pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Disulfide Bonds

[Warren L. D. <wa...@su...>]

On Fri, 20 Sep 2002, Kaushik Raha wrote:

> Warren,
>
> Thanks for the h-bond tip. A related question, I was wondering if PyMOL
> can protonate  ligands on its own. In other words can it perceive  the
> atom-type. I have been trying to integrate a perception algorithm

If your ligands come in with valid valencies and formal charges, PyMOL's
h_add command can protonate ligands.  (NOTE that there is a minor
technical hiccup with SD-files which are loaded by default as immutable
"discrete" objects.)  Suffice it to say that in order to make changes to
the chemical structure, an object must be loaded with the "discrete" flag
set to zero.

> similar to babel with other programs and would like to do it with PyMOL
> as well. However  I could not find  details/examples on the attach
> command in the manual (I did not look through the code yet, I am a new
> user). So can you please give an example of attach command.

Unfortunately, much of the molecular editing stuff remains to be
documented.  Here's an example sequence, but I'm not sure it will help to
much...as indicated in the manual, this is immature functionality with
some major gaps.  Attach in particular is very limited...

# show valences
set valence=0.05

# load cysteine fragment
fragment cys

# remove hydrogens
remove (hydro)

# edit gamma S
edit cys////sg

# add hydrogen
attach H,1,1

# add planer, trivalent nitrogen onto C terminus
edit cys////C
attach N,3,3

# edit that nitrogen
edit (elem N and neighbor cys////C)

# attach a tetrahedral methyl (note random position)
attach C,4,4

# here's an example of adding a whole residue from the library
edit cys////N
editor.attach_amino_acid("pk1","ace")

# now restore missing hydrogens (note that the names are off...)
h_add

> Well, the reason I wanted the parser was some programs like  AMBER
> (leap) requires different  names for linked cysteines. It would be
> helpful to get this information from the PDB file since it has it. Also
> there is other information in the PDB file which can be useful if
> displayed somewhere on the viewer like sequence etc. In other words a
> hierarchy window similar to the web-lab viewer. Maybe it does  and just
> have not figured out how to make it work it.

Hmm...I can't think of any smart way to use the selection language to get
it off the top of my head.  You can use the alter command to change the
residue names as follows:

alter cys/,name='CYX'

or for specific residues

alter 146+167+156/,name='CYX'

save modified.pdb

but that's not general...

> In any case I think this is a terrific program and although I have just
> started using it I am realizing its potential.

It will take a few years, but I'm hoping that the open-source version
of PyMOL will become a useful and ubiquitous tool for a variety of common
molecular tasks like setting up molecules for Amber, tweaking hydrogens,
or fixing atom names, etc.

Cheers,
Warren

> Kaushik.
>
> On Friday, September 20, 2002, at 05:24 PM, DeLano, Warren wrote:
>
> > Regarding H-bonds. Funny you should ask -- Hans and I just worked out
> > how to do this here at Sunesis...
> >
> > There isn't a built-in function yet (it is coming), but you can show
> > H-bonds between two objects using  atom selections so long as hydrogens
> > are present in both molecules.  If you don't have hydrogens, you can
> > use h_add on the proteins or provide ligands with valence information
> > and then use h_add.
> >
> > Two examples are below.  For clarity, they draw dashes between the
> > heavy atoms and hide the hydrogens.
> >
> > # EXAMPLE 1: Show hydrogen bonds between protein
> > # and docked ligands (which must have hydrogens)
> >
> > load target.pdb,prot
> > load docked_ligs.sdf,lig
> >
> > # add hydrogens to protein
> >
> > h_add prot
> >
> > select don, (elem n,o and (neighbor hydro))
> > select acc, (elem o or (elem n and not (neighbor hydro)))
> > dist HBA, (lig and acc),(prot and don), 3.2
> > dist HBD, (lig and don),(prot and acc), 3.2
> > delete don
> > delete acc
> > hide (hydro)
> >
> > hide labels,HBA
> > hide labels,HBD
> >
> > # EXAMPLE 2
> > # Show hydrogen bonds between two proteins
> >
> > load prot1.pdb
> > load prot2.pdb
> >
> > h_add prot1
> > h_add prot2
> >
> > select don, (elem n,o and (neighbor hydro))
> > select acc, (elem o or (elem n and not (neighbor hydro)))
> > dist HBA, (prot1 and acc),(prot2 and don), 3.2
> > dist HBD, (prot1 and don),(prot2 and acc), 3.2
> > delete don
> > delete acc
> > hide (hydro)
> >
> > hide labels,HBA
> > hide labels,HBD
> >
> > # NOTE: that you could also use this approach between two
> > # non-overlapping selections within a single object.
> >
> > As far as SSBOND records go, no PyMOL doesn't currently parse
> > these...does it need to?
> >
> > Warren
> >
> > --
> > mailto:wa...@su...
> > Warren L. DeLano, Ph.D.
> >
> >> -----Original Message-----
> >> From: Kaushik Raha [mailto:kx...@ps...]
> >> Sent: Friday, September 20, 2002 1:36 PM
> >> To: pym...@li...
> >> Subject: Re: [PyMOL] Disulfide Bonds
> >>
> >>
> >> A similar question: Does PyMOL have a PDB file parser that can read
> >> disulphide linkages from the file and connect the atoms or one has to
> >> explicitly issue bond commands. Also, can PyMOL display
> >> hydrogen bonds
> >> without the user having to write out a list?
> >>
> >> thanks,
> >>
> >> Kaushik Raha.
> >> Penn State University.
> >>
> >> On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote:
> >>
> >>> Alex,
> >>>
> >>> 	If the sulfurs are within disulfide bonding distance,
> >> PyMOL should
> >>> connect them by default.  If this is not happening, please
> >> send me the
> >>> PDB file so I can take a look-see.
> >>>
> >>>       Otherwise, you can use the "bond" command to attach them:
> >>>
> >>> bond 24/sg,26/sg
> >>> bond 56/sb,99/sg
> >>>
> >>> unpick
> >>>
> >>> (unpick will hide the bond baton which gets displayed)
> >>>
> >>> Cheers,
> >>> Warren
> >>>
> >>> --
> >>> mailto:wa...@su...
> >>> Warren L. DeLano, Ph.D.
> >>>
> >>>> -----Original Message-----
> >>>> From: Alex Morla [mailto:al...@ui...]
> >>>> Sent: Friday, September 20, 2002 8:48 AM
> >>>> To: pym...@li...
> >>>> Subject: [PyMOL] Disulfide Bonds
> >>>>
> >>>>
> >>>> Sorry if this is a novice question, but how do I display the
> >>>> disulfide bonds
> >>>> in my models?
> >>>>
> >>>> Thanks, and keep up the great work!!
> >>>>
> >>>> Alex Morla
> >>>> Univ. of Illinois, Rockford.
> >>>>
> >
> >
> > -------------------------------------------------------
> > This sf.net email is sponsored by:ThinkGeek
> > Welcome to geek heaven.
> > http://thinkgeek.com/sf
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Re: [PyMOL] Disulfide Bonds

[Kaushik R. <kx...@ps...>]

Warren,

Thanks for the h-bond tip. A related question, I was wondering if PyMOL 
can protonate  ligands on its own. In other words can it perceive  the 
atom-type. I have been trying to integrate a perception algorithm 
similar to babel with other programs and would like to do it with PyMOL 
as well. However  I could not find  details/examples on the attach 
command in the manual (I did not look through the code yet, I am a new 
user). So can you please give an example of attach command.

Well, the reason I wanted the parser was some programs like  AMBER 
(leap) requires different  names for linked cysteines. It would be 
helpful to get this information from the PDB file since it has it. Also 
there is other information in the PDB file which can be useful if 
displayed somewhere on the viewer like sequence etc. In other words a 
hierarchy window similar to the web-lab viewer. Maybe it does  and just 
have not figured out how to make it work it.

In any case I think this is a terrific program and although I have just 
started using it I am realizing its potential.

Kaushik.

On Friday, September 20, 2002, at 05:24 PM, DeLano, Warren wrote:

> Regarding H-bonds. Funny you should ask -- Hans and I just worked out 
> how to do this here at Sunesis...
>
> There isn't a built-in function yet (it is coming), but you can show 
> H-bonds between two objects using  atom selections so long as hydrogens 
> are present in both molecules.  If you don't have hydrogens, you can 
> use h_add on the proteins or provide ligands with valence information 
> and then use h_add.
>
> Two examples are below.  For clarity, they draw dashes between the 
> heavy atoms and hide the hydrogens.
>
> # EXAMPLE 1: Show hydrogen bonds between protein
> # and docked ligands (which must have hydrogens)
>
> load target.pdb,prot
> load docked_ligs.sdf,lig
>
> # add hydrogens to protein
>
> h_add prot
>
> select don, (elem n,o and (neighbor hydro))
> select acc, (elem o or (elem n and not (neighbor hydro)))
> dist HBA, (lig and acc),(prot and don), 3.2
> dist HBD, (lig and don),(prot and acc), 3.2
> delete don
> delete acc
> hide (hydro)
>
> hide labels,HBA
> hide labels,HBD
>
> # EXAMPLE 2
> # Show hydrogen bonds between two proteins
>
> load prot1.pdb
> load prot2.pdb
>
> h_add prot1
> h_add prot2
>
> select don, (elem n,o and (neighbor hydro))
> select acc, (elem o or (elem n and not (neighbor hydro)))
> dist HBA, (prot1 and acc),(prot2 and don), 3.2
> dist HBD, (prot1 and don),(prot2 and acc), 3.2
> delete don
> delete acc
> hide (hydro)
>
> hide labels,HBA
> hide labels,HBD
>
> # NOTE: that you could also use this approach between two
> # non-overlapping selections within a single object.
>
> As far as SSBOND records go, no PyMOL doesn't currently parse 
> these...does it need to?
>
> Warren
>
> --
> mailto:wa...@su...
> Warren L. DeLano, Ph.D.
>
>> -----Original Message-----
>> From: Kaushik Raha [mailto:kx...@ps...]
>> Sent: Friday, September 20, 2002 1:36 PM
>> To: pym...@li...
>> Subject: Re: [PyMOL] Disulfide Bonds
>>
>>
>> A similar question: Does PyMOL have a PDB file parser that can read
>> disulphide linkages from the file and connect the atoms or one has to
>> explicitly issue bond commands. Also, can PyMOL display
>> hydrogen bonds
>> without the user having to write out a list?
>>
>> thanks,
>>
>> Kaushik Raha.
>> Penn State University.
>>
>> On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote:
>>
>>> Alex,
>>>
>>> 	If the sulfurs are within disulfide bonding distance,
>> PyMOL should
>>> connect them by default.  If this is not happening, please
>> send me the
>>> PDB file so I can take a look-see.
>>>
>>>       Otherwise, you can use the "bond" command to attach them:
>>>
>>> bond 24/sg,26/sg
>>> bond 56/sb,99/sg
>>>
>>> unpick
>>>
>>> (unpick will hide the bond baton which gets displayed)
>>>
>>> Cheers,
>>> Warren
>>>
>>> --
>>> mailto:wa...@su...
>>> Warren L. DeLano, Ph.D.
>>>
>>>> -----Original Message-----
>>>> From: Alex Morla [mailto:al...@ui...]
>>>> Sent: Friday, September 20, 2002 8:48 AM
>>>> To: pym...@li...
>>>> Subject: [PyMOL] Disulfide Bonds
>>>>
>>>>
>>>> Sorry if this is a novice question, but how do I display the
>>>> disulfide bonds
>>>> in my models?
>>>>
>>>> Thanks, and keep up the great work!!
>>>>
>>>> Alex Morla
>>>> Univ. of Illinois, Rockford.
>>>>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

RE: [PyMOL] electron density maps

[DeLano, W. <wa...@su...>]

Scott,

isomesh msh1, map1, 1.5, myobject, carve=3D2.1

The postfix "carve=3D2.1" will trim density which is more than 2.1 A =
from myobject. =20

You may want to play around with the exact cutoff...

Cheers,
Warren




> -----Original Message-----
> From: Scott Classen [mailto:cl...@uc...]
> Sent: Friday, September 20, 2002 3:11 PM
> To: pym...@li...
> Subject: [PyMOL] electron density maps
>=20
>=20
> Hello fellow PyMOL users,
> 	I am trying to display a ccp4 map over just a ligand. I have=20
> successfully read in the map and displayed it around the ligand with:
>=20
> isomesh msh1, map1, 1.5, myobject
>=20
> but the map has bits and peices of the surrounding sidechains.
> Is there a way to only display the map around my ligand?
> Thanks,
> Scott
>=20
>=20
>=20
> =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>    Scott Classen
>    cl...@uc...
>    University of California, Berkeley
>    Department of Molecular & Cell Biology
>    229 Stanley Hall #3206
>    Berkeley, CA 94720-3206
>    LAB 510.643.9491
>    FAX 510.643.9290
> =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] electron density maps

[Scott C. <cl...@uc...>]

Hello fellow PyMOL users,
	I am trying to display a ccp4 map over just a ligand. I have 
successfully read in the map and displayed it around the ligand with:

isomesh msh1, map1, 1.5, myobject

but the map has bits and peices of the surrounding sidechains.
Is there a way to only display the map around my ligand?
Thanks,
Scott



==============================================
   Scott Classen
   cl...@uc...
   University of California, Berkeley
   Department of Molecular & Cell Biology
   229 Stanley Hall #3206
   Berkeley, CA 94720-3206
   LAB 510.643.9491
   FAX 510.643.9290
==============================================

RE: [PyMOL] Disulfide Bonds

[DeLano, W. <wa...@su...>]

Regarding H-bonds. Funny you should ask -- Hans and I just worked out =
how to do this here at Sunesis...

There isn't a built-in function yet (it is coming), but you can show =
H-bonds between two objects using  atom selections so long as hydrogens =
are present in both molecules.  If you don't have hydrogens, you can use =
h_add on the proteins or provide ligands with valence information and =
then use h_add.

Two examples are below.  For clarity, they draw dashes between the heavy =
atoms and hide the hydrogens.

# EXAMPLE 1: Show hydrogen bonds between protein=20
# and docked ligands (which must have hydrogens)

load target.pdb,prot
load docked_ligs.sdf,lig

# add hydrogens to protein

h_add prot

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (lig and acc),(prot and don), 3.2
dist HBD, (lig and don),(prot and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# EXAMPLE 2
# Show hydrogen bonds between two proteins

load prot1.pdb
load prot2.pdb

h_add prot1
h_add prot2

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (prot1 and acc),(prot2 and don), 3.2
dist HBD, (prot1 and don),(prot2 and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# NOTE: that you could also use this approach between two
# non-overlapping selections within a single object.

As far as SSBOND records go, no PyMOL doesn't currently parse =
these...does it need to?

Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> -----Original Message-----
> From: Kaushik Raha [mailto:kx...@ps...]
> Sent: Friday, September 20, 2002 1:36 PM
> To: pym...@li...
> Subject: Re: [PyMOL] Disulfide Bonds
>=20
>=20
> A similar question: Does PyMOL have a PDB file parser that can read=20
> disulphide linkages from the file and connect the atoms or one has to=20
> explicitly issue bond commands. Also, can PyMOL display=20
> hydrogen bonds=20
> without the user having to write out a list?
>=20
> thanks,
>=20
> Kaushik Raha.
> Penn State University.
>=20
> On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote:
>=20
> > Alex,
> >
> > 	If the sulfurs are within disulfide bonding distance,=20
> PyMOL should=20
> > connect them by default.  If this is not happening, please=20
> send me the=20
> > PDB file so I can take a look-see.
> >
> >       Otherwise, you can use the "bond" command to attach them:
> >
> > bond 24/sg,26/sg
> > bond 56/sb,99/sg
> >
> > unpick
> >
> > (unpick will hide the bond baton which gets displayed)
> >
> > Cheers,
> > Warren
> >
> > --
> > mailto:wa...@su...
> > Warren L. DeLano, Ph.D.
> >
> >> -----Original Message-----
> >> From: Alex Morla [mailto:al...@ui...]
> >> Sent: Friday, September 20, 2002 8:48 AM
> >> To: pym...@li...
> >> Subject: [PyMOL] Disulfide Bonds
> >>
> >>
> >> Sorry if this is a novice question, but how do I display the
> >> disulfide bonds
> >> in my models?
> >>
> >> Thanks, and keep up the great work!!
> >>
> >> Alex Morla
> >> Univ. of Illinois, Rockford.
> >>

Re: [PyMOL] Disulfide Bonds

[Kaushik R. <kx...@ps...>]

A similar question: Does PyMOL have a PDB file parser that can read 
disulphide linkages from the file and connect the atoms or one has to 
explicitly issue bond commands. Also, can PyMOL display hydrogen bonds 
without the user having to write out a list?

thanks,

Kaushik Raha.
Penn State University.

On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote:

> Alex,
>
> 	If the sulfurs are within disulfide bonding distance, PyMOL should 
> connect them by default.  If this is not happening, please send me the 
> PDB file so I can take a look-see.
>
>       Otherwise, you can use the "bond" command to attach them:
>
> bond 24/sg,26/sg
> bond 56/sb,99/sg
>
> unpick
>
> (unpick will hide the bond baton which gets displayed)
>
> Cheers,
> Warren
>
> --
> mailto:wa...@su...
> Warren L. DeLano, Ph.D.
>
>> -----Original Message-----
>> From: Alex Morla [mailto:al...@ui...]
>> Sent: Friday, September 20, 2002 8:48 AM
>> To: pym...@li...
>> Subject: [PyMOL] Disulfide Bonds
>>
>>
>> Sorry if this is a novice question, but how do I display the
>> disulfide bonds
>> in my models?
>>
>> Thanks, and keep up the great work!!
>>
>> Alex Morla
>> Univ. of Illinois, Rockford.
>>
>>
>>
>> -------------------------------------------------------
>> This sf.net email is sponsored by:ThinkGeek
>> Welcome to geek heaven.
>> http://thinkgeek.com/sf
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

RE: [PyMOL] Disulfide Bonds

[DeLano, W. <wa...@su...>]

Alex,

	If the sulfurs are within disulfide bonding distance, PyMOL should =
connect them by default.  If this is not happening, please send me the =
PDB file so I can take a look-see.

      Otherwise, you can use the "bond" command to attach them:

bond 24/sg,26/sg
bond 56/sb,99/sg

unpick

(unpick will hide the bond baton which gets displayed)

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> -----Original Message-----
> From: Alex Morla [mailto:al...@ui...]
> Sent: Friday, September 20, 2002 8:48 AM
> To: pym...@li...
> Subject: [PyMOL] Disulfide Bonds
>=20
>=20
> Sorry if this is a novice question, but how do I display the=20
> disulfide bonds
> in my models?
>=20
> Thanks, and keep up the great work!!
>=20
> Alex Morla
> Univ. of Illinois, Rockford.
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Disulfide Bonds

[Alex M. <al...@ui...>]

Sorry if this is a novice question, but how do I display the disulfide bonds
in my models?

Thanks, and keep up the great work!!

Alex Morla
Univ. of Illinois, Rockford.

[PyMOL] Re: NVidia Linux Stereo Drivers

[Marc S. <mar...@mp...>]

pym...@li... wrote:

 > It looks like nVidia may have finally answered our pleas for stereo
 > under Linux : )
 >
 > Forwarded from Peter Wolanin (with permission):

Could you ask him a few questions regarding this?


 > --
 >
 > In case you're interested, I was able to get quad-buffered stereo 3D
 > graphics with pymol on a linux (Redhat 7.3) system after a couple
 > weeks of false starts.  The system is a Dell Precision with an nVidia
 > GeForce2 card.  After getting the very latest nVidia drivers

1. Is this really a Geforce2 or a Quadro 2??

nVidia claims that Quadro is stereo-enabled, not Geforce (according to 
their relase notes in the latest driver (v.1.0-3123)).

2. Is there some patch neccessary to fool the driver (like the 
Windows-version)?

3. How does the emitter works (something like the beamsplitter available 
from NuVision)??

4. Does this emitter allow for stereo in a window (instead of 
fullscreen-stereo)?



-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

[PyMOL] Problems getting Linux Nvidia stereo working

[Hariharan J. <ha...@bl...>]

Hi thanks for forwarding Peter Wolanins email about working stereo on
linux with the latest driver from nvdidia on a Geforce2. I have some
problems getting the same working on a geforce3 with Mandrake linux 8.1
kernel version 2.4.8-26mdk . 
I successfully installed the latest driver 31.23 using the appropriate
precompiled binary rpm from the nvidia website. After installation Made
sure that the application gears was working fine and that the installation
was using the right libraries , also pymol works fine . Now I added the 
Option "Stereo" "1"
Line in the config file as suggested in the email and hinted in the
README ,And restarted X 
Howvever pymol responds saying that Stereo support is not available. Also
the XFree86.0.log (for version Xfree version 4.1.0)says
that stereo is available only on Quadro cards

(**) NVIDIA(0): Option "Stereo" "1"
(**) NVIDIA(0): DDC stereo requested

AND LATER DOWN in the log  IT SAYS

(II) Module ramdac: vendor="The XFree86 Project"
	compiled for 4.1.0, module version = 0.1.0
	ABI class: XFree86 Video Driver, version 0.4
(WW) NVIDIA(0): Stereo is only available on Quadro cards


The readme from nvidia also says that stereo is supported only on quadro
cards.
Just wondering whether any other "fix" is required to enable stereo on my
geforce3 assuming that the geforce3 like the geforce2 is not a quadro
based card. 

I know that previously there were products like softquadro ( for
PC-win2000)that patched the nvidia driver to fool it into thinking we have
a quadro (Incidentally thats the solution i use to get pymol stereo under
windows on the same machine) 

Any help to get this working ,will be greatly appreciated..
Thanks
Hari



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

On Tue, 17 Sep 2002, DeLano, Warren wrote:

> 
> It looks like nVidia may have finally answered our pleas for stereo under Linux : ) 
> 
> Forwarded from Peter Wolanin (with permission):
> 
> --
> 
> In case you're interested, I was able to get quad-buffered stereo 3D
> graphics with pymol on a linux (Redhat 7.3) system after a couple weeks of
> false starts.  The system is a Dell Precision with an nVidia GeForce2
> card.  After getting the very latest nVidia drivers installed, and
> installing some *very* reasonably priced LCD goggles from Eye3D I thought
> I was home free.  However, it didn't work until I read the nVidia README
> in detail and discovered that you have to put in the XF86Config-4 file the
> driver option: Option "Stereo" "1"  to enable hardware stereo.  The
> emitter has to be manually switched (since it only has drivers for
> Windows), but otherwise everthing seems perfect.  If only I'd had a few
> extra hints along the way, it would only have taken an hour to get
> working.
> 
> -Peter
> 
> --
> 
> FYI: the vendor for the Eye3D glasses he mentions is http://www.demensional.com/. I noticed they've linked VMD on their site -- perhaps we could convince them to include a reference to PyMOL as well?  
> 
> --
> mailto:wa...@su...
> Warren L. DeLano, Ph.D.
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.NET email is sponsored by: AMD - Your access to the experts
> on Hammer Technology! Open Source & Linux Developers, register now
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> 

[PyMOL] RE: stereo 3d with pymol (NVidia cards)

[DeLano, W. <wa...@su...>]

> From: Peter M. Wolanin [mailto:pwo...@Pr...]

> One other thing with pymol and 3D stereo:  on our system, at least, it
> seems as though the on-screen rendering is much faster and smoother in
> stero mode than in regular mode.  Pymol in its usual mode=20
> seem much slower
> than spdbv.  Is there something that needs to be set in order=20
> to use the
> hardware rendering?

This is a defect in all of the nVidia based solutions I've tested, and =
one of the reasons I don't recommend nVidia cards for stereographics.  =
ATI FireGL or Radeon (+XiG) cards work fine as do various cards from =
3DLabs.  Since this is clearly an nVidia chipset/driver specific issue, =
it is troubling that nVidia doesn't offer an appropriate email address =
or forum where we could report these kinds of low-level problems.

The same behavior is seen with their chipsets under Windows or Linux as =
well and with a few other GLUT-based stereo-capable programs (such as O, =
I believe).  If you have enabled the card's stereo capability, then when =
you create a stereo OpenGL context, you only get good performance when =
the program is actually rendering in stereo mode.  None of the other =
stereo graphics cards in this market seem to suffer this limitation.

The workaround for nVidia cards is to run PyMOL in stereo mode at all =
times but to zero out the stereo parameters when you are not actually =
wearing 3D glasses.  You end up drawing two identical images and =
everything looks peachy.

Here is some Python code which you can run on startup in order to get =
better mono performace with stereo-enabled nVidia cards.  The F1 key =
then becomes the stereo toggle.

Save in a ".py" file, such as $HOME/.pymolrc.py

# nvidia.py : NVidia stereo/mono performance workaround
# (put in your .pymolrc.py file or run this .py program manually)

from pymol import cmd

def nvidia_stereo():
   cmd.stereo("on") # always on
   if float(cmd.get_setting_tuple("stereo_angle")[1][0])!=3D0.0:
      cmd.set("stereo_angle",0)
      cmd.set("stereo_shift",0)
      print "nVidia stereo off"
   else:
      cmd.set("stereo_angle",2.1)
      cmd.set("stereo_shift",2)
      print "nVidia stereo on"
           =20
cmd.set_key("F1",nvidia_stereo)

nvidia_stereo()=20

# end of code

Hope this helps,

Warren

cc: PyMOL Mailing List
    in...@nv...

[PyMOL] NVidia Linux Stereo Drivers

[DeLano, W. <wa...@su...>]

It looks like nVidia may have finally answered our pleas for stereo =
under Linux : )=20

Forwarded from Peter Wolanin (with permission):

--

In case you're interested, I was able to get quad-buffered stereo 3D
graphics with pymol on a linux (Redhat 7.3) system after a couple weeks =
of
false starts.  The system is a Dell Precision with an nVidia GeForce2
card.  After getting the very latest nVidia drivers installed, and
installing some *very* reasonably priced LCD goggles from Eye3D I =
thought
I was home free.  However, it didn't work until I read the nVidia README
in detail and discovered that you have to put in the XF86Config-4 file =
the
driver option: Option "Stereo" "1"  to enable hardware stereo.  The
emitter has to be manually switched (since it only has drivers for
Windows), but otherwise everthing seems perfect.  If only I'd had a few
extra hints along the way, it would only have taken an hour to get
working.

-Peter

--

FYI: the vendor for the Eye3D glasses he mentions is =
http://www.demensional.com/. I noticed they've linked VMD on their site =
-- perhaps we could convince them to include a reference to PyMOL as =
well? =20

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

RE: [PyMOL] PyMOL movie question

[DeLano, W. <wa...@su...>]

Okay I found the problem...

This fails:

"mpng mov # will create mov0001.png, mov0002.png, etc."

but this:

"mpng mov
 # will create mov0001.png, mov0002.png, etc."

works fine.=20

The problem is that PyMOL isn't yet 100% tolerant of comments which =
follow PyMOL commands on the same line.  Unfortunately, I can't make the =
uniform assumption that everything after a "#" is a comment, since "#" =
is a valid SMILES character, and I need to leave room for SMILES =
capabilities down the road.

For the time being, to be absolutely safe, put comments on their own =
separate lines in PyMOL command scripts (not Python programs, which are =
unaffected by this limitation). =20

Sorry for the inconvenience this may cause. =20

Cheers,
Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Jennifer Ekstrom [mailto:jek...@Ph...]
> Sent: Friday, September 13, 2002 9:41 AM
> To: 'pym...@li...'
> Subject: [PyMOL] PyMOL movie question
>=20
>=20
> Hello,=20
> I'm a new PyMOL user, and am trying to make my first=20
> molecular movie. =20
>=20
> I've inserted the following into my script:=20
>=20
> 	mset 1 x120                 =20
> 	util.mroll(1,120,1)         =20
> 	set ray_trace_frames=3D1
> 	set cache_frames=3D0
> 	mclear
> 	mpng mov=20
>=20
> and I'm getting the following output:
>=20
> PyMOL>mset 1 x120                 =20
> PyMOL>util.mroll(1,120,1)         =20
> PyMOL>set ray_trace_frames=3D1
>  Setting: ray_trace_frames set to 1.00000.
> PyMOL>set cache_frames=3D0
>  Setting: cache_frames set to 0.00000.
> PyMOL>mclear
> PyMOL>mpng mov=20
> Traceback (most recent call last):
>   File "C:\Program Files\DeLano=20
> Scientific\PyMOL/modules\pymol\parser.py",
> lin
> e 126, in parse
>     result=3Dapply(kw[nest][0],args[nest],kw_args[nest])
>   File "C:\Program Files\DeLano=20
> Scientific\PyMOL/modules\pymol\moving.py",
> lin
> e 178, in mpng
>     r =3D cmd._mpng(prefix,int(first)-1,int(last)-1)
> ValueError: invalid literal for int(): mov0002.png
>=20
>=20
> Any suggestions?=20
>=20
> Thanks,=20
> Jennifer=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

RE: [PyMOL] PyMOL movie question

[DeLano, W. <wa...@su...>]

Jennifer,

   That looks like some blatantly buggy behavior in PyMOL.  Strange =
thing is, I don't get the same behavior on the version I have installed. =
 Thus, I may have inadvertently fixed this problem...
=20
What version of PyMOL are you using? (under Windows obviously...)

Thanks,
Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Jennifer Ekstrom [mailto:jek...@Ph...]
> Sent: Friday, September 13, 2002 9:41 AM
> To: 'pym...@li...'
> Subject: [PyMOL] PyMOL movie question
>=20
>=20
> Hello,=20
> I'm a new PyMOL user, and am trying to make my first=20
> molecular movie. =20
>=20
> I've inserted the following into my script:=20
>=20
> 	mset 1 x120                 =20
> 	util.mroll(1,120,1)         =20
> 	set ray_trace_frames=3D1
> 	set cache_frames=3D0
> 	mclear
> 	mpng mov=20
>=20
> and I'm getting the following output:
>=20
> PyMOL>mset 1 x120                 =20
> PyMOL>util.mroll(1,120,1)         =20
> PyMOL>set ray_trace_frames=3D1
>  Setting: ray_trace_frames set to 1.00000.
> PyMOL>set cache_frames=3D0
>  Setting: cache_frames set to 0.00000.
> PyMOL>mclear
> PyMOL>mpng mov=20
> Traceback (most recent call last):
>   File "C:\Program Files\DeLano=20
> Scientific\PyMOL/modules\pymol\parser.py",
> lin
> e 126, in parse
>     result=3Dapply(kw[nest][0],args[nest],kw_args[nest])
>   File "C:\Program Files\DeLano=20
> Scientific\PyMOL/modules\pymol\moving.py",
> lin
> e 178, in mpng
>     r =3D cmd._mpng(prefix,int(first)-1,int(last)-1)
> ValueError: invalid literal for int(): mov0002.png
>=20
>=20
> Any suggestions?=20
>=20
> Thanks,=20
> Jennifer=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] PyMOL movie question

[Jennifer E. <jek...@Ph...>]

Hello, 
I'm a new PyMOL user, and am trying to make my first molecular movie.  

I've inserted the following into my script: 

	mset 1 x120                  
	util.mroll(1,120,1)          
	set ray_trace_frames=1
	set cache_frames=0
	mclear
	mpng mov 

and I'm getting the following output:

PyMOL>mset 1 x120                  
PyMOL>util.mroll(1,120,1)          
PyMOL>set ray_trace_frames=1
 Setting: ray_trace_frames set to 1.00000.
PyMOL>set cache_frames=0
 Setting: cache_frames set to 0.00000.
PyMOL>mclear
PyMOL>mpng mov 
Traceback (most recent call last):
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py",
lin
e 126, in parse
    result=apply(kw[nest][0],args[nest],kw_args[nest])
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\moving.py",
lin
e 178, in mpng
    r = cmd._mpng(prefix,int(first)-1,int(last)-1)
ValueError: invalid literal for int(): mov0002.png


Any suggestions? 

Thanks, 
Jennifer 

[PyMOL] Secondary Structure, DSSP etc

[Michel F. <mic...@mb...>]

Hi,=20
I currently have an implementation of DSSP in C++ with lots of
improvements such as correctly identifying Pi-helices.=20


The output of the program is pseudo-PDB, so you could paste it to the
top of your PDB file and most programs, including PyMol would read it
accurately. The output additionally includes geometrical parameters for
each helix, and direction vectors as well as chirality to distinguish
right from left handed helices.=20
--sample output start --=20


REMARK   ------------------------------------------------------------------=
-----
REMARK    Secondary Structure Definition program - (c) Michel N. Fodje, 200=
1-02=20
REMARK      Based on method described in:                                  =
    =20
REMARK        Fodje and Al-Karadaghi (2002)                                =
    =20
REMARK              Protein Engineering vol.15 no.5 pp.335-358             =
    =20
REMARK   ------------------------------------------------------------------=
-----
HEADER    LYASE                                   22-DEC-99   1DOZ         =
    =20
REMARK                                PDB    helix                   K&S   =
    =20
REMARK            from         to     class geometry     axis dir  Chiral l=
ength
REMARK   HLX-# |-resid -|  |-resid -|  |   r   d   n    x    y    z   |    =
    =20
HELIX    1   1 ILE A   22  ILE A   29  1  2.3 1.5 3.7  0.4  0.4 -0.8 H+    =
8   =20
HELIX    2   2 PRO A   37  ALA A   49  1  2.3 1.5 3.6  0.6 -0.1  0.8 H+   1=
3   =20
HELIX    3   3 PRO A   55  ILE A   74  1  2.3 1.5 3.7  0.6  0.7  0.3 H+   2=
0   =20
HELIX    4   4 ILE A   93  LYS A  102  1  2.3 1.5 3.6  0.0  0.8  0.6 H+   1=
0   =20
HELIX    5   5 VAL A  122  LEU A  136  1  2.3 1.5 3.7 -0.5  0.8  0.2 H+   1=
5   =20
HELIX    6   6 PRO A  151  SER A  167  1  2.3 1.5 3.6  0.1 -1.0  0.2 H+   1=
7   =20
HELIX    7   7 GLU A  170  ARG A  173  1  2.2 1.6 3.6  0.1  0.6 -0.8 H+    =
4   =20
HELIX    8   8 TYR A  196  GLY A  210  1  2.3 1.5 3.7  0.6 -0.4  0.7 H+   1=
5   =20
HELIX    9   9 VAL A  235  LYS A  246  1  2.4 1.4 3.8  0.7 -0.7 -0.1 H+   1=
2   =20
HELIX   10  10 LEU A  263  LEU A  266  1  2.4 1.5 3.9  0.4 -0.9 -0.2 H+    =
4   =20
HELIX   11  11 GLU A  272  ASP A  279  1  2.3 1.5 3.6  0.4 -0.9 -0.2 H+    =
8   =20
HELIX   12  12 PRO A  294  LYS A  307  1  2.3 1.5 3.6  0.2  0.9 -0.5 H+   1=
4   =20
HELIX   13  13 LEU A  266  CYS A  273  3  2.7 1.2 4.2  0.4 -0.9 -0.3 I+    =
8   =20
HELIX   14  14 GLU A   19  ASP A   21  5  2.1 1.8 3.4 -0.1  0.2 -1.0 G+    =
3   =20
HELIX   15  15 ILE A   29  GLY A   32  5  2.2 1.8 3.5  0.9  0.1  0.3 G+    =
4   =20
HELIX   16  16 GLU A  187  PHE A  192  5  2.1 1.8 3.2  0.6  0.8 -0.2 G+    =
6   =20
SHEET    1   A 4 LYS A   4  ALA A  12 -1                                   =
    =20
SHEET    2   A 4 ILE A  78  LEU A  86 -1                                   =
    =20
SHEET    3   A 4 GLU A 107  VAL A 112 -1                                   =
    =20
SHEET    4   A 4 THR A 140  SER A 143 -1                                   =
    =20
SHEET    1   B 4 MET A 177  HIS A 183 -1                                   =
    =20
SHEET    2   B 4 TYR A 216  GLN A 221 -1                                   =
    =20
SHEET    3   B 4 ALA A 250  VAL A 254 -1                                   =
    =20
SHEET    4   B 4 SER A 283  TYR A 285 -1                                   =
    =20

--sample output end   --=20


You can currently access it from the web at: =20
http://www.mbfys.lu.se/Services/SecStr/
The source code should be available at the same site in the near future
when the documentation is complete. =20

My pythonese is not up to notch, otherwise I would really like to
contribute code to this fine project.=20

/Michel=20

On Tue, 2002-09-10 at 15:48, Gareth Stockwell wrote:=20
> David,
>=20
> Have a look at the rTools package on Kristian Rother's page
>=20
> 	http://www.rubor.de/bioinf/
>=20
> (I haven't used this myself, and it appears to have some external
> dependencies - notably Java, but it may be what you want)
>=20
> Gareth
>=20
>=20
> On Tue, 2002-09-10 at 14:11, David Guerra Aragao wrote:
> > Hello to all,
> >=20
> > I would like to use DSSP secondary structure assignments but I don't
> > know how to incorporate DSSP output in pdb format for PyMOL.
> >=20
> > I have found plenty of information arround but none about this
issue.
> >=20
> > Can i get some help ?
> >=20
> > David
> >=20
> > --=20
> > David Aragao
> > Linux User n=BA 237333 on http://counter.li.org/
> > "You will pay for your sins.  If you have already paid, please
disregard
> > this message."
> >=20
> >=20
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > This sf.net email is sponsored by: OSDN - Tired of that same old
> > cell phone?  Get a new here for FREE!
> >
https://www.inphonic.com/r.asp?r___________________________________________=
____
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> --=20
>
---------------------------------------------------------------------------=
--
>  Gareth Stockwell
>  EMBL - European Bioinformatics Institute
>  Wellcome Trust Genome Campus
>  Hinxton
>  Cambridge CB10 1SD                                       =20
> ga...@eb...
>  Tel 01223 492548            Personal homepage:
> http://www.ebi.ac.uk/~gareth
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: OSDN - Tired of that same old
> cell phone?  Get a new here for FREE!
> https://www.inphonic.com/r.asp?r=3Dsourceforge1&refcode1=3Dvs3390
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
_______________________
Michel N. Fodje
Molecular Biophysics,
Lund University, Sweden

phone: +46 46 222 45 13
email:    mic...@mb...
web:     http://www.mbfys.lu.se
_______________________

[PyMOL] Possible glass-free 3D monitor for OSX PyMol?

[Luca J. <luc...@ma...>]

Hello PyMol users,

I've just come across a short report in the October issue of MacWorld 
about a double LCD monitor from Deep View Imaging, which apparently 
produces a 3D effect without the need for special glasses. At the moment 
it doesn't seem like a very cheap solution (they say model price ranges 
from 3000 to 6000 USD), but I wonder how PyMol (and O) would work with 
this system...
Have a look at:

	http://www.actualdepth.com/

Ciao, Luca

PS: I am in no way affiliated with this company!!!

--------------------------------------------------------
Luca Jovine, Ph.D.
Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620  FAX: +1.509.356-2832
E-Mail: luc...@ma...
W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------

Re: [PyMOL] picture size and resolution

[Ben C. <ac...@em...>]

David,

Type 'help ray'.

What you want is 'ray 3000,2400', followed by 'png foo.png'.

Regards,

Ben

On Thursday, September 12, 2002, at 11:01 AM, David Guerra Aragao wrote:

> Dear all,
>
> Thanks to Gareth i solved my problem about SS prediction using rTools
> package. My Thanks to Kristian Rother also.
>
> I have another question:
>
> I need to produce a 3000x2400 pixel image (for 300dpi with 10x8 =20
> inches).
> It seams I can only save a picture with the screen size. For example I
> have 1600x1400 desktop size so the maximum picture that can be save =20=

> it's
> that ? Can't I save picture bigger ?
>
> Thanks in advance for any help,
>
> David
>
> On Tue, 2002-09-10 at 14:48, Gareth Stockwell wrote:
>> David,
>>
>> Have a look at the rTools package on Kristian Rother's page
>>
>> 	http://www.rubor.de/bioinf/
>>
>> (I haven't used this myself, and it appears to have some external
>> dependencies - notably Java, but it may be what you want)
>>
>> Gareth
>>
>>
>> On Tue, 2002-09-10 at 14:11, David Guerra Aragao wrote:
>>> Hello to all,
>>>
>>> I would like to use DSSP secondary structure assignments but I don't
>>> know how to incorporate DSSP output in pdb format for PyMOL.
>>>
>>> I have found plenty of information arround but none about this =
issue.
>>>
>>> Can i get some help ?
>>>
>>> David
>>>
>>> -- =20
>>> David Aragao
>>> Linux User n=BA 237333 on http://counter.li.org/
>>> "You will pay for your sins.  If you have already paid, please =20
>>> disregard
>>> this message."
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This sf.net email is sponsored by: OSDN - Tired of that same old
>>> cell phone?  Get a new here for FREE!
>>> https://www.inphonic.com/=20
>>> r.asp?r_______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> --=20
>> =
----------------------------------------------------------------------=20=

>> -------
>>  Gareth Stockwell
>>  EMBL - European Bioinformatics Institute
>>  Wellcome Trust Genome Campus
>>  Hinxton
>>  Cambridge CB10 1SD
>> ga...@eb...
>>  Tel 01223 492548            Personal homepage:
>> http://www.ebi.ac.uk/~gareth
>>
>>
>>
>>
>> -------------------------------------------------------
>> This sf.net email is sponsored by: OSDN - Tired of that same old
>> cell phone?  Get a new here for FREE!
>> https://www.inphonic.com/r.asp?r=3Dsourceforge1&refcode1=3Dvs3390
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] picture size and resolution

[Evan S. <st...@sa...>]

The pymol ray tracer can generate an image of any size.

ray height,width

In your case:

ray 3000,2400
png filename.png

For more options, try 'help ray'

--
Evan Stein
Structural Biology Program
Skirball Institute / NYU School of Medicine
540 First Avenue Lab 3-4
New York, NY 10016

phone: (212) 263-8968
fax: (212) 263-8951
email: st...@sa...
URL: http://saturn.med.nyu.edu/~stein


> From: David Guerra Aragao <da...@ar...>
> Date: Thu, 12 Sep 2002 16:01:11 +0100
> To: pym...@li...
> Subject: [PyMOL] picture size and resolution
>=20
> Dear all,
>=20
> Thanks to Gareth i solved my problem about SS prediction using rTools
> package. My Thanks to Kristian Rother also.
>=20
> I have another question:
>=20
> I need to produce a 3000x2400 pixel image (for 300dpi with 10x8 inches).
> It seams I can only save a picture with the screen size. For example I
> have 1600x1400 desktop size so the maximum picture that can be save it's
> that ? Can't I save picture bigger ?
>=20
> Thanks in advance for any help,
>=20
> David =20
>=20
> On Tue, 2002-09-10 at 14:48, Gareth Stockwell wrote:
>> David,
>>=20
>> Have a look at the rTools package on Kristian Rother's page
>>=20
>> http://www.rubor.de/bioinf/
>>=20
>> (I haven't used this myself, and it appears to have some external
>> dependencies - notably Java, but it may be what you want)
>>=20
>> Gareth
>>=20
>>=20
>> On Tue, 2002-09-10 at 14:11, David Guerra Aragao wrote:
>>> Hello to all,
>>>=20
>>> I would like to use DSSP secondary structure assignments but I don't
>>> know how to incorporate DSSP output in pdb format for PyMOL.
>>>=20
>>> I have found plenty of information arround but none about this issue.
>>>=20
>>> Can i get some help ?
>>>=20
>>> David
>>>=20
>>> --=20
>>> David Aragao
>>> Linux User n=BA 237333 on http://counter.li.org/
>>> "You will pay for your sins.  If you have already paid, please disregar=
d
>>> this message."
>>>=20
>>>=20
>>>=20
>>>=20
>>>=20
>>> -------------------------------------------------------
>>> This sf.net email is sponsored by: OSDN - Tired of that same old
>>> cell phone?  Get a new here for FREE!
>>> https://www.inphonic.com/r.asp?r_______________________________________=
_____
>>> ___
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> --=20
>> ------------------------------------------------------------------------=
-----
>> Gareth Stockwell
>> EMBL - European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> ga...@eb...
>> Tel 01223 492548            Personal homepage:
>> http://www.ebi.ac.uk/~gareth
>>=20
>>=20
>>=20
>>=20
>> -------------------------------------------------------
>> This sf.net email is sponsored by: OSDN - Tired of that same old
>> cell phone?  Get a new here for FREE!
>> https://www.inphonic.com/r.asp?r=3Dsourceforge1&refcode1=3Dvs3390
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>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] picture size and resolution

[David G. A. <da...@ar...>]

Dear all,

Thanks to Gareth i solved my problem about SS prediction using rTools
package. My Thanks to Kristian Rother also.

I have another question:

I need to produce a 3000x2400 pixel image (for 300dpi with 10x8 inches).
It seams I can only save a picture with the screen size. For example I
have 1600x1400 desktop size so the maximum picture that can be save it's
that ? Can't I save picture bigger ?

Thanks in advance for any help,

David =20

On Tue, 2002-09-10 at 14:48, Gareth Stockwell wrote:
> David,
>=20
> Have a look at the rTools package on Kristian Rother's page
>=20
> 	http://www.rubor.de/bioinf/
>=20
> (I haven't used this myself, and it appears to have some external
> dependencies - notably Java, but it may be what you want)
>=20
> Gareth
>=20
>=20
> On Tue, 2002-09-10 at 14:11, David Guerra Aragao wrote:
> > Hello to all,
> >=20
> > I would like to use DSSP secondary structure assignments but I don't
> > know how to incorporate DSSP output in pdb format for PyMOL.
> >=20
> > I have found plenty of information arround but none about this issue.
> >=20
> > Can i get some help ?
> >=20
> > David
> >=20
> > --=20
> > David Aragao
> > Linux User n=BA 237333 on http://counter.li.org/
> > "You will pay for your sins.  If you have already paid, please disregar=
d
> > this message."
> >=20
> >=20
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > This sf.net email is sponsored by: OSDN - Tired of that same old
> > cell phone?  Get a new here for FREE!
> > https://www.inphonic.com/r.asp?r_______________________________________=
________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> --=20
> -------------------------------------------------------------------------=
----
>  Gareth Stockwell
>  EMBL - European Bioinformatics Institute
>  Wellcome Trust Genome Campus
>  Hinxton
>  Cambridge CB10 1SD                                       =20
> ga...@eb...
>  Tel 01223 492548            Personal homepage:
> http://www.ebi.ac.uk/~gareth
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: OSDN - Tired of that same old
> cell phone?  Get a new here for FREE!
> https://www.inphonic.com/r.asp?r=3Dsourceforge1&refcode1=3Dvs3390
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Emulate 3-button mouse in pymol

[Bronwyn C. <br...@bi...>]

I tried doing this and you can't.  Not successfully anyway - there is a 
key combination that lets you zoom, but it's unpredictable and does odd 
things to clipping planes and then you can't zoom the other way.  So you 
either have to use commands or get a mouse and plug it in.

Bronwyn

On Wednesday, September 11, 2002, at 05:22  AM, Yu Chen wrote:

> Hi,
>
> I installed pymol on MAC G4 laptop, since it only has a 1-button touch
> pad, how do I emulate a 3-button mouse using some keys combined with the
> one button, juse like under Xdarwin I can configure it with option+click
> and command+click.
>
> Thanks!
>
> ===========================================
> Yu Chen
> Howard Hughes Medical Institute
> University of Maryland Baltimore County
> 1000 Hilltop Circle
> Baltimore, MD 21250
>
> phone: (410)455-6347
> fax: (410)455-1174
> email: ch...@hh...
> ===========================================
>
> -------------------------------------------------------
> This sf.net email is sponsored by: OSDN - Tired of that same old
> cell phone?  Get a new here for FREE!
> https://www.inphonic.com/r.asp?r=sourceforge1&refcode1=vs3390
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
Bronwyn Carlisle
Biochemistry Department
University of Otago
Dunedin
New Zealand

Tel 64 3 479 7704

[PyMOL] Emulate 3-button mouse in pymol

[Yu C. <ch...@hh...>]

Hi, 

I installed pymol on MAC G4 laptop, since it only has a 1-button touch 
pad, how do I emulate a 3-button mouse using some keys combined with the 
one button, juse like under Xdarwin I can configure it with option+click 
and command+click. 

Thanks!





===========================================
Yu Chen
Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250

phone: (410)455-6347
fax: (410)455-1174
email: ch...@hh...
===========================================

Re: [PyMOL] Using DSSP output

[Gareth S. <ga...@eb...>]

David,

Have a look at the rTools package on Kristian Rother's page

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

(I haven't used this myself, and it appears to have some external
dependencies - notably Java, but it may be what you want)

Gareth


On Tue, 2002-09-10 at 14:11, David Guerra Aragao wrote:
> Hello to all,
>=20
> I would like to use DSSP secondary structure assignments but I don't
> know how to incorporate DSSP output in pdb format for PyMOL.
>=20
> I have found plenty of information arround but none about this issue.
>=20
> Can i get some help ?
>=20
> David
>=20
> --=20
> David Aragao
> Linux User n=BA 237333 on http://counter.li.org/
> "You will pay for your sins.  If you have already paid, please disregard
> this message."
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: OSDN - Tired of that same old
> cell phone?  Get a new here for FREE!
> https://www.inphonic.com/r.asp?r_________________________________________=
______
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
--=20
---------------------------------------------------------------------------=
--
 Gareth Stockwell
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                       =20
ga...@eb...
 Tel 01223 492548            Personal homepage:
http://www.ebi.ac.uk/~gareth

[PyMOL] Using DSSP output

[David G. A. <da...@ar...>]

Hello to all,

I would like to use DSSP secondary structure assignments but I don't
know how to incorporate DSSP output in pdb format for PyMOL.

I have found plenty of information arround but none about this issue.

Can i get some help ?

David

--=20
David Aragao
Linux User n=BA 237333 on http://counter.li.org/
"You will pay for your sins.  If you have already paid, please disregard
this message."

Re [PyMOL] Re: mice for OSX PyMOL

[Richard G. <re...@co...>]

On Monday, September 9, 2002, at 06:33 PM, Luca Jovine wrote:

> I use a basic Logitech 2 button + wheel mouse, and it seems to work 
> just fine...
> -Luca
>
>
I have the same mouse and love it.  I've always thought it would be 
really nice if you could rotate
models using the wheel. (Perhaps PyMol already does this, I'm not that 
familiar).
Crystallographers have really liked dials for years, but they are hard 
to find these
days and I think people have forgotten how nice they were. Ideally, a 
button
press or mouse click could change mode so the wheel would rotate a 
different
axis or bond. I'll probably eventually implement this in OpenDX. Anyone 
have
thoughts for PyMol?