pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] displaying protein with propeptide

[Eric Z. <zo...@ca...>]

Is there a similar command to force PyMOL to use only CONECT lines in=20
the pdb file instead of generating connectivity by distance?

Eric

Warren DeLano wrote:
> A quick fix is to use the "retain_order" setting.
>=20
> set retain_order
>=20
> which will force PyMOL to honor the order of ATOMs in the PDB file over=
 the numeric ordering of residue identifiers.
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>=20
> . 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
>=20
>=20
>>-----Original Message-----
>>From: pym...@li...=20
>>[mailto:pym...@li...] On Behalf Of=20
>>Joel Tyndall
>>Sent: Thursday, November 17, 2005 12:15 PM
>>To: Anne M=F8lgaard; pym...@li...
>>Subject: Re: [PyMOL] displaying protein with propeptide
>>
>>Hi Ann,
>>
>>I would change the chain id of the propeptide in a text=20
>>editor, to say P and remove the P from after the residue numbers.
>>
>>J
>>
>>Anne M=F8lgaard wrote:
>>
>>
>>>Hi,
>>>
>>>I am having problems displaying proteins with unusual residue=20
>>>numbering, such as proteins with propeptides. An example is=20
>>
>>1cs8, which=20
>>
>>>starts off like
>>>this:
>>>
>>>ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
>>>N =20
>>>ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
>>>C =20
>>>ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
>>>C =20
>>>ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
>>>O =20
>>>ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
>>>C =20
>>>ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
>>>O
>>>.
>>>.
>>>.
>>>And later on comes the sequence corresponding to the mature protein:
>>>
>>>ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
>>>N =20
>>>ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
>>>C =20
>>>ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
>>>C =20
>>>ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
>>>O =20
>>>ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
>>>C
>>>Etc.=20
>>>
>>>If I open 1cs8 with PyMol, I can see everything in the "lines",=20
>>>"sticks" and "surface" representation, but in ribbon or cartoon mode=20
>>>only part of the protein is shown. What do I have to do to=20
>>
>>show the whole sequence?
>>
>>>How do I select residues with a "P" appended to the residue=20
>>
>>number? If=20
>>
>>>I say "select resi 1P-5P" I get both 1P-5P and 1-5.
>>>
>>>Any help will be appreciated! (I am using PyMol version 0.98=20
>>
>>for Windows).
>>
>>>- Anne
>>>
>>>--------------------------------------------
>>>Anne M=F8lgaard, Ph.D.
>>>Center for Biological Sequence Analysis BioCentrum-DTU, Building 208=20
>>>DK-2800 Lyngby
>>>
>>>Email:  an...@cb...
>>>Phone:  (+45)4525 2472
>>>--------------------------------------------
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
>>>Register for a JBoss Training Course.  Free Certification Exam
>>>for All Training Attendees Through End of 2005. For more info visit:
>>>http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick
>>>_______________________________________________
>>>PyMOL-users mailing list
>>>PyM...@li...
>>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>
>>>=20
>>>
>>
>>--=20
>>Joel Tyndall, PhD
>>
>>Lecturer
>>National School of Pharmacy
>>University of Otago
>>PO Box 913 Dunedin
>>New Zealand                    =20
>>
>>Pukenga
>>Te Kura Taiwhanga Putaiao
>>Te Whare Wananga o Otago
>>Pouaka Poutapeta 913 Otepoti
>>Aotearoa
>>
>>Ph / Waea               +64 3 4797293=20
>>Fax / Waeawhakaahua     +64 3 4797034
>>
>>
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
>>Register for a JBoss Training Course.  Free Certification Exam
>>for All Training Attendees Through End of 2005. For more info visit:
>>http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick
>>_______________________________________________
>>PyMOL-users mailing list
>>PyM...@li...
>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> Register for a JBoss Training Course.  Free Certification Exam
> for All Training Attendees Through End of 2005. For more info visit:
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

RE: [PyMOL] displaying protein with propeptide

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

A quick fix is to use the "retain_order" setting.

set retain_order

which will force PyMOL to honor the order of ATOMs in the PDB file over =
the numeric ordering of residue identifiers.

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
> Joel Tyndall
> Sent: Thursday, November 17, 2005 12:15 PM
> To: Anne M=F8lgaard; pym...@li...
> Subject: Re: [PyMOL] displaying protein with propeptide
>=20
> Hi Ann,
>=20
> I would change the chain id of the propeptide in a text=20
> editor, to say P and remove the P from after the residue numbers.
>=20
> J
>=20
> Anne M=F8lgaard wrote:
>=20
> >Hi,
> >
> >I am having problems displaying proteins with unusual residue=20
> >numbering, such as proteins with propeptides. An example is=20
> 1cs8, which=20
> >starts off like
> >this:
> >
> >ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
> >N =20
> >ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
> >C =20
> >ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
> >C =20
> >ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
> >O =20
> >ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
> >C =20
> >ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
> >O
> >.
> >.
> >.
> >And later on comes the sequence corresponding to the mature protein:
> >
> >ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
> >N =20
> >ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
> >C =20
> >ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
> >C =20
> >ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
> >O =20
> >ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
> >C
> >Etc.=20
> >
> >If I open 1cs8 with PyMol, I can see everything in the "lines",=20
> >"sticks" and "surface" representation, but in ribbon or cartoon mode=20
> >only part of the protein is shown. What do I have to do to=20
> show the whole sequence?
> >
> >How do I select residues with a "P" appended to the residue=20
> number? If=20
> >I say "select resi 1P-5P" I get both 1P-5P and 1-5.
> >
> >Any help will be appreciated! (I am using PyMol version 0.98=20
> for Windows).
> >
> >- Anne
> >
> >--------------------------------------------
> >Anne M=F8lgaard, Ph.D.
> >Center for Biological Sequence Analysis BioCentrum-DTU, Building 208=20
> >DK-2800 Lyngby
> >
> >Email:  an...@cb...
> >Phone:  (+45)4525 2472
> >--------------------------------------------
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> >Register for a JBoss Training Course.  Free Certification Exam
> >for All Training Attendees Through End of 2005. For more info visit:
> >http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick
> >_______________________________________________
> >PyMOL-users mailing list
> >PyM...@li...
> >https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> > =20
> >
>=20
> --=20
> Joel Tyndall, PhD
>=20
> Lecturer
> National School of Pharmacy
> University of Otago
> PO Box 913 Dunedin
> New Zealand                    =20
>=20
> Pukenga
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 913 Otepoti
> Aotearoa
>=20
> Ph / Waea               +64 3 4797293=20
> Fax / Waeawhakaahua     +64 3 4797034
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> Register for a JBoss Training Course.  Free Certification Exam
> for All Training Attendees Through End of 2005. For more info visit:
> http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] combine align and rms_cur to calculate rms for complexes

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

Hi all,
could someone confirm this:
I have some complexes protein+ligand and I'd like to perform rms
calculation for the position of the ligand. This what I have done:

load reference.pdb
select proteinreference, segi A
select ligreference, segi B
load compare.pdb
select proteincomapre, segi A
select ligcompare, segi B
align proteinreference,proteincompare
rms_cur ligreference,ligcompare

is rms_cur the right command to calculate the rms for the ligand
position? then, is the procedure "chemically" correct?

thanks

regards,

andrea

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

Re: [PyMOL] displaying protein with propeptide

[Joel T. <joe...@ot...>]

Hi Ann,

I would change the chain id of the propeptide in a text editor, to say P =

and remove the P from after the residue numbers.

J

Anne M=F8lgaard wrote:

>Hi,
>
>I am having problems displaying proteins with unusual residue numbering,=

>such as proteins with propeptides. An example is 1cs8, which starts off =
like
>this:
>
>ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
>N =20
>ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
>C =20
>ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
>C =20
>ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
>O =20
>ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
>C =20
>ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
>O =20
>.
>.
>.
>And later on comes the sequence corresponding to the mature protein:
>
>ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
>N =20
>ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
>C =20
>ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
>C =20
>ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
>O =20
>ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
>C =20
>Etc.=20
>
>If I open 1cs8 with PyMol, I can see everything in the "lines", "sticks"=
 and
>"surface" representation, but in ribbon or cartoon mode only part of the=

>protein is shown. What do I have to do to show the whole sequence?
>
>How do I select residues with a "P" appended to the residue number? If I=
 say
>"select resi 1P-5P" I get both 1P-5P and 1-5.=20
>
>Any help will be appreciated! (I am using PyMol version 0.98 for Windows=
).
>
>- Anne=20
>
>--------------------------------------------
>Anne M=F8lgaard, Ph.D.
>Center for Biological Sequence Analysis
>BioCentrum-DTU, Building 208
>DK-2800 Lyngby
>
>Email:  an...@cb...=20
>Phone:  (+45)4525 2472
>--------------------------------------------=20
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
>Register for a JBoss Training Course.  Free Certification Exam
>for All Training Attendees Through End of 2005. For more info visit:
>http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> =20
>

--=20
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                    =20

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293=20
Fax / Waeawhakaahua     +64 3 4797034

[PyMOL] Transparent background

[Kerff <fk...@ul...>]

Hi pymol users,

I'd like to make a figure with a transparent background. Is it possible
with pymol?
Thanks for your help.

Fred

[PyMOL] displaying protein with propeptide

[<an...@cb...>]

Hi,

I am having problems displaying proteins with unusual residue numbering,
such as proteins with propeptides. An example is 1cs8, which starts off =
like
this:

ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
N =20
ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
C =20
ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
C =20
ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
O =20
ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
C =20
ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
O =20
.
.
.
And later on comes the sequence corresponding to the mature protein:

ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
N =20
ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
C =20
ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
C =20
ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
O =20
ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
C =20
Etc.=20

If I open 1cs8 with PyMol, I can see everything in the "lines", "sticks" =
and
"surface" representation, but in ribbon or cartoon mode only part of the
protein is shown. What do I have to do to show the whole sequence?

How do I select residues with a "P" appended to the residue number? If I =
say
"select resi 1P-5P" I get both 1P-5P and 1-5.=20

Any help will be appreciated! (I am using PyMol version 0.98 for =
Windows).

- Anne=20

--------------------------------------------
Anne M=F8lgaard, Ph.D.
Center for Biological Sequence Analysis
BioCentrum-DTU, Building 208
DK-2800 Lyngby

Email:  an...@cb...=20
Phone:  (+45)4525 2472
--------------------------------------------=20

[PyMOL] PyMol Wiki Needs You!

[tree <jav...@ut...>]

Dear PyMol Users,

Due to the increasing popularity of the PyMol Wiki, and the fact that
I'll be hard to reach until Dec. 2nd, we need some people to do very
simple, daily, checks on the PyMol Wiki to make sure that no spammers
have attacked the Wiki.  

Recently, we have had attempts to seed the PyMol Wiki with illegal or
inappropriate material (read: links to drugs and porn); thus, we need
the users to patrol the site and look for inappropriate additions.

It's EASY to look for malfeasance-- just click on "Recent Changes" or
the link http://www.pymolwiki.org/index.php/Special:Recentchanges
and see if the last entries were PyMol related or not.  If not, please
remove the inappropriate content ASAP.  These reprobates use Wikis as
Google seeding sites to increase their PageRank.  If you look at the
page you won't see the content they add, because they use devious tricks
-- so you need to look at the differences.

Much thanks,

-- Jason

-- 
Jason Vertrees (jav...@ut...)
BSCB Graduate Student @ UTMB, Galveston
http://www.bscb.utmb.edu :: BSCB @ UTMB
http://best.utmb.edu :: B.E.S.T. @ UTMB
http://pymolwiki.org :: PyMol Wiki

[PyMOL] Light source questions

[Christopher F. <cd...@em...>]

Hello-

 

I have a few questions about lighting in PyMol v0.98. First, is there anyway
to increase the intensity of the light source? I ask because I would like to
try to backlight my molecule, but whenever I do move the light to behind it,
It comes up very dim. I have tried to output a file for use in POV-RAY (huge
file, even after limiting the quality of cartoons and surfaces a bit) to add
additional pointlights, but the file is so large It takes forever to even
try to ray-trace the image. If anyone knows how to add more light sources in
PyMol, that would be best but it looks like that is imposible. Any hints?

 

Thanks, Chris

 

Christopher D. Fleming

Graduate Student

Redinbo Laboratory

Dept. of Biochemistry & Biophysics

UNC-Chapel Hill

w. 919-962-8270

 

RE: [PyMOL] File size?

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

Simon,

When PyMOL starts up, it prints out the OpenGL rendering information to
standard output  GL_VENDOR, GL_RENDERER, etc.

If it mentions Mesa, then acceleration is disabled.  If it mentions
nVidia, then you should be getting acceleration.  PyMOL's speed depends
mainly on the quality of your graphics accelerator, so if it still seems
slow after acceleration is enabled, then your only recourse is to buy a
more powerful graphics card. =20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Vsevolod (Simon) Ilyushchenko [mailto:si...@cs...]=20
> Sent: Tuesday, November 15, 2005 8:43 AM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: Re: [PyMOL] File size?
>=20
> Warren,
>=20
> Thank you for your answer. I have an Nvidia card on my=20
> desktop with Nvidia drivers which I think include OpenGL=20
> support. PyMOL is still slow. How can I find out whether=20
> PyMOL is using hardware OpenGL or not?
>=20
> Also, if I'm running PyMOL on a Linux server from, say, a=20
> Windows desktop, do I have to have hardware OpenGL support in=20
> Linux or in Windows?
>=20
> Thanks,
> Simon
>=20
> Warren DeLano wrote on 11/14/2005 08:17 PM:
> > Simon,
> >=20
> > Most likely you need to install vendor-specific OpenGL drivers to=20
> > enable hardware acceleration (Linux can't ship with them=20
> because they=20
> > aren't open-source).  Refer to the web site for your=20
> graphics card vendor.
> >=20
> > Without such drivers, PyMOL falls back on software OpenGL=20
> rendering,=20
> > which is much slower than RasMOL's more specialized=20
> molecule rendering=20
> > engine.  With a decent OpenGL graphics card and installed drivers,=20
> > PyMOL's performance should meet or exceed RasMOL.
>=20
> --=20
>=20
> Simon (Vsevolod ILyushchenko)   si...@cs...
> 				http://www.simonf.com
>=20
> "Think like a man of action, act like a man of thought."
>=20
> 		         Henri Bergson
>=20
>=20
>=20
>=20

Re: [PyMOL] File size?

[Vsevolod (S. I. <si...@cs...>]

Warren,

Thank you for your answer. I have an Nvidia card on my desktop with 
Nvidia drivers which I think include OpenGL support. PyMOL is still 
slow. How can I find out whether PyMOL is using hardware OpenGL or not?

Also, if I'm running PyMOL on a Linux server from, say, a Windows 
desktop, do I have to have hardware OpenGL support in Linux or in Windows?

Thanks,
Simon

Warren DeLano wrote on 11/14/2005 08:17 PM:
> Simon,
> 
> Most likely you need to install vendor-specific OpenGL drivers to enable
> hardware acceleration (Linux can't ship with them because they aren't
> open-source).  Refer to the web site for your graphics card vendor.  
> 
> Without such drivers, PyMOL falls back on software OpenGL rendering,
> which is much slower than RasMOL's more specialized molecule rendering
> engine.  With a decent OpenGL graphics card and installed drivers,
> PyMOL's performance should meet or exceed RasMOL.

-- 

Simon (Vsevolod ILyushchenko)   si...@cs...
				http://www.simonf.com

"Think like a man of action, act like a man of thought."

		         Henri Bergson

RE: [PyMOL] File size?

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

Simon,

Most likely you need to install vendor-specific OpenGL drivers to enable
hardware acceleration (Linux can't ship with them because they aren't
open-source).  Refer to the web site for your graphics card vendor. =20

Without such drivers, PyMOL falls back on software OpenGL rendering,
which is much slower than RasMOL's more specialized molecule rendering
engine.  With a decent OpenGL graphics card and installed drivers,
PyMOL's performance should meet or exceed RasMOL.

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
> Vsevolod (Simon) Ilyushchenko
> Sent: Monday, November 14, 2005 5:09 PM
> To: pym...@li...
> Subject: [PyMOL] File size?
>=20
> Hi,
>=20
> I've installed pymol on a 3 Ghz 32-bit Linux box with 2.6 Gb=20
> of RAM, and a user complained that pymol is very slow=20
> compared to rasmol. Could you please give me an idea of the=20
> upper limit on usable file size/complexity? Is it normal for=20
> pymol to be slower than rasmol?
>=20
> Thanks,
> Simon
> --=20
>=20
> Simon (Vsevolod ILyushchenko)   si...@cs...
> 				http://www.simonf.com
>=20
> "Think like a man of action, act like a man of thought."
>=20
> 		         Henri Bergson
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today Register for a JBoss Training Course.  Free=20
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] Wall Eye stereo widgets

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

Aaron,

Very recent betas can do this:  http://delsci.com/beta  Use the command:

stereo geowall

and then

stereo swap=20

If you want crosseye instead of walleye.

There is no developers manual yet...

Cheers,
Waren


--
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
> Aaron Bryden
> Sent: Monday, November 14, 2005 4:17 PM
> To: pym...@li...
> Subject: [PyMOL] Wall Eye stereo widgets
>=20
> Hey,
> =20
> Is their any way to make the wall eye stereo mode draw the=20
> various controls for each eye.  Specifically I am talking=20
> about the panel on the right and the sequence=20
> display/selection control.  Where in the code tree should I=20
> consider looking in order to add this functionality. =20
> =20
> Also does a developers manual exist anywhere?  Or is it=20
> pretty much read the code in order to understand the structure.
> =20
> =20
> Thank you for your time,
> =20
> Aaron
>=20

[PyMOL] File size?

[Vsevolod (S. I. <si...@cs...>]

Hi,

I've installed pymol on a 3 Ghz 32-bit Linux box with 2.6 Gb of RAM, and 
a user complained that pymol is very slow compared to rasmol. Could you 
please give me an idea of the upper limit on usable file 
size/complexity? Is it normal for pymol to be slower than rasmol?

Thanks,
Simon
-- 

Simon (Vsevolod ILyushchenko)   si...@cs...
				http://www.simonf.com

"Think like a man of action, act like a man of thought."

		         Henri Bergson

[PyMOL] Wall Eye stereo widgets

[Aaron B. <br...@wi...>]

Hey,
 Is their any way to make the wall eye stereo mode draw the various control=
s
for each eye. Specifically I am talking about the panel on the right and th=
e
sequence display/selection control. Where in the code tree should I conside=
r
looking in order to add this functionality.
 Also does a developers manual exist anywhere? Or is it pretty much read th=
e
code in order to understand the structure.
  Thank you for your time,
 Aaron

[PyMOL] Aminoacid lining of a tube

[Michael M. <dwa...@ya...>]

Hi everyone,
Is there an easier way to select the aminoacid lining
of a tube rather than selecting them manually?
Any help will be appreciated.


		
__________________________________ 
Yahoo! FareChase: Search multiple travel sites in one click.
http://farechase.yahoo.com

[PyMOL] WG: [o-info] Re: freeglut

[Blaesse, M. <Bl...@pr...>]

Hallo,

sorry for the crossposting, but I got no answer on the O mailing list.
I get the below mentioned error message running O since I have compiled=20
and installed PYMOL on a dual Opteron machine with a NVIDIA=20
Quadro FX 1100, running SuSE 9.3. After setting STEREO off=20
lin_ono works well. And also stereo mode of COOT stopped working ("This =
computer seems not to be able to do hardware stereo").

>>I had to activate hardware stereo modes in xorg.conf
>>
>>Section "Device"
>>
>>#       Driver      "nv"
>>         Identifier  "Videocard0"
>>         Driver      "nvidia"
>>         VendorName  "Videocard vendor"
>>         BoardName   "NVIDIA Quadro FX (generic)"
>>         Option      "Stereo" "3"  #<< this what you need to stop=20
>>freeglut complaining
>>regards,Dmitry

This is just what I have there.

>>William Scott wrote:
>>> Have you installed freeglut?  If not, this is probably=20
>>> telling you that
>>> you need to install it, glut, or some such variant.
>>>=20

I have reinstalled both freeglut packages (32 and 64bit).

>>>>O/data# lin_ono fxn_3.o
>>>>  Stereo enabled, hit F1
>>>>  Gamepad disabled
>>>>lin_ono: freeglut_window.c:300: fgOpenWindow: Assertion
>>>>`window->Window.VisualInfo !=3D ((void *)
>>>>                                                            =20
>>  0)' failed.
>>>>Abort

What could have been changed by the PYMOL installation? Any advice would =
be greatly appreciated.=20

Thanks,
Michael Blaesse

RE: [PyMOL] movie from chempy objets

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

Raul,

Load them in to the same object in a serial fashion -- i.e. where you =
specify the object state for each molecule loaded.  You may also want to =
set the discrete object to 1 in order to avoid extra bonds.

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
> Ra=FAl Mera
> Sent: Wednesday, November 09, 2005 9:37 AM
> To: pym...@li...
> Subject: [PyMOL] movie from chempy objets
>=20
> Greetings
>=20
> I need to create pseudo-atoms with Van der Waals radius=20
> defined by me, I know how to do it using chempy, and loading=20
> the chempy objets into pymol, but i need to create several=20
> chempy objets and show them in pymol as frames of a movie.=20
> (i.e getting a movie of an objetc which VdW radius changes in=20
> time) How can I do this?  How can I make a movie from a serie=20
> of chempy objects?
> I would really appreciate if someone could help me with this.
> thanks in advanced, and sorry bout my english (Not a natives speaker)
>=20
> __________________________________________________
> Correo Yahoo!
> Espacio para todos tus mensajes, antivirus y antispam =A1gratis!=20
> Reg=EDstrate ya - http://correo.espanol.yahoo.com/=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
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> http://sourceforge.net/geronimo.php
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

[PyMOL] movie from chempy objets

[<but...@ya...>]

Greetings

I need to create pseudo-atoms with Van der Waals
radius defined by me, I know how to do it using
chempy, and loading the chempy objets into pymol, but
i need to create several chempy objets and show them
in pymol as frames of a movie. (i.e getting a movie of
an objetc which VdW radius changes in time) How can I
do this?  How can I make a movie from a serie of
chempy objects?
I would really appreciate if someone could help me
with this.
thanks in advanced, and sorry bout my english (Not a
natives speaker)

__________________________________________________
Correo Yahoo!
Espacio para todos tus mensajes, antivirus y antispam ¡gratis! 
Regístrate ya - http://correo.espanol.yahoo.com/ 

[PyMOL] Re: transpose_selection

[Leigh W. <le...@rs...>]

Of course within minutes of posting my question about transpose_selection, I 
have found the answer for myself.  There are a couple of new flags added to the 
command, which is now:

def transform_selection(selection,matrix,state=0,log=0,homogenous=0,transpose=0)


When I call it with the flag transpose=1, I get the result that I expect.


Leigh Willard
le...@rs...

[PyMOL] transform_selection

[Leigh W. <le...@rs...>]

I know that the transform_selection command is "unsupported", but I have used it 
in my program, which worked great under pymol v 0.97.  Now with  version 0.98 
the transform_selection command seems to have changed, as it no longer produces 
the same results.  The old syntax was:

cmd.transform_selection(string selection, list-of-16-floats matrix, int 
state-number)

Can you tell me what has changed?  I don't get error messages, but the transform 
is not what I am expecting.  Has the format of the matrix changed?

Thanks,
Leigh Willard
le...@rs...

Re: [PyMOL] Geowall Testing

[D. J. A. <de...@ia...>]

On Mon, Oct 17, 2005 at 02:43:42PM -0700, Warren DeLano wrote:
> 
> You'll only need the new PyMOL build if you are using a
> non-quadro graphics card to drive your geowall.

Can dual-head Macs drive a two-display GeoWall-type setup under
PyMOL?

-- 
D. Joe

Re: [PyMOL] MacPyMOL 0.99beta29

[Gilleain T. <gil...@gm...>]

Hi,

The link to the beta99:

http://delsci.com/beta/macpymol-0_99beta29.tar.gz

says "Page not found".

I wouldn't normally worry, but since using recent betas, my screen  
goes odd when waking from sleep. Which isn't much to worry about  
either (assuming it is caused by pymol, which I don't know for sure  
anyway).

gilleain

On 8 Nov 2005, at 03:39, Warren DeLano wrote:

> MacPyMOL Users,
>
> For those experiencing performance and/or flicker issues under 10.4.3,
> please update to 0.99Beta29 -- this should be the fastest, most stable
> MacPyMOL to date (~2-4X faster than betas 26-28).
>
> http://delsci.com/beta
>
> 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...
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.  
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Question about custom CGO objects

[Gilleain T. <gil...@gm...>]

Hi,

As I understand it, you can either make cgo's that are 'static' in  
shape (like a 3D stamp) or use pymol.callback objects, which can use  
arbitrary opengl commands (such as matrix rotations).

I actually made a cone, in response to someone's query, only I had to  
use callbacks to get triangle fans, and it appears that macpymol  
doesn't have opengl compiled in by default or something.

Here is my Cone class (mostly nicked from a tutorial on the web):

import math
from pymol.opengl.gl import *
from pymol.callback import Callback
from pymol import cmd

class Cone(Callback):

     def get_extent(self):
         return [[-10.0, -10.0, -10.0], [10.0, 10.0, 10.0]]

     def __call__(self):
         glPushMatrix()
         glRotatef(xRot, 1.0, 0.0, 0.0)
         glRotatef(yRot, 0.0, 1.0, 0.0)

         # Begin a triangle fan
         glBegin(GL_TRIANGLE_FAN)

         # Pinnacle of cone is shared vertex for fan, moved up z-axis
         # to produce a cone instead of a circle
         glVertex3f(0.0, 0.0, 75.0)

         # Loop around in a circle and specify even points along the  
circle
         # as the vertices of the triangle fan
         angle = 0.0
         while angle < 2.0 * math.pi:

             # Calculate x and y position of the next vertex
             x = 50.0 * math.sin(angle)
             y = 50.0 * math.cos(angle)

             # Alternate color between red and green
             if((iPivot %2) == 0):
                 glColor3f(0.0, 1.0, 0.0)
             else:
                 glColor3f(1.0, 0.0, 0.0)

             # Increment pivot to change color next time
             iPivot += 1

             # Specify the next vertex for the triangle fan
             glVertex2f(x, y)
             angle += (math.pi / 8.0)

         # Done drawing fan for cone
         glEnd()

         # Begin a new triangle fan to cover the bottom
         glBegin(GL_TRIANGLE_FAN)

         # Center of fan is at the origin
         glVertex2f(0.0, 0.0)
         angle = 0.0
         while angle < 2.0 * math.pi:
             # Calculate x and y position of the next vertex
             x = 50.0 * math.sin(angle)
             y = 50.0 * math.cos(angle)

             # Alternate color between red and green
             if((iPivot %2) == 0):
                 glColor3f(0.0, 1.0, 0.0)
             else:
                 glColor3f(1.0, 0.0, 0.0)

             # Increment pivot to change color next time
             iPivot += 1

             # Specify the next vertex for the triangle fan
             glVertex2f(x, y)
             angle += (math.pi / 8.0)

         # Done drawing the fan that covers the bottom
         glEnd()

         # Restore transformations
         glPopMatrix()


rx, ry, rz = 1, 2, 3
cmd.load_callback(Cone(), 'cone')


Gilleain Torrance

On 8 Nov 2005, at 06:44, Andrew Wollacott wrote:

> Hey all,
> I recently made a cone class that will display cones using pymol
> cgo's.  I built the cones using triangles as suggested by Warren  Now
> I need to get the cones oriented properly, so I was wondering if it's
> possible to apply a GL or rotation matrix when making the cgo.  I
> guess if I can't do this then I can rotate the vertices of each
> individual triangle, but I only want to do this as a last resort.
>
> Any help would be appreciated.
>
> Thanks,
>
> Andrew Wollacott, PhD
> Baker Research Group
> The University of Washington
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.  
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] Question about custom CGO objects

[Andrew W. <sen...@gm...>]

Hey all,
I recently made a cone class that will display cones using pymol
cgo's.  I built the cones using triangles as suggested by Warren  Now
I need to get the cones oriented properly, so I was wondering if it's
possible to apply a GL or rotation matrix when making the cgo.  I
guess if I can't do this then I can rotate the vertices of each
individual triangle, but I only want to do this as a last resort.

Any help would be appreciated.

Thanks,

Andrew Wollacott, PhD
Baker Research Group
The University of Washington

RE: [PyMOL] MacPyMOL 0.99beta29

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

Chris and Others,

Yes, there is at least one outstanding issue with the "new" MacPyMOL
that is unrelated to OpenGL.  If you experience a crash on startup, then
please email crash logs to me (copy and paste from the report error
window), along with a system profile. =20

Apple Menu->About This Mac->More Info->File->Save.

Cheers,
Warren

PS./Aside  For max performance with 0.99beta29 (on machine where it
works):

set texture_fonts
set use_display_lists

--
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: Christopher Yip [mailto:chr...@sy...]=20
> Sent: Monday, November 07, 2005 8:03 PM
> To: Warren DeLano
> Subject: Re: [PyMOL] MacPyMOL 0.99beta29
>=20
> Has anyone reported problems with these beta versions where=20
> they launch but when you click on the windows, the=20
> application seems to quit - using 10.4.3 but this problem=20
> stemmed back to earlier 0.99 beta version...
>=20
> Thanks
>=20
> Chris
> ....
>=20
> On Nov 7, 2005, at 10:39 PM, Warren DeLano wrote:
>=20
>=20
> 	MacPyMOL Users,
>=20
> 	For those experiencing performance and/or flicker=20
> issues under 10.4.3,
> 	please update to 0.99Beta29 -- this should be the=20
> fastest, most stable
> 	MacPyMOL to date (~2-4X faster than betas 26-28).
>=20
> 	http://delsci.com/beta
>=20
> 	Cheers,
> 	Warren
>=20
> 	--
> 	Warren L. DeLano, Ph.D.                    =20
> 	Principal Scientist
>=20
> 	. 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
>=20
>=20
> 	-------------------------------------------------------
> 	SF.Net email is sponsored by:
> 	Tame your development challenges with Apache's Geronimo=20
> App Server. Download
> 	it for free - -and be entered to win a 42" plasma tv or=20
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> 	_______________________________________________
> 	PyMOL-users mailing list
> 	PyM...@li...
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
> Christopher M. Yip, Ph.D., P.Eng.
>=20
> Associate Professor - Canada Research Chair in Molecular Imaging
>=20
> Department of Chemical Engineering and Applied Chemistry
>=20
> Department of Biochemistry
>=20
> Institute of Biomaterials and Biomedical Engineering
>=20
> The Terrence Donnelly Centre for Cellular and Biomolecular Research
>=20
> University of Toronto
>=20
> Room 404 160 College St.
> Toronto, ON, CANADA M5S 3E1
>=20
> (416) 978-7853
>=20
> (416) 978-4317 (fax)
>=20
> chr...@ut...
>=20
> http://bigten.ibme.utoronto.ca
>=20
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