res 3'

save aa.pdb, all
-----------------------

Thanks a lot for any help.

Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

Re: [PyMOL] PyMOL in CAVE

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

Hi Joe Zhou,

Wow, four times CAVE in four lines of text :)
I'm not completely sure, but I thought we had (have) a CAVEable version of
Pymol here. You could contact Frans van Hoesel (
F.H.J.van.Hoeselremoving-the-usual-junk at
rug.nl ). He will surely know.

Cheers,

Tsjerk

On 3/13/06, Joe Zhou <jz...@de...> wrote:
> Dear PyMOLers,
>
> Does anybody work on porting PyMOL to CAVE? Any plan or status for that?
> VMD has a CAVE-enabled version, our clients would love to run
> PyMOL in our CAVE. I am willing to do some porting and testing in
> the CAVE.
>
> Best regards,
>
> Joe Zhou
>
> Delta Search Labs
> 400 Technology Square,
> Cambridge, MA 02139
> http://www.deltasearchlabs.com/
>
>
>
> -------------------------------------------------------
> 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=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> _______________________________________________
> 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

[PyMOL] Surface Vertex Coordinates

[Ewgenij P. <pro...@st...>]

Hello everybody,

I am interested in the coordinates of the vertices of the mesh 
representation of the molecular surface. Is there any method to read 
them out?

Thanks

Ewgenij

[PyMOL] PyMOL in CAVE

[Joe Z. <jz...@de...>]

Dear PyMOLers,

Does anybody work on porting PyMOL to CAVE? Any plan or status for that?
VMD has a CAVE-enabled version, our clients would love to run
PyMOL in our CAVE. I am willing to do some porting and testing in
the CAVE.

Best regards,

Joe Zhou

Delta Search Labs
400 Technology Square,
Cambridge, MA 02139
http://www.deltasearchlabs.com/

[PyMOL] Re: OSX quad buffered stereo possible on older G5 with GeForce FX5200!

[Dan W. <da...@ch...>]

Dear All,

after reading the post below, for a new quad buffered stereo plugin =20
for OSIRIX,
I though I would try it out on my older apple G5 with  GeForce =20
FX5200, just for a giggle, not expecting it to work
on this older graphics card.  OSX 10.4.5

As far as I am aware, the only card apple recommends for quad =20
buffered stereo is
the new quadro card that comes in the new high end G5 quad?

However, to my amazement, after plugging in my Stereographics Enabler =20=

between the VGA out of the mac graphics card and the monitor cable, =20
and hooking up the Stereographics E2 emitter box to that
(stolen off my linux box which uses a quadro XGL 980. I had to plug =20
the enabler PS2 power supply cable in to an adjacent SGI indigo2 =20
keyboard port, how ironic!)
when I turned on the plugin to use quad buffered stereo (force blue =20
line checked), the emitter box light up,
and yes, there was a quad buffered stereo image on the screen (an old =20=

21 inch SGI CRT monitor)

I can get 1280x1024 at 90Hz (a bit flickery of course)
and
1280x960 at 96 Hz (flicker not too bad)
(and an unuseable but flicker free 1280x492 at 120 Hz)

Works with Pymol and Osirix!!! Maybe it will work with O, VMD and =20
others too....
(now I just need to fix our software www.BioImageXD.org
to make it work properly too....)

I thought I needed the special  Mac version of the emitter box and =20
enabler   from stereographics,
but apparently the normal windows/linux one works with this =20
GeForceFX5200 with blue line quad buffered stereo.

cheers  go out to Jonathon Mah for inspiting me to try it!!!

Dan


Begin forwarded message:

> Begin forwarded message:
>
>> I'm Jonathon Mah, a student studying third year Computer Systems
>> Engineering at the University of Adelaide -- and also a Cocoa nut.
>> Over the (Australian) summer break I've been working at SAPAC
>> <http://www.sapac.edu.au/>. As you may remember, back in last
>> September/October Craig Hill contacted you about stereo support in
>> OsiriX. Specifically, quad-buffered stereo was desired.
>>
>> "Quad-buf... what?"
>> I had no idea what quad-buffered stereo was, either. Quad-buffered
>> is where you write the left and right images to the graphics card.
>> Since OpenGL uses a front buffer (on-screen) and back buffer (off-
>> screen), adding stereo to these gives you four buffers (front-left,
>> front-right, back-left, back-right). Thus, "quad-buffered". Once
>> the graphics card has the left and right images, it can display
>> them for shutter glasses, output them to different monitors, and so
>> on, depending on the card's driver.
>>
>> I was able to add support for this to OsiriX. VTK already provides
>> some support for this, but it doesn't work as-is. Since Objective-C
>> is so nicely dynamic, I was able to implement this as a plug-in
>> (although it should eventually be merged into the main app). I've
>> also added support for exporting stereo movies (left and right
>> separately). We've been using it for a couple of months now, so I
>> think the major problems have all been fixed. Stereo rendering
>> looks really very nice!
>>
>> You'll find the source and binary at <http://www.JonathonMah.com/
>> temp/QuadBufferedStereo.zip>. Please put it up on the OsiriX plug-
>> ins page. It'd be great if you could copy it to your own server, as
>> that address will only be temporary. There's a ReadMe file included
>> which should answer most questions. It compiles for Intel too, but
>> I don't have a machine here to test it on -- I assume it works. :)
>> The quad-buffered mode will show the left and right images
>> flickering back and forth, which is necessary for shutter glasses.
>> I also put an interlaced option in there, "because I can".

Dr. Daniel James White BSc. (Hons.) PhD
Bioimaging Coordinator
Nanoscience Centre and Department of Biological and Environmental =20
Sciences
Division of Molecular Recognition
Ambiotica C242
PO Box 35
University of Jyv=E4skyl=E4
Jyv=E4skyl=E4
FIN 40014
Finland

+358 14 260 4183 (work)
+358 468102840 (mobile)
http://www.bioimagexd.org
http://www.chalkie.org.uk
da...@ch...
wh...@cc...

Re: [PyMOL] manipulate standard error ?

[Sebastien M. <seb...@ig...>]

> Hi,
>=20
> If you are getting unwanted PyMOL standard errors you can turn them off=
=20
> using the cmd.feedback() commands:
>=20
> cmd.feedback('disable', 'selector', 'everything')
> cmd.feedback('disable', 'executive', 'everything')
>=20
>=20
> to turn them on again:
>=20
> cmd.feedback('enable', 'selector', 'everything')
> cmd.feedback('enable', 'executive', 'everything')
>=20
> cmd.feedback('disable', 'all', 'everything') will do exactly as it says=
=20
> on the tin.
>=20
> otherwise maybe use a Python try:/except: clause?
>=20
> eg:
>=20
> try:
>     Instructions to load the map (cmd.load(map)?)
> except:
>     raise IOError('')
>=20
>=20
> Jules

It's this kind of manipulation I want.
Thanks

>>> Hello,
>>>
>>> yes. maybe. if you are talking about printing to standard error, then=
 :
>>>
>>>    import sys
>>>    sys.stderr.write("hello, stderr!")
>>>
>>> will do it.
>>>
>>> if, on the other hand, you mean something more complicated to do with=
=20
>>> manipulating the shell ("redirection"...?) than I don't know, sorry.
>>>
>>> gilleain torrance
>>
>>
>> I would like to change the current path for stderr to /dev/null by=20
>> example.
>>
>> I have a plugin which creates a legend box from a fake (empty) apdb=20
>> map. Instruction, which loads the map, sends an error message and I=20
>> would like to hide it.
>>
>> How can I do ?
>>
>> Thanks
>>
>>>
>>>     Hello,
>>>     I would like to know if there is a way to manipulate standard err=
or
>>>     redirection into pymol scripting language ?
>>>
>>>     Thanks

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS UPR 2589
163 Avenue de Luminy, case 934
13288 Marseille cedex 9 (France)

Re: [PyMOL] manipulate standard error ?

[Sebastien M. <seb...@ig...>]

Lind, Kenneth wrote:
> Hi Sebastien,
>=20
> This sounds like a strange thing to do.  First, I would ask why are you=
 getting an error?  Rather than hiding the error, you should fix it...
>=20
> If that is not possible, a typical python way of doing this is to use a=
 try/except wrapping.  for example:
>=20
> try:
>     print 1/0
> except ZeroDivisionError:
>     pass
>=20
> If you *really* want to manipulate sys.stderr, you can do it.  Somethin=
g like:
>=20
> errF =3D open("stdout.err", "w")
> sys.stderr =3D errF
>=20
> Hope that helps.  Best,
> Ken

It's this kind of manipulation I want.
Thanks

>>Hello,
>>
>>yes. maybe. if you are talking about printing to standard error, then :
>>
>>   import sys
>>   sys.stderr.write("hello, stderr!")
>>
>>will do it.
>>
>>if, on the other hand, you mean something more complicated to do with=20
>>manipulating the shell ("redirection"...?) than I don't know, sorry.
>>
>>gilleain torrance
>=20
>=20
> I would like to change the current path for stderr to /dev/null by exam=
ple.
>=20
> I have a plugin which creates a legend box from a fake (empty) apdb map=
.=20
> Instruction, which loads the map, sends an error message and I would=20
> like to hide it.
>=20
> How can I do ?
>=20
> Thanks
>=20
>=20
>>    Hello,
>>    I would like to know if there is a way to manipulate standard error
>>    redirection into pymol scripting language ?
>>
>>    Thanks

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS UPR 2589
163 Avenue de Luminy, case 934
13288 Marseille cedex 9 (France)

[PyMOL] cmd.get_povray stereo segfault

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

Hi Warren,

First of all, I really love the stereoview rendering in Pymol 0.99. Still,
I'd like some more control on the lighting and the surfaces and would like
to output to povray. However, cmd.get_povray first processes the stereo
scene, building the primitives for each panel (as desired), but then it
segfaults. Maybe I shouldn't be wanting to get my povray stereo scene like
this, but a segfault is never a neat way to quit an application. In
addition, you may want to consider to allow cmd.get_povray to process both
panels properly, which essentially means that one gets two povray headers o=
r
two camera definitions. Or actually, since Pymol uses a camera space..., it
does mean two complete scenes.

Just for the record, I'm running Pymol 0.99rc1 with Suse Linux 10.0.

Cheers,

Tsjerk

--

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

Re: [PyMOL] manipulate standard error ?

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

>
> I would like to change the current path for stderr to /dev/null by
> example.
>
> I have a plugin which creates a legend box from a fake (empty) apdb map.
> Instruction, which loads the map, sends an error message and I would
> like to hide it.
>
> How can I do ?

Create a new script (pymol.bash) containing these lines:

#!/usr/bin/env bash
pymol.com 2>/dev/null

This could probably be done within pymol.com itself as well, but someone
else will have to point out how to do that (aka I don't know how).

As a side question, why have a csh script with a .com extension?

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] RE: selecting surface residues only

[Aaron N. <aar...@gm...>]

Jean,

I have been playing around with the Caver plugin to map concave areas on th=
e
molecule.  The program makes a mesh map of the "tunnel" that you can then
use as an object to select nearby atoms that tend to be on or near the
surface.

If anyone knows an easier way, please let us know.

Aaron New

Re: [PyMOL] manipulate standard error ?

[Jules J. <jo...@he...>]

Hi,

If you are getting unwanted PyMOL standard errors you can turn them off 
using the cmd.feedback() commands:

cmd.feedback('disable', 'selector', 'everything')
cmd.feedback('disable', 'executive', 'everything')


to turn them on again:

cmd.feedback('enable', 'selector', 'everything')
cmd.feedback('enable', 'executive', 'everything')

cmd.feedback('disable', 'all', 'everything') will do exactly as it says on 
the tin.

otherwise maybe use a Python try:/except: clause?

eg:

try:
     Instructions to load the map (cmd.load(map)?)
except:
     raise IOError('')


Jules

Sebastien Moretti wrote:
>> Hello,
>>
>> yes. maybe. if you are talking about printing to standard error, then :
>>
>>    import sys
>>    sys.stderr.write("hello, stderr!")
>>
>> will do it.
>>
>> if, on the other hand, you mean something more complicated to do with 
>> manipulating the shell ("redirection"...?) than I don't know, sorry.
>>
>> gilleain torrance
> 
> I would like to change the current path for stderr to /dev/null by example.
> 
> I have a plugin which creates a legend box from a fake (empty) apdb map. 
> Instruction, which loads the map, sends an error message and I would 
> like to hide it.
> 
> How can I do ?
> 
> Thanks
> 
>>
>>     Hello,
>>     I would like to know if there is a way to manipulate standard error
>>     redirection into pymol scripting language ?
>>
>>     Thanks
> 

Re: [PyMOL] manipulate standard error ?

[Sebastien M. <seb...@ig...>]

> Hello,
>=20
> yes. maybe. if you are talking about printing to standard error, then :
>=20
>    import sys
>    sys.stderr.write("hello, stderr!")
>=20
> will do it.
>=20
> if, on the other hand, you mean something more complicated to do with=20
> manipulating the shell ("redirection"...?) than I don't know, sorry.
>=20
> gilleain torrance

I would like to change the current path for stderr to /dev/null by exampl=
e.

I have a plugin which creates a legend box from a fake (empty) apdb map.=20
Instruction, which loads the map, sends an error message and I would=20
like to hide it.

How can I do ?

Thanks

>=20
>     Hello,
>     I would like to know if there is a way to manipulate standard error
>     redirection into pymol scripting language ?
>=20
>     Thanks

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS UPR 2589
163 Avenue de Luminy, case 934
13288 Marseille cedex 9 (France)

Re: [PyMOL] manipulate standard error ?

[gilleain t. <gil...@gm...>]

Hello,

yes. maybe. if you are talking about printing to standard error, then :

   import sys
   sys.stderr.write("hello, stderr!")

will do it.

if, on the other hand, you mean something more complicated to do with
manipulating the shell ("redirection"...?) than I don't know, sorry.

gilleain torrance

On 3/9/06, Sebastien Moretti <seb...@ig...> wrote:
>
> Hello,
> I would like to know if there is a way to manipulate standard error
> redirection into pymol scripting language ?
>
> Thanks
>
> --
> S=E9bastien Moretti
> http://www.igs.cnrs-mrs.fr/
> CNRS - IGS UPR 2589
> 163 Avenue de Luminy, case 934
> 13288 Marseille cedex 9 (France)
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting
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> that extends applications into web and mobile media. Attend the live
> webcast
> and join the prime developer group breaking into this new coding
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
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>

[PyMOL] manipulate standard error ?

[Sebastien M. <seb...@ig...>]

Hello,
I would like to know if there is a way to manipulate standard error=20
redirection into pymol scripting language ?

Thanks

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS UPR 2589
163 Avenue de Luminy, case 934
13288 Marseille cedex 9 (France)

[PyMOL] red - blue stereo mode

[bgbg b. <bg...@gm...>]

Is it possible to add the possibilty to make PyMol's stereo mode work with
old fasioned red/bkue(or green or whatever) glasses? Something like this:
http://www.3dchem.com/stereoglasses.asp

[PyMOL] selecting surface residues only

[jean <je...@sc...>]

Hi everybody

Is there an easy way to select only surface residues in Pymol?

I want to generate an image with labels on the surface residues only.
  I've read all the advice on this list on how to make pretty labels, but
in order to do that I first need to identify&select all the surface
residues.  The best solutions I've come up with so far are:

Either  label everything and make the surface transparent, then take
notes of which residues are on the surface - very messy with lots of labels

Or turn off the labels, show lines under the transparent surface and
just mouse-click on each residue..

Both of these require lots of time and some careful adjustment of the
clipping plane if I want to be able to see anything..

If there's a quicker way, I'd love to know about it!

Thanks in advance

Jean