pymol-users Mailing List for PyMOL Molecular Graphics System

On Jun 30, 2004, at 11:39, Gabriel C. Lander wrote:

> Anyone know if pymol can in any way handle rendering very large 
> molecules (like viral capsids)?  I've got a molecule with 392,095 
> atoms, and an additional 78,406 - atom molecule with 155 different 
> states.  Pymol loads the line rendering just fine, but when I go to 
> cartoon rendering, Pymol crashes.  I'm using 2 dual-processor G5's.
> Is there any way to get this to work?
> thanks,
> -gabe

Hi Gabe,

I don't know about viral capsids, but I could render the whole 50S 
subunit (~90000 atoms) with no problems (see 
http://www.mssm.edu/students/jovinl02/images/50s_large.jpg ) - that is, 
after reducing the hash_max parameter to 70 (default is 120) to prevent 
PyMOL from crashing.
Another two parameters you might want to reduce are stick_quality 
(default is 8) and cartoon_sampling (default is 7); lowering these will 
save a lot of memory and not highly affect the quality of an overall 
view of something as large as a virus... I doubt people will check 
individual strands within such a picture!

Hope this helps, good luck - Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Brookdale 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... - luc...@ms...
W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------

Anyone know if pymol can in any way handle rendering very large 
molecules (like viral capsids)?  I've got a molecule with 392,095 
atoms, and an additional 78,406 - atom molecule with 155 different 
states.  Pymol loads the line rendering just fine, but when I go to 
cartoon rendering, Pymol crashes.  I'm using 2 dual-processor G5's.
Is there any way to get this to work?
thanks,
-gabe

Madhavi,

I think the following will work:

load 1HPV.pdb, 1hpv
load 1HSG.pdb, 1hsv

pair_fit 1hpv//A+B/1-9+86-99/CA, 1hsg//A+B/1-9+86-99/CA

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Nalam, Madhavi
> Sent: Friday, June 25, 2004 1:48 PM
> To: Warren DeLano; pym...@li...
> Subject: RE: [PyMOL] superposition of structures
> 
> Hi Warren,
> Thanks for the email. I want to superimpose two structures 
> (pdb codes 1HPV, 1HSG) using residues 1-9, 86-99 @ca in both 
> chain A and chain B (total of 46 atoms). How do I do this?
> So long,
> Madhavi 
> 
> -----Original Message-----
> From: Warren DeLano [mailto:wa...@de...]
> Sent: Friday, June 25, 2004 4:21 PM
> To: Nalam, Madhavi; pym...@li...
> Subject: RE: [PyMOL] superposition of structures
> 
> Nalam,
> 
> Yes, the pair_fit command is probably the easiest way to 
> specify a few CA atoms over which to fit...
> 
> For example:
> 
>   load prot1.pdb
>   load prot2.pdb
> 
>   pair_fit prot1///11-26/CA, prot2///34-49/CA
> 
> would superimpose prot1 on prot2 using C-alphas from residues 11-26 in
> prot1
> and 34-49 in prot2.
> 
> Cheers,
> Warren
> 
> 
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154 
> Fax   (650)-593-4020
>   
> 
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf 
> Of Nalam, 
> > Madhavi
> > Sent: Friday, June 25, 2004 10:55 AM
> > To: pym...@li...
> > Subject: [PyMOL] superposition of structures
> > 
> > Hello,
> > I would like to superimpose two structures using c-alpha 
> atoms of few 
> > residues (not all c-alpha atoms). Can I do this in PyMOL?
> > Thanks,
> > Madhavi
> > 
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of 
> > pym...@li...
> > Sent: Friday, June 25, 2004 2:29 AM
> > To: pym...@li...
> > Subject: PyMOL-users digest, Vol 1 #630 - 5 msgs
> > 
> > Send PyMOL-users mailing list submissions to
> > 	pym...@li...
> > 
> > To subscribe or unsubscribe via the World Wide Web, visit
> > 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> > or, via email, send a message with subject or body 'help' to
> > 	pym...@li...
> > 
> > You can reach the person managing the list at
> > 	pym...@li...
> > 
> > When replying, please edit your Subject line so it is more specific 
> > than "Re: Contents of PyMOL-users digest..."
> > 
> > 
> > Today's Topics:
> > 
> >    1. RE: Orient molecule (Warren DeLano)
> >    2. cartoon and alternates (Robert Schwarzenbacher)
> >    3. RE: cartoon and alternates (Warren DeLano)
> >    4. Question about rotation (Qun Wan)
> >    5. Questions about rotation view (Qun Wan)
> > 
> > --__--__--
> > 
> > Message: 1
> > From: "Warren DeLano" <wa...@de...>
> > To: "'Steve Bowlus'" <che...@go...>,
> > 	<che...@cc...>
> > Cc: <pym...@li...>
> > Date: Wed, 23 Jun 2004 22:59:43 -0700
> > Subject: [PyMOL] RE: Orient molecule
> > 
> > Steve,
> > 
> > This is something PyMOL can do with a little help from Python...
> >   
> > # PyMOL script: view2coord.pml
> > 
> > # get the current camera matrix
> > v=cmd.get_view()
> > 
> > # translate atoms to the current origin of rotation alter_state 1, 
> > all, \
> > (x,y,z) = (x-v[12],y-v[13],z-v[14])
> > 
> > # apply the rotation (matrix multiplication) alter_state 1, all, \
> > (x,y,z) = (x*v[0]+y*v[3]+z*v[6], \
> > x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8])
> > 
> > # end script
> > 
> > After loading a molecule and choosing a view (either with 
> the mouse, 
> > or using commands like "orient", "turn", "move", "center", 
> etc.), you 
> > then simply run the script and save the new coordinates:
> > 
> > load original_mol.pdb
> > orient
> > center 10/ca
> > @view2coord.pml
> > save transformed_mol.pdb
> > quit
> > 
> > Oh, and yes, PyMOL is still free unless you choose to pay for it.
> > 
> > Cheers,
> > Warren
> > 
> > --
> > mailto:wa...@de...
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154 
> > Fax   (650)-593-4020
> >   
> > 
> > > -----Original Message-----
> > > From: Computational Chemistry List
> > > [mailto:che...@cc...] On Behalf Of Steve Bowlus
> > > Sent: Wednesday, June 23, 2004 8:42 PM
> > > To: che...@cc...
> > > Subject: CCL:Orient molecule
> > > 
> > > I am frantically searching for a simple piece of code that
> > will allow
> > > me to:
> > > 
> > > Read a standard file (mol, pdb, Sybyl ...) select an atom 
> to put at 
> > > the Cartesian origin select an atom to put on the X axis 
> select an 
> > > atom to put in the XY plane Do a rigid rotation Do 
> sequential rigid 
> > > rotations about Cartesian axes Freeze the molecule in the new 
> > > orientation Output the NEW, transformed coordinates.
> > > 
> > > This is equivalent to the Sybyl "orient" command, plus rigid 
> > > rotations, plus "Freeze molecule". But I have not found a 
> free (or 
> > > even cheap) package that will freeze a molecule in the new
> > coordinates
> > > before output.
> > > 
> > > Thanks in advance for any pointers,
> > > Steve
> > > 
> > > 
> > > -= This is automatically added to each message by the
> > mailing script
> > > =- To send e-mail to subscribers of CCL put the string
> > > CCL: on your Subject: line and send your message to:  
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> > > 
> > > Send your subscription/unsubscription requests to: 
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> > > HOME Page: http://www.ccl.net   | Jobs Page: 
> > http://www.ccl.net/jobs
> > > 
> > > If your mail is bouncing from CCL.NET domain send it to the
> > > maintainer:
> > > Jan Labanowski,  jla...@nd... (read about it on CCL Home Page)
> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> > > -+-+-+-+-+
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > 
> > --__--__--
> > 
> > Message: 2
> > From: Robert Schwarzenbacher <ro...@sd...>
> > Date: Wed, 23 Jun 2004 23:46:50 -0700
> > To: Warren DeLano  <wa...@de...>
> > Cc: pym...@li...
> > Subject: [PyMOL] cartoon and alternates
> > 
> > hi there,
> > 
> > I get broken cartoons with alternate conformations. Is 
> there a quick 
> > way to solve this problem?
> > 
> > thanks,
> > 
> > robert
> > 
> > ---
> > Robert Schwarzenbacher, PhD
> > The Joint Center for Structural Genomics
> > phone: 858 822 3637
> > 
> > 
> > --__--__--
> > 
> > Message: 3
> > From: "Warren DeLano" <wa...@de...>
> > To: <pym...@li...>
> > Subject: RE: [PyMOL] cartoon and alternates
> > Date: Thu, 24 Jun 2004 08:27:49 -0700
> > 
> > Robert,
> > 
> > This sounds like a potential bug.  You might be able to 
> work around it 
> > by removing all but one alternate conformation...
> > 
> > remove not alt ''+A
> > rebuild
> > 
> > But I'd like to take a look at the file to understand why PyMOL is 
> > having trouble.  Could you send me a copy (directly, not via the 
> > mailing list) or let me know what PDB code to look for?
> > 
> > Cheers,
> > Warren
> > 
> > --
> > mailto:wa...@de...
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154 
> > Fax   (650)-593-4020
> > 
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On 
> Behalf Of Robert 
> > > Schwarzenbacher
> > > Sent: Wednesday, June 23, 2004 11:47 PM
> > > To: Warren DeLano
> > > Cc: pym...@li...
> > > Subject: [PyMOL] cartoon and alternates
> > > 
> > > hi there,
> > > 
> > > I get broken cartoons with alternate conformations. Is 
> there a quick 
> > > way to solve this problem?
> > > 
> > > thanks,
> > > 
> > > robert
> > > 
> > > ---
> > > Robert Schwarzenbacher, PhD
> > > The Joint Center for Structural Genomics
> > > phone: 858 822 3637
> > > 
> > > 
> > > -------------------------------------------------------
> > > This SF.Net email sponsored by Black Hat Briefings & Training.
> > > Attend Black Hat Briefings & Training, Las Vegas July 24-29 - 
> > > digital self defense, top technical experts, no vendor pitches, 
> > > unmatched networking opportunities. Visit www.blackhat.com 
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > 
> > 
> > 
> > 
> > 
> > --__--__--
> > 
> > Message: 4
> > Date: Thu, 24 Jun 2004 12:08:14 -0400
> > From: Qun Wan <Qu...@uv...>
> > To: <pym...@li...>
> > Subject: [PyMOL] Question about rotation
> > 
> > 1.When I want to get the exact rotation of my current view, 
> I did as 
> > the following instruction, but Pymol programe says: invalid 
> syntax. I 
> > do not know why that happens. Could you figure it out for me?
> > 
> > Getting the right view in the script:
> > 
> > When creating the script, it is nice to have the view come 
> up in the 
> > right orientation. To do this, you need to get the coordinates.
> > First, position the molecule the way you would like it to 
> appear, this 
> > can include zooming and rotating the molecule. Once it is in the 
> > correct position, click on the "Get View" button In the 
> PyMOL window 
> > (the one that doesn't show the molecule), a set_view 
> command will be 
> > created for you and you simply cut (from either the PyMol window or 
> > the Terminal window) and paste this text into your script.
> > 
> > 2. If I want to get a particular rotation, what can I do? 
> For example, 
> > if I want to rotation the the current view by 50 degree in 
> the x-axis, 
> > what is the syntax?
> > 
> > 
> > 
> > --__--__--
> > 
> > Message: 5
> > Date: Thu, 24 Jun 2004 13:54:29 -0400
> > From: Qun Wan <Qu...@uv...>
> > To: <pym...@li...>
> > Subject: [PyMOL] Questions about rotation view
> > 
> > 1.When I want to get the exact rotation of my current view, 
> I did as 
> > the following instruction, but Pymol programe says: invalid 
> syntax. I 
> > do not know why that happens. Could you figure it out for me?
> > 
> > Getting the right view in the script:
> > 
> > When creating the script, it is nice to have the view come 
> up in the 
> > right orientation. To do this, you need to get the coordinates.
> > First, position the molecule the way you would like it to 
> appear, this 
> > can include zooming and rotating the molecule. Once it is in the 
> > correct position, click on the "Get View" button In the 
> PyMOL window 
> > (the one that doesn't show the molecule), a set_view 
> command will be 
> > created for you and you simply cut (from either the PyMol window or 
> > the Terminal window) and paste this text into your script.
> > 
> > 2. If I want to get a particular rotation, what can I do? 
> For example, 
> > if I want to rotation the the current view by 50 degree in 
> the x-axis, 
> > what is the syntax?
> > 
> > 
> > 
> > 
> > 
> > --__--__--
> > 
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > 
> > 
> > End of PyMOL-users Digest
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email sponsored by Black Hat Briefings & Training.
> > Attend Black Hat Briefings & Training, Las Vegas July 24-29 
> - digital 
> > self defense, top technical experts, no vendor pitches, unmatched 
> > networking opportunities. Visit www.blackhat.com 
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 - 
> digital self defense, top technical experts, no vendor 
> pitches, unmatched networking opportunities. Visit 
> www.blackhat.com _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hi Warren,
Thanks for the email. I want to superimpose two structures (pdb codes
1HPV, 1HSG) using residues 1-9, 86-99 @ca in both chain A and chain B
(total of 46 atoms). How do I do this?
So long,
Madhavi=20

-----Original Message-----
From: Warren DeLano [mailto:wa...@de...]=20
Sent: Friday, June 25, 2004 4:21 PM
To: Nalam, Madhavi; pym...@li...
Subject: RE: [PyMOL] superposition of structures

Nalam,

Yes, the pair_fit command is probably the easiest way to specify a few
CA
atoms over which to fit...

For example:

  load prot1.pdb
  load prot2.pdb

  pair_fit prot1///11-26/CA, prot2///34-49/CA

would superimpose prot1 on prot2 using C-alphas from residues 11-26 in
prot1
and 34-49 in prot2.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Nalam, Madhavi
> Sent: Friday, June 25, 2004 10:55 AM
> To: pym...@li...
> Subject: [PyMOL] superposition of structures
>=20
> Hello,
> I would like to superimpose two structures using c-alpha=20
> atoms of few residues (not all c-alpha atoms). Can I do this in PyMOL?
> Thanks,
> Madhavi
>=20
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of=20
> pym...@li...
> Sent: Friday, June 25, 2004 2:29 AM
> To: pym...@li...
> Subject: PyMOL-users digest, Vol 1 #630 - 5 msgs
>=20
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
>=20
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
>=20
> You can reach the person managing the list at
> 	pym...@li...
>=20
> When replying, please edit your Subject line so it is more=20
> specific than "Re: Contents of PyMOL-users digest..."
>=20
>=20
> Today's Topics:
>=20
>    1. RE: Orient molecule (Warren DeLano)
>    2. cartoon and alternates (Robert Schwarzenbacher)
>    3. RE: cartoon and alternates (Warren DeLano)
>    4. Question about rotation (Qun Wan)
>    5. Questions about rotation view (Qun Wan)
>=20
> --__--__--
>=20
> Message: 1
> From: "Warren DeLano" <wa...@de...>
> To: "'Steve Bowlus'" <che...@go...>,
> 	<che...@cc...>
> Cc: <pym...@li...>
> Date: Wed, 23 Jun 2004 22:59:43 -0700
> Subject: [PyMOL] RE: Orient molecule
>=20
> Steve,
>=20
> This is something PyMOL can do with a little help from Python...
>  =20
> # PyMOL script: view2coord.pml
>=20
> # get the current camera matrix
> v=3Dcmd.get_view()
>=20
> # translate atoms to the current origin of rotation=20
> alter_state 1, all, \
> (x,y,z) =3D (x-v[12],y-v[13],z-v[14])
>=20
> # apply the rotation (matrix multiplication) alter_state 1, all, \
> (x,y,z) =3D (x*v[0]+y*v[3]+z*v[6], \
> x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8])
>=20
> # end script
>=20
> After loading a molecule and choosing a view (either with the=20
> mouse, or using commands like "orient", "turn", "move",=20
> "center", etc.), you then simply run the script and save the=20
> new coordinates:
>=20
> load original_mol.pdb
> orient
> center 10/ca
> @view2coord.pml
> save transformed_mol.pdb
> quit
>=20
> Oh, and yes, PyMOL is still free unless you choose to pay for it.
>=20
> Cheers,
> Warren
>=20
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154=20
> Fax   (650)-593-4020
>  =20
>=20
> > -----Original Message-----
> > From: Computational Chemistry List
> > [mailto:che...@cc...] On Behalf Of Steve Bowlus
> > Sent: Wednesday, June 23, 2004 8:42 PM
> > To: che...@cc...
> > Subject: CCL:Orient molecule
> >=20
> > I am frantically searching for a simple piece of code that=20
> will allow=20
> > me to:
> >=20
> > Read a standard file (mol, pdb, Sybyl ...) select an atom to put at=20
> > the Cartesian origin select an atom to put on the X axis select an=20
> > atom to put in the XY plane Do a rigid rotation Do sequential rigid=20
> > rotations about Cartesian axes Freeze the molecule in the new=20
> > orientation Output the NEW, transformed coordinates.
> >=20
> > This is equivalent to the Sybyl "orient" command, plus rigid=20
> > rotations, plus "Freeze molecule". But I have not found a free (or=20
> > even cheap) package that will freeze a molecule in the new=20
> coordinates=20
> > before output.
> >=20
> > Thanks in advance for any pointers,
> > Steve
> >=20
> >=20
> > -=3D This is automatically added to each message by the=20
> mailing script=20
> > =3D- To send e-mail to subscribers of CCL put the string
> > CCL: on your Subject: line and send your message to: =20
> > CHE...@cc...
> >=20
> > Send your subscription/unsubscription requests to:=20
> > CHE...@cc...=20
> > HOME Page: http://www.ccl.net   | Jobs Page:=20
> http://www.ccl.net/jobs=20
> >=20
> > If your mail is bouncing from CCL.NET domain send it to the
> > maintainer:
> > Jan Labanowski,  jla...@nd... (read about it on CCL Home Page)
> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> > -+-+-+-+-+
> >=20
> >=20
> >=20
> >=20
> >=20
> >=20
>=20
>=20
>=20
>=20
> --__--__--
>=20
> Message: 2
> From: Robert Schwarzenbacher <ro...@sd...>
> Date: Wed, 23 Jun 2004 23:46:50 -0700
> To: Warren DeLano  <wa...@de...>
> Cc: pym...@li...
> Subject: [PyMOL] cartoon and alternates
>=20
> hi there,
>=20
> I get broken cartoons with alternate conformations. Is there=20
> a quick way to solve this problem?
>=20
> thanks,
>=20
> robert
>=20
> ---
> Robert Schwarzenbacher, PhD
> The Joint Center for Structural Genomics
> phone: 858 822 3637
>=20
>=20
> --__--__--
>=20
> Message: 3
> From: "Warren DeLano" <wa...@de...>
> To: <pym...@li...>
> Subject: RE: [PyMOL] cartoon and alternates
> Date: Thu, 24 Jun 2004 08:27:49 -0700
>=20
> Robert,
>=20
> This sounds like a potential bug.  You might be able to work around it
> by
> removing all but one alternate conformation...
>=20
> remove not alt ''+A
> rebuild
>=20
> But I'd like to take a look at the file to understand why PyMOL is
> having
> trouble.  Could you send me a copy (directly, not via the=20
> mailing list)
> or
> let me know what PDB code to look for?
>=20
> Cheers,
> Warren
>=20
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154=20
> Fax   (650)-593-4020
>=20
> > -----Original Message-----
> > From: pym...@li...=20
> > [mailto:pym...@li...] On Behalf Of=20
> > Robert Schwarzenbacher
> > Sent: Wednesday, June 23, 2004 11:47 PM
> > To: Warren DeLano
> > Cc: pym...@li...
> > Subject: [PyMOL] cartoon and alternates
> >=20
> > hi there,
> >=20
> > I get broken cartoons with alternate conformations. Is there=20
> > a quick way to solve this problem?
> >=20
> > thanks,
> >=20
> > robert
> >=20
> > ---
> > Robert Schwarzenbacher, PhD
> > The Joint Center for Structural Genomics
> > phone: 858 822 3637
> >=20
> >=20
> > -------------------------------------------------------
> > This SF.Net email sponsored by Black Hat Briefings & Training.
> > Attend Black Hat Briefings & Training, Las Vegas July 24-29 -=20
> > digital self defense, top technical experts, no vendor pitches,=20
> > unmatched networking opportunities. Visit www.blackhat.com
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
>=20
>=20
>=20
>=20
> --__--__--
>=20
> Message: 4
> Date: Thu, 24 Jun 2004 12:08:14 -0400
> From: Qun Wan <Qu...@uv...>
> To: <pym...@li...>
> Subject: [PyMOL] Question about rotation
>=20
> 1.When I want to get the exact rotation of my current view, I did as
> the following instruction, but Pymol programe says: invalid syntax. I
> do not know why that happens. Could you figure it out for me?
>=20
> Getting the right view in the script:
>=20
> When creating the script, it is nice to have the view come up in the
> right orientation. To do this, you need to get the coordinates.
> First, position the molecule the way you would like it to appear,
> this can include zooming and rotating the molecule. Once it is in the
> correct position, click on the "Get View" button In the PyMOL window
> (the one that doesn't show the molecule), a set_view command will be
> created for you and you simply cut (from either the PyMol window or
> the Terminal window) and paste this text into your script.
>=20
> 2. If I want to get a particular rotation, what can I do? For
> example, if I want to rotation the the current view by 50 degree in
> the x-axis, what is the syntax?
>=20
>=20
>=20
> --__--__--
>=20
> Message: 5
> Date: Thu, 24 Jun 2004 13:54:29 -0400
> From: Qun Wan <Qu...@uv...>
> To: <pym...@li...>
> Subject: [PyMOL] Questions about rotation view
>=20
> 1.When I want to get the exact rotation of my current view, I did as
> the following instruction, but Pymol programe says: invalid syntax. I
> do not know why that happens. Could you figure it out for me?
>=20
> Getting the right view in the script:
>=20
> When creating the script, it is nice to have the view come up in the
> right orientation. To do this, you need to get the coordinates.
> First, position the molecule the way you would like it to appear,
> this can include zooming and rotating the molecule. Once it is in the
> correct position, click on the "Get View" button In the PyMOL window
> (the one that doesn't show the molecule), a set_view command will be
> created for you and you simply cut (from either the PyMol window or
> the Terminal window) and paste this text into your script.
>=20
> 2. If I want to get a particular rotation, what can I do? For
> example, if I want to rotation the the current view by 50 degree in
> the x-axis, what is the syntax?
>=20
>=20
>=20
>=20
>=20
> --__--__--
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
> End of PyMOL-users Digest
>=20
>=20
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 -=20
> digital self defense, top technical experts, no vendor pitches,=20
> unmatched networking opportunities. Visit www.blackhat.com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Nalam,

Yes, the pair_fit command is probably the easiest way to specify a few CA
atoms over which to fit...

For example:

  load prot1.pdb
  load prot2.pdb

  pair_fit prot1///11-26/CA, prot2///34-49/CA

would superimpose prot1 on prot2 using C-alphas from residues 11-26 in prot1
and 34-49 in prot2.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Nalam, Madhavi
> Sent: Friday, June 25, 2004 10:55 AM
> To: pym...@li...
> Subject: [PyMOL] superposition of structures
> 
> Hello,
> I would like to superimpose two structures using c-alpha 
> atoms of few residues (not all c-alpha atoms). Can I do this in PyMOL?
> Thanks,
> Madhavi
> 
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of 
> pym...@li...
> Sent: Friday, June 25, 2004 2:29 AM
> To: pym...@li...
> Subject: PyMOL-users digest, Vol 1 #630 - 5 msgs
> 
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
> 
> You can reach the person managing the list at
> 	pym...@li...
> 
> When replying, please edit your Subject line so it is more 
> specific than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>    1. RE: Orient molecule (Warren DeLano)
>    2. cartoon and alternates (Robert Schwarzenbacher)
>    3. RE: cartoon and alternates (Warren DeLano)
>    4. Question about rotation (Qun Wan)
>    5. Questions about rotation view (Qun Wan)
> 
> --__--__--
> 
> Message: 1
> From: "Warren DeLano" <wa...@de...>
> To: "'Steve Bowlus'" <che...@go...>,
> 	<che...@cc...>
> Cc: <pym...@li...>
> Date: Wed, 23 Jun 2004 22:59:43 -0700
> Subject: [PyMOL] RE: Orient molecule
> 
> Steve,
> 
> This is something PyMOL can do with a little help from Python...
>   
> # PyMOL script: view2coord.pml
> 
> # get the current camera matrix
> v=cmd.get_view()
> 
> # translate atoms to the current origin of rotation 
> alter_state 1, all, \
> (x,y,z) = (x-v[12],y-v[13],z-v[14])
> 
> # apply the rotation (matrix multiplication) alter_state 1, all, \
> (x,y,z) = (x*v[0]+y*v[3]+z*v[6], \
> x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8])
> 
> # end script
> 
> After loading a molecule and choosing a view (either with the 
> mouse, or using commands like "orient", "turn", "move", 
> "center", etc.), you then simply run the script and save the 
> new coordinates:
> 
> load original_mol.pdb
> orient
> center 10/ca
> @view2coord.pml
> save transformed_mol.pdb
> quit
> 
> Oh, and yes, PyMOL is still free unless you choose to pay for it.
> 
> Cheers,
> Warren
> 
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154 
> Fax   (650)-593-4020
>   
> 
> > -----Original Message-----
> > From: Computational Chemistry List
> > [mailto:che...@cc...] On Behalf Of Steve Bowlus
> > Sent: Wednesday, June 23, 2004 8:42 PM
> > To: che...@cc...
> > Subject: CCL:Orient molecule
> > 
> > I am frantically searching for a simple piece of code that 
> will allow 
> > me to:
> > 
> > Read a standard file (mol, pdb, Sybyl ...) select an atom to put at 
> > the Cartesian origin select an atom to put on the X axis select an 
> > atom to put in the XY plane Do a rigid rotation Do sequential rigid 
> > rotations about Cartesian axes Freeze the molecule in the new 
> > orientation Output the NEW, transformed coordinates.
> > 
> > This is equivalent to the Sybyl "orient" command, plus rigid 
> > rotations, plus "Freeze molecule". But I have not found a free (or 
> > even cheap) package that will freeze a molecule in the new 
> coordinates 
> > before output.
> > 
> > Thanks in advance for any pointers,
> > Steve
> > 
> > 
> > -= This is automatically added to each message by the 
> mailing script 
> > =- To send e-mail to subscribers of CCL put the string
> > CCL: on your Subject: line and send your message to:  
> > CHE...@cc...
> > 
> > Send your subscription/unsubscription requests to: 
> > CHE...@cc... 
> > HOME Page: http://www.ccl.net   | Jobs Page: 
> http://www.ccl.net/jobs 
> > 
> > If your mail is bouncing from CCL.NET domain send it to the
> > maintainer:
> > Jan Labanowski,  jla...@nd... (read about it on CCL Home Page)
> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> > -+-+-+-+-+
> > 
> > 
> > 
> > 
> > 
> > 
> 
> 
> 
> 
> --__--__--
> 
> Message: 2
> From: Robert Schwarzenbacher <ro...@sd...>
> Date: Wed, 23 Jun 2004 23:46:50 -0700
> To: Warren DeLano  <wa...@de...>
> Cc: pym...@li...
> Subject: [PyMOL] cartoon and alternates
> 
> hi there,
> 
> I get broken cartoons with alternate conformations. Is there 
> a quick way to solve this problem?
> 
> thanks,
> 
> robert
> 
> ---
> Robert Schwarzenbacher, PhD
> The Joint Center for Structural Genomics
> phone: 858 822 3637
> 
> 
> --__--__--
> 
> Message: 3
> From: "Warren DeLano" <wa...@de...>
> To: <pym...@li...>
> Subject: RE: [PyMOL] cartoon and alternates
> Date: Thu, 24 Jun 2004 08:27:49 -0700
> 
> Robert,
> 
> This sounds like a potential bug.  You might be able to work around it
> by
> removing all but one alternate conformation...
> 
> remove not alt ''+A
> rebuild
> 
> But I'd like to take a look at the file to understand why PyMOL is
> having
> trouble.  Could you send me a copy (directly, not via the 
> mailing list)
> or
> let me know what PDB code to look for?
> 
> Cheers,
> Warren
> 
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154 
> Fax   (650)-593-4020
> 
> > -----Original Message-----
> > From: pym...@li... 
> > [mailto:pym...@li...] On Behalf Of 
> > Robert Schwarzenbacher
> > Sent: Wednesday, June 23, 2004 11:47 PM
> > To: Warren DeLano
> > Cc: pym...@li...
> > Subject: [PyMOL] cartoon and alternates
> > 
> > hi there,
> > 
> > I get broken cartoons with alternate conformations. Is there 
> > a quick way to solve this problem?
> > 
> > thanks,
> > 
> > robert
> > 
> > ---
> > Robert Schwarzenbacher, PhD
> > The Joint Center for Structural Genomics
> > phone: 858 822 3637
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email sponsored by Black Hat Briefings & Training.
> > Attend Black Hat Briefings & Training, Las Vegas July 24-29 - 
> > digital self defense, top technical experts, no vendor pitches, 
> > unmatched networking opportunities. Visit www.blackhat.com
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > 
> 
> 
> 
> 
> --__--__--
> 
> Message: 4
> Date: Thu, 24 Jun 2004 12:08:14 -0400
> From: Qun Wan <Qu...@uv...>
> To: <pym...@li...>
> Subject: [PyMOL] Question about rotation
> 
> 1.When I want to get the exact rotation of my current view, I did as
> the following instruction, but Pymol programe says: invalid syntax. I
> do not know why that happens. Could you figure it out for me?
> 
> Getting the right view in the script:
> 
> When creating the script, it is nice to have the view come up in the
> right orientation. To do this, you need to get the coordinates.
> First, position the molecule the way you would like it to appear,
> this can include zooming and rotating the molecule. Once it is in the
> correct position, click on the "Get View" button In the PyMOL window
> (the one that doesn't show the molecule), a set_view command will be
> created for you and you simply cut (from either the PyMol window or
> the Terminal window) and paste this text into your script.
> 
> 2. If I want to get a particular rotation, what can I do? For
> example, if I want to rotation the the current view by 50 degree in
> the x-axis, what is the syntax?
> 
> 
> 
> --__--__--
> 
> Message: 5
> Date: Thu, 24 Jun 2004 13:54:29 -0400
> From: Qun Wan <Qu...@uv...>
> To: <pym...@li...>
> Subject: [PyMOL] Questions about rotation view
> 
> 1.When I want to get the exact rotation of my current view, I did as
> the following instruction, but Pymol programe says: invalid syntax. I
> do not know why that happens. Could you figure it out for me?
> 
> Getting the right view in the script:
> 
> When creating the script, it is nice to have the view come up in the
> right orientation. To do this, you need to get the coordinates.
> First, position the molecule the way you would like it to appear,
> this can include zooming and rotating the molecule. Once it is in the
> correct position, click on the "Get View" button In the PyMOL window
> (the one that doesn't show the molecule), a set_view command will be
> created for you and you simply cut (from either the PyMol window or
> the Terminal window) and paste this text into your script.
> 
> 2. If I want to get a particular rotation, what can I do? For
> example, if I want to rotation the the current view by 50 degree in
> the x-axis, what is the syntax?
> 
> 
> 
> 
> 
> --__--__--
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> End of PyMOL-users Digest
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 - 
> digital self defense, top technical experts, no vendor pitches, 
> unmatched networking opportunities. Visit www.blackhat.com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hello,
I would like to superimpose two structures using c-alpha atoms of few
residues (not all c-alpha atoms). Can I do this in PyMOL?
Thanks,
Madhavi

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of
pym...@li...
Sent: Friday, June 25, 2004 2:29 AM
To: pym...@li...
Subject: PyMOL-users digest, Vol 1 #630 - 5 msgs

Send PyMOL-users mailing list submissions to
	pym...@li...

To subscribe or unsubscribe via the World Wide Web, visit
	https://lists.sourceforge.net/lists/listinfo/pymol-users
or, via email, send a message with subject or body 'help' to
	pym...@li...

You can reach the person managing the list at
	pym...@li...

When replying, please edit your Subject line so it is more specific
than "Re: Contents of PyMOL-users digest..."


Today's Topics:

   1. RE: Orient molecule (Warren DeLano)
   2. cartoon and alternates (Robert Schwarzenbacher)
   3. RE: cartoon and alternates (Warren DeLano)
   4. Question about rotation (Qun Wan)
   5. Questions about rotation view (Qun Wan)

--__--__--

Message: 1
From: "Warren DeLano" <wa...@de...>
To: "'Steve Bowlus'" <che...@go...>,
	<che...@cc...>
Cc: <pym...@li...>
Date: Wed, 23 Jun 2004 22:59:43 -0700
Subject: [PyMOL] RE: Orient molecule

Steve,

This is something PyMOL can do with a little help from Python...
 =20
# PyMOL script: view2coord.pml

# get the current camera matrix
v=3Dcmd.get_view()

# translate atoms to the current origin of rotation
alter_state 1, all, \
(x,y,z) =3D (x-v[12],y-v[13],z-v[14])

# apply the rotation (matrix multiplication)
alter_state 1, all, \
(x,y,z) =3D (x*v[0]+y*v[3]+z*v[6], \
x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8])

# end script

After loading a molecule and choosing a view (either with the mouse, or
using commands like "orient", "turn", "move", "center", etc.), you then
simply run the script and save the new coordinates:

load original_mol.pdb
orient
center 10/ca
@view2coord.pml
save transformed_mol.pdb
quit

Oh, and yes, PyMOL is still free unless you choose to pay for it.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
 =20

> -----Original Message-----
> From: Computational Chemistry List=20
> [mailto:che...@cc...] On Behalf Of Steve Bowlus
> Sent: Wednesday, June 23, 2004 8:42 PM
> To: che...@cc...
> Subject: CCL:Orient molecule
>=20
> I am frantically searching for a simple piece of code that=20
> will allow me to:
>=20
> Read a standard file (mol, pdb, Sybyl ...) select an atom to=20
> put at the Cartesian origin select an atom to put on the X=20
> axis select an atom to put in the XY plane Do a rigid=20
> rotation Do sequential rigid rotations about Cartesian axes=20
> Freeze the molecule in the new orientation Output the NEW,=20
> transformed coordinates.
>=20
> This is equivalent to the Sybyl "orient" command, plus rigid=20
> rotations, plus "Freeze molecule". But I have not found a=20
> free (or even cheap) package that will freeze a molecule in=20
> the new coordinates before output.
>=20
> Thanks in advance for any pointers,
> Steve
>=20
>=20
> -=3D This is automatically added to each message by the mailing=20
> script =3D- To send e-mail to subscribers of CCL put the string=20
> CCL: on your Subject: line and send your message to: =20
> CHE...@cc...
>=20
> Send your subscription/unsubscription requests to:=20
> CHE...@cc...=20
> HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs=20
>=20
> If your mail is bouncing from CCL.NET domain send it to the=20
> maintainer:
> Jan Labanowski,  jla...@nd... (read about it on CCL Home Page)
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+
>=20
>=20
>=20
>=20
>=20
>=20




--__--__--

Message: 2
From: Robert Schwarzenbacher <ro...@sd...>
Date: Wed, 23 Jun 2004 23:46:50 -0700
To: Warren DeLano  <wa...@de...>
Cc: pym...@li...
Subject: [PyMOL] cartoon and alternates

hi there,

I get broken cartoons with alternate conformations. Is there a quick
way to solve this problem?

thanks,

robert

---
Robert Schwarzenbacher, PhD
The Joint Center for Structural Genomics=20
phone: 858 822 3637


--__--__--

Message: 3
From: "Warren DeLano" <wa...@de...>
To: <pym...@li...>
Subject: RE: [PyMOL] cartoon and alternates
Date: Thu, 24 Jun 2004 08:27:49 -0700

Robert,

This sounds like a potential bug.  You might be able to work around it
by
removing all but one alternate conformation...

remove not alt ''+A
rebuild

But I'd like to take a look at the file to understand why PyMOL is
having
trouble.  Could you send me a copy (directly, not via the mailing list)
or
let me know what PDB code to look for?

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Robert Schwarzenbacher
> Sent: Wednesday, June 23, 2004 11:47 PM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: [PyMOL] cartoon and alternates
>=20
> hi there,
>=20
> I get broken cartoons with alternate conformations. Is there=20
> a quick way to solve this problem?
>=20
> thanks,
>=20
> robert
>=20
> ---
> Robert Schwarzenbacher, PhD
> The Joint Center for Structural Genomics
> phone: 858 822 3637
>=20
>=20
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 -=20
> digital self defense, top technical experts, no vendor pitches,=20
> unmatched networking opportunities. Visit www.blackhat.com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20




--__--__--

Message: 4
Date: Thu, 24 Jun 2004 12:08:14 -0400
From: Qun Wan <Qu...@uv...>
To: <pym...@li...>
Subject: [PyMOL] Question about rotation

1.When I want to get the exact rotation of my current view, I did as
the following instruction, but Pymol programe says: invalid syntax. I
do not know why that happens. Could you figure it out for me?

Getting the right view in the script:

When creating the script, it is nice to have the view come up in the
right orientation. To do this, you need to get the coordinates.
First, position the molecule the way you would like it to appear,
this can include zooming and rotating the molecule. Once it is in the
correct position, click on the "Get View" button In the PyMOL window
(the one that doesn't show the molecule), a set_view command will be
created for you and you simply cut (from either the PyMol window or
the Terminal window) and paste this text into your script.

2. If I want to get a particular rotation, what can I do? For
example, if I want to rotation the the current view by 50 degree in
the x-axis, what is the syntax?



--__--__--

Message: 5
Date: Thu, 24 Jun 2004 13:54:29 -0400
From: Qun Wan <Qu...@uv...>
To: <pym...@li...>
Subject: [PyMOL] Questions about rotation view

1.When I want to get the exact rotation of my current view, I did as
the following instruction, but Pymol programe says: invalid syntax. I
do not know why that happens. Could you figure it out for me?

Getting the right view in the script:

When creating the script, it is nice to have the view come up in the
right orientation. To do this, you need to get the coordinates.
First, position the molecule the way you would like it to appear,
this can include zooming and rotating the molecule. Once it is in the
correct position, click on the "Get View" button In the PyMOL window
(the one that doesn't show the molecule), a set_view command will be
created for you and you simply cut (from either the PyMol window or
the Terminal window) and paste this text into your script.

2. If I want to get a particular rotation, what can I do? For
example, if I want to rotation the the current view by 50 degree in
the x-axis, what is the syntax?





--__--__--

_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users


End of PyMOL-users Digest

1.When I want to get the exact rotation of my current view, I did as
the following instruction, but Pymol programe says: invalid syntax. I
do not know why that happens. Could you figure it out for me?

Getting the right view in the script:

When creating the script, it is nice to have the view come up in the
right orientation. To do this, you need to get the coordinates.
First, position the molecule the way you would like it to appear,
this can include zooming and rotating the molecule. Once it is in the
correct position, click on the "Get View" button In the PyMOL window
(the one that doesn't show the molecule), a set_view command will be
created for you and you simply cut (from either the PyMol window or
the Terminal window) and paste this text into your script.

2. If I want to get a particular rotation, what can I do? For
example, if I want to rotation the the current view by 50 degree in
the x-axis, what is the syntax?

1.When I want to get the exact rotation of my current view, I did as
the following instruction, but Pymol programe says: invalid syntax. I
do not know why that happens. Could you figure it out for me?

Getting the right view in the script:

When creating the script, it is nice to have the view come up in the
right orientation. To do this, you need to get the coordinates.
First, position the molecule the way you would like it to appear,
this can include zooming and rotating the molecule. Once it is in the
correct position, click on the "Get View" button In the PyMOL window
(the one that doesn't show the molecule), a set_view command will be
created for you and you simply cut (from either the PyMol window or
the Terminal window) and paste this text into your script.

2. If I want to get a particular rotation, what can I do? For
example, if I want to rotation the the current view by 50 degree in
the x-axis, what is the syntax?

Robert,

This sounds like a potential bug.  You might be able to work around it by
removing all but one alternate conformation...

remove not alt ''+A
rebuild

But I'd like to take a look at the file to understand why PyMOL is having
trouble.  Could you send me a copy (directly, not via the mailing list) or
let me know what PDB code to look for?

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Robert Schwarzenbacher
> Sent: Wednesday, June 23, 2004 11:47 PM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: [PyMOL] cartoon and alternates
> 
> hi there,
> 
> I get broken cartoons with alternate conformations. Is there 
> a quick way to solve this problem?
> 
> thanks,
> 
> robert
> 
> ---
> Robert Schwarzenbacher, PhD
> The Joint Center for Structural Genomics
> phone: 858 822 3637
> 
> 
> -------------------------------------------------------
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hi there,

I get broken cartoons with alternate conformations. Is there a quick
way to solve this problem?

thanks,

robert

---
Robert Schwarzenbacher, PhD
The Joint Center for Structural Genomics 
phone: 858 822 3637

Steve,

This is something PyMOL can do with a little help from Python...
  
# PyMOL script: view2coord.pml

# get the current camera matrix
v=cmd.get_view()

# translate atoms to the current origin of rotation
alter_state 1, all, \
(x,y,z) = (x-v[12],y-v[13],z-v[14])

# apply the rotation (matrix multiplication)
alter_state 1, all, \
(x,y,z) = (x*v[0]+y*v[3]+z*v[6], \
x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8])

# end script

After loading a molecule and choosing a view (either with the mouse, or
using commands like "orient", "turn", "move", "center", etc.), you then
simply run the script and save the new coordinates:

load original_mol.pdb
orient
center 10/ca
@view2coord.pml
save transformed_mol.pdb
quit

Oh, and yes, PyMOL is still free unless you choose to pay for it.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: Computational Chemistry List 
> [mailto:che...@cc...] On Behalf Of Steve Bowlus
> Sent: Wednesday, June 23, 2004 8:42 PM
> To: che...@cc...
> Subject: CCL:Orient molecule
> 
> I am frantically searching for a simple piece of code that 
> will allow me to:
> 
> Read a standard file (mol, pdb, Sybyl ...) select an atom to 
> put at the Cartesian origin select an atom to put on the X 
> axis select an atom to put in the XY plane Do a rigid 
> rotation Do sequential rigid rotations about Cartesian axes 
> Freeze the molecule in the new orientation Output the NEW, 
> transformed coordinates.
> 
> This is equivalent to the Sybyl "orient" command, plus rigid 
> rotations, plus "Freeze molecule". But I have not found a 
> free (or even cheap) package that will freeze a molecule in 
> the new coordinates before output.
> 
> Thanks in advance for any pointers,
> Steve
> 
> 
> -= This is automatically added to each message by the mailing 
> script =- To send e-mail to subscribers of CCL put the string 
> CCL: on your Subject: line and send your message to:  
> CHE...@cc...
> 
> Send your subscription/unsubscription requests to: 
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> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+
> 
> 
> 
> 
> 
> 

Just a quick tip: I came across a PDB file containing a number of NMR 
structures. Besides the actual protein atoms, the file also contained "pseudo 
atoms" corresponding to the geometrical average of groups of equivalent
hydrogen atoms (or something like that). I found that these extra atoms can
be quickly selected with a command like

select dummies,(name QA,QB,QD,QD1,QD2,QE,QE2,QG, \ 
QG1,QG2,QH1,QH2,QQD,QQG,QR,QZ)

The atoms can then be deleted using the "remove atoms" command on the 
"dummies" selection in the PyMOL menu.

-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel

On Jun 22, 2004, at 19:29, Konrad Hinsen wrote:

> So now I am trying chempy.brick. I just installed NumPy into the 
> internal Python (business as usual). However, while I can generate 
> bricks, any isomesh I make from

After recompiling PyMOL, it works fine. Who needs weird file formats 
when one can just pass Python arrays? Python rules!

Konrad.

On Tue, 22 Jun 2004, Konrad Hinsen wrote:

> Bad news. My map has a grid spacing of 2 angstrom, I need better
> resolution than that for placing it.
>
> So now I am trying chempy.brick.

If you're using the CVS version of PyMOL, you might try DX multigrid
formatted files.  You can find some brief documentation here

http://agave.wustl.edu/apbs/doc/html/user-guide/x2539.html

and there's sure to be more at opendx.org (you probably won't need more,
though).

-michael

> I just installed NumPy into the
> internal Python (business as usual). However, while I can generate
> bricks, any isomesh I make from them always has zero lines. This is
> true already for the example script (brick01.py), which generates eight
> meshes that are all empty. Is this a bug?
>
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire L=E9on Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: hi...@ll...
> ---------------------------------------------------------------------
>
>
>
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 -
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>

On Jun 22, 2004, at 16:52, Warren DeLano wrote:

> 	Using crystallographic formats like XPLOR for generic volume
> visualization is tricky because ultimately the map must be aligned on=20=

> a grid
> which passes through the origin.  In other words, the grid spacing =
must

Bad news. My map has a grid spacing of 2 angstrom, I need better=20
resolution than that for placing it.

So now I am trying chempy.brick. I just installed NumPy into the=20
internal Python (business as usual). However, while I can generate=20
bricks, any isomesh I make from them always has zero lines. This is=20
true already for the example script (brick01.py), which generates eight=20=

meshes that are all empty. Is this a bug?

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hi...@ll...
---------------------------------------------------------------------

Peter,

Assuming you have an existing selection

   load my_prot.pdb
   select my_sel, resi 100

You can use the within/of operation...

   color cyan, my_prot within 15 of my_sel
   color red, my_prot within 10 of my_sel

If you needed to exclude the region immediately around the selection, you
could do so with

   color green, (my_prot within 7 of my_sel) and not (my_sel expand 4)

By residue is also an option for coloring complete residues.

   color yellow, byres (my_prot within 7 of my_sel) 

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Peter Teriete
> Sent: Tuesday, June 22, 2004 8:33 AM
> To: pym...@li...
> Subject: [PyMOL] Coloring surfaces by distance
> 
> Hi All,
>  
> I know there was a question regarding this some time ago, but 
> didn't see any reply saying how to do it or a suggesting a 
> possible workaround.
>  
> I have a surface coloured by the underlying residues and am 
> wondering if it is possible to colour an additional part of 
> the surface if it's within a certain distance of the selected 
> residues. 
>  
> Thanks,
>  
> Peter
>  
>  
> Dr Peter Teriete
> Laboratory of Molecular Biophysics
> Department of Biochemistry
> University of Oxford
> South Parks Rd.
> Oxford
> OX1 3QU
>  
> Tel: +44 1865 275742
> Fax: +44 1865 275182
>  
> 

Hi All,
 
I know there was a question regarding this some time ago, but didn't see
any reply
saying how to do it or a suggesting a possible workaround.
 
I have a surface coloured by the underlying residues and am wondering if
it is possible
to colour an additional part of the surface if it's within a certain
distance of the selected
residues. 
 
Thanks,
 
Peter
 
 
Dr Peter Teriete
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Rd.
Oxford
OX1 3QU
 
Tel: +44 1865 275742
Fax: +44 1865 275182
 

Konrad,

	Using crystallographic formats like XPLOR for generic volume
visualization is tricky because ultimately the map must be aligned on a =
grid
which passes through the origin.  In other words, the grid spacing must
include the origin even if the map itself does not.  In order to shift =
the
map away from the origin, you need to move the interval away from the
origin.

For example, to get a map covering the interval 25 to 75 along an axis =
in
XPLOR format, you would need to provide the information as follows:

There unit cell axis is 50 Angstroms.
There are 50 divisions per unit cell.
The range for this axis is 25 to 75.

etc.

Cheers,
Warren



--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Konrad Hinsen
> Sent: Tuesday, June 22, 2004 3:58 AM
> To: <pym...@li...>=20
> <pym...@li...>
> Subject: Re: [PyMOL] Electronic density maps
>=20
> On Jun 22, 2004, at 11:41, Konrad Hinsen wrote:
>=20
> > I'll see if I can get CCP4 format to work in a reasonable amount of=20
> > time...
>=20
> Actually I went for XPlor in the end, after getting a useful hint:
>=20
> 	http://cns.csb.yale.edu/v1.1/tutorial/text.html
>=20
> Problem: the XPlor format does not specify the absolute=20
> position of the map in space. PyMOL must choose it somehow.=20
> Unfortunately, it makes the choice in such a way that my=20
> protein (in a PDB file) is outside the map.
>=20
> Is it possible to shift the map (by a numerically specified=20
> distance) after it has been loaded? I'd rather shift the=20
> single map than redoing a few dozen PDB files.
>=20
> Konrad
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire L=E9on Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: hi...@ll...
> ---------------------------------------------------------------------
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 -=20
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> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

On Jun 22, 2004, at 11:41, Konrad Hinsen wrote:

> I'll see if I can get CCP4 format to work in a reasonable amount of=20
> time...

Actually I went for XPlor in the end, after getting a useful hint:

	http://cns.csb.yale.edu/v1.1/tutorial/text.html

Problem: the XPlor format does not specify the absolute position of the=20=

map in space. PyMOL must choose it somehow. Unfortunately, it makes the=20=

choice in such a way that my protein (in a PDB file) is outside the=20
map.

Is it possible to shift the map (by a numerically specified distance)=20
after it has been loaded? I'd rather shift the single map than redoing=20=

a few dozen PDB files.

Konrad
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hi...@ll...
---------------------------------------------------------------------

On Jun 21, 2004, at 17:36, Warren DeLano wrote:

> Konrad,
>
> There are several options for loading map data into PyMOL now:
>
> XPLOR (format=xplor)
> CCP4  (format=ccpy)
> O/BRIX (format=brix)

Good to know! At least the CCP4 one is documented, but being a binary 
format, it's a bit of a pain to use.

> You can also bypass the file entirely and load an orthogonal "ChemPy 
> brick"
> into PyMOL via NumPy.  Example code for this can be found in

That sounds a lot better!

> examples/devel/brick01.py.  Note that you must use a PyMOL build that
> included numeric Python in order for this to work (the RPMs and Linux
> binaries do not have it, so you may need to build from source using the
> _PYMOL_NUMPY define).  There's also a "ChemPy Map" approach, which 
> expects
> opaque packed C float data.

Well... My choice is PyMOL 0.86 under Linux with NumPy (but 0.86 
doesn't seem to have the ChemPy Brick stuff yet), or 0.95 under MacOS 
(the hybrid build, without NumPy). So I am out of luck... and I can't 
mess around with installations at the moment.

I'll see if I can get CCP4 format to work in a reasonable amount of 
time...

<rant>
Why can't the crystallography community agree on one file format and 
document it properly?
</rant>

Konrad.

Mark,

You don't have to reboot, go to the process tab of windows task manager 
and end the python image underlying PyMOl.

Jules

Mark Wilke wrote:
> Is there any way of stopping a ray trace once it has been started without
> closing pymol?  Some of my ray trace jobs take too long and I want to stop
> them.  I've also noticed that pymol doesn't close very elegently during a
> ray trace job.  I'm working on a windows pc and the "end task" approach
> sometimes doesn't seem to work at all, forcing me to reboot.  
> 
> -Mark
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 - 
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Is there any way of stopping a ray trace once it has been started without
closing pymol?  Some of my ray trace jobs take too long and I want to stop
them.  I've also noticed that pymol doesn't close very elegently during a
ray trace job.  I'm working on a windows pc and the "end task" approach
sometimes doesn't seem to work at all, forcing me to reboot.  

-Mark

Konrad,

There are several options for loading map data into PyMOL now:

XPLOR (format=3Dxplor)
CCP4  (format=3Dccpy)
O/BRIX (format=3Dbrix)

In addition, you can use the following non-crystallographic formats:

Delphi/Grasp PHI files (format=3Dphi)
AVS FLD files (as output from MEAD) (format=3Dfld)

and in the current CVS, we have support for DX files output by APBS
(format=3Ddx).

You can also bypass the file entirely and load an orthogonal "ChemPy =
brick"
into PyMOL via NumPy.  Example code for this can be found in
examples/devel/brick01.py.  Note that you must use a PyMOL build that
included numeric Python in order for this to work (the RPMs and Linux
binaries do not have it, so you may need to build from source using the
_PYMOL_NUMPY define).  There's also a "ChemPy Map" approach, which =
expects
opaque packed C float data.

Once in PyMOL, you can then use "isomesh" and "isosurface" to create =
mesh
and solid isocontours.  Or use "ramp_new" and=20
"color" to color by the potential found in the map.

Sorry about the lack of documentation -- it will improve.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Konrad Hinsen
> Sent: Monday, June 21, 2004 7:10 AM
> To: <pym...@li...>=20
> <pym...@li...>
> Subject: [PyMOL] Electronic density maps
>=20
> I am trying to visualize electronic densities that I prepare=20
> in my own code. This means that I have to write them in XPlor=20
> format in order to load them into PyMOL. Is there anywhere a=20
> detailed description of that format, preferably with some=20
> example files? The best I could find is a summary.
>=20
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire L=E9on Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: hi...@ll...
> ---------------------------------------------------------------------
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by The 2004 JavaOne(SM)=20
> Conference Learn from the experts at JavaOne(SM), Sun's=20
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

I am trying to visualize electronic densities that I prepare in my own=20=

code. This means that I have to write them in XPlor format in order to=20=

load them into PyMOL. Is there anywhere a detailed description of that=20=

format, preferably with some example files? The best I could find is a=20=

summary.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hi...@ll...
---------------------------------------------------------------------

Bill,

	Fit is an extremely finicky command...it only works when the two
objects have matched identifiers for each atom to be superimposed (name,
resi, resn, chain, segi, alt).  Align won't help you because you're using
RNA.  So you'll need to use pair_fit, which requires that you specify a set
of paired atoms in each structure.  Fortunately, you no longer have to
specify each pair separately, so long as the ordering is the same in each
selection (almost always true).  

pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and
name P )

should do the trick.

Cheers,
Warren



--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> William Scott
> Sent: Saturday, June 19, 2004 10:53 PM
> To: pym...@li...
> Subject: [PyMOL] superposition of two molecules
> 
>   This is driving me nuts.  I am trying to superimpose two 
> RNA molecules:
> 
> 
> PyMOL>load trna10.pdb
> ....
> Executive: object "trna10" created.
> PyMOL>load ref4.pdb
> ....
>   Executive: object "ref4" created.
> PyMOL>color blue
>   Executive: Colored 2668 atoms.
> PyMOL>color yellow, ( trna10 and resid 10:15 and name P )
>   Executive: Colored 6 atoms.
> PyMOL>color red, ( ref4 and resid 10:15 and name P )
>   Executive: Colored 6 atoms.
> 
> All of the above works without incident, so the atom 
> selection syntax must be ok.
> 
> Then I want to fit the two sets of colored phosphorus atoms, 
> selecting with the same syntax:
> 
> 
> PyMOL>fit  ( trna10 and resid 10:15 and name P ), ( ref4 and resid 
> 10:15 and name P )
> ExecutiveRMS-Error: No atoms selected.
> 
> same error if I replace fit with rms
> 
> What am I doing wrong?
> 
> 
> 
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