pymol-users Mailing List for PyMOL Molecular Graphics System

By match do you mean, that the new pdb has no more or no less atoms, 
all with the same names so that only the coords and Bs have changed?

Dave


At 3:09 PM -0800 1/31/08, DeLano Scientific wrote:
>David,
>
>So long as the PDB files match, you should be able to:
>
>load new_pdb.pdb, new_object
>
>update old_object, new_object
>
>delete new_object
>
>Cheers,
>Warren
>
>
>--
>DeLano Scientific LLC
>Subscriber Support Services
>mailto:de...@de...
>
>
>>  -----Original Message-----
>>  From: pym...@li...
>>  [mailto:pym...@li...] On Behalf
>>  Of David Garboczi
>>  Sent: Thursday, January 31, 2008 2:54 PM
>>  To: pym...@li...
>>  Subject: [PyMOL] .pse file and new pdb
>>
>>  Suppose one is mouse-oriented and script-averse.
>>
>>  He makes a nice figure with a not-fully-refined model and
>>  saves the .pse file.
>>
>>  Later, refinement is done and he has a new pdb file.
>>
>>  He would like to have that same figure that is encoded in the
>>  .pse file, but using the final pdb file, without repeating
>>  all the mouse-ing.
>>
>>  Is there a way or is he destined to repeat the mouse work? 
>>  He should have turned on the log while he was mouse-ing?
>>
>>  thanks,
>>
>>  Dave
>>
>>  --
>>  David N. Garboczi, PhD
>>  Phone: 301-496-4773
>>  Investigator, Structural Biology Section (SBS) Laboratory of
>>  Immunogenetics (LIG) National Institute of Allergy and
>>  Infectious Diseases (NIAID) National Institutes of Health
>>  (NIH) Twinbrook 2/Room 110
>>  12441 Parklawn Drive
>>  Rockville, Maryland 20852-1742
>>  Fax:    301-402-0284
>>  Email: dga...@ni...
>>
>>
>>
>>
>>  The information in this e-mail and any of its attachments is
>>  confidential and may contain sensitive information. It should not be
>>  used by anyone who is not the original intended recipient. 
>>  If you have
>>  received this e-mail in error please inform the sender and delete it
>>  from your mailbox or any other storage devices.  The National
>>  Institute
>>  of Allergy and Infectious Diseases (NIAID)  shall not accept liability
>>  for any statement made that are the sender's own and not
>>  expressly made
>>  on behalf of the NIAID by one of its representatives.
>>
>>  --------------------------------------------------------------
>>  -----------
>>  This SF.net email is sponsored by: Microsoft
>>  Defy all challenges. Microsoft(R) Visual Studio 2008.
>>  http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>>  _______________________________________________
>>  PyMOL-users mailing list
>>  PyM...@li...
>>  https://lists.sourceforge.net/lists/listinfo/pymol-users


-- 
David N. Garboczi, PhD
Phone: 301-496-4773
Investigator, Structural Biology Section (SBS)
Laboratory of Immunogenetics (LIG)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742	   
Fax:    301-402-0284
Email: dga...@ni...




The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be
used by anyone who is not the original intended recipient.  If you have
received this e-mail in error please inform the sender and delete it
from your mailbox or any other storage devices.  The National Institute
of Allergy and Infectious Diseases (NIAID)  shall not accept liability
for any statement made that are the sender's own and not expressly made
on behalf of the NIAID by one of its representatives.

David,

So long as the PDB files match, you should be able to:

load new_pdb.pdb, new_object

update old_object, new_object

delete new_object

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of David Garboczi
> Sent: Thursday, January 31, 2008 2:54 PM
> To: pym...@li...
> Subject: [PyMOL] .pse file and new pdb
> 
> Suppose one is mouse-oriented and script-averse.
> 
> He makes a nice figure with a not-fully-refined model and 
> saves the .pse file.
> 
> Later, refinement is done and he has a new pdb file.
> 
> He would like to have that same figure that is encoded in the 
> .pse file, but using the final pdb file, without repeating 
> all the mouse-ing.
> 
> Is there a way or is he destined to repeat the mouse work?  
> He should have turned on the log while he was mouse-ing?
> 
> thanks,
> 
> Dave
> 
> --
> David N. Garboczi, PhD
> Phone: 301-496-4773
> Investigator, Structural Biology Section (SBS) Laboratory of 
> Immunogenetics (LIG) National Institute of Allergy and 
> Infectious Diseases (NIAID) National Institutes of Health 
> (NIH) Twinbrook 2/Room 110
> 12441 Parklawn Drive
> Rockville, Maryland 20852-1742
> Fax:    301-402-0284
> Email: dga...@ni...
> 
> 
> 
> 
> The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be
> used by anyone who is not the original intended recipient.  
> If you have
> received this e-mail in error please inform the sender and delete it
> from your mailbox or any other storage devices.  The National 
> Institute
> of Allergy and Infectious Diseases (NIAID)  shall not accept liability
> for any statement made that are the sender's own and not 
> expressly made
> on behalf of the NIAID by one of its representatives.
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Suppose one is mouse-oriented and script-averse.

He makes a nice figure with a not-fully-refined model and saves the .pse file.

Later, refinement is done and he has a new pdb file.

He would like to have that same figure that is encoded in the .pse 
file, but using the final pdb file, without repeating all the 
mouse-ing.

Is there a way or is he destined to repeat the mouse work?  He should 
have turned on the log while he was mouse-ing?

thanks,

Dave

-- 
David N. Garboczi, PhD
Phone: 301-496-4773
Investigator, Structural Biology Section (SBS)
Laboratory of Immunogenetics (LIG)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742
Fax:    301-402-0284
Email: dga...@ni...




The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be
used by anyone who is not the original intended recipient.  If you have
received this e-mail in error please inform the sender and delete it
from your mailbox or any other storage devices.  The National Institute
of Allergy and Infectious Diseases (NIAID)  shall not accept liability
for any statement made that are the sender's own and not expressly made
on behalf of the NIAID by one of its representatives.

Hi people!

I'm trying to apply a transformation matrix to a few atoms in a
representation. By now I'm using a python script that modify the
position vector directly in the pdb, and then load the new pdb, but I
think that should exist some other way to apply the matrix direct with
the pymol.

Something like

   create a,resi 10
   apply_transformation_matrix a, [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]]

Or I'm just dreaming?

Thanks!

-- 
"Two of the most famous products of Berkeley are LSD and Unix. I don't
think that this is a coincidence."
http://servomac.blogspot.com

A little oops!

On Wed, 30 Jan 2008 16:33:00 -0500, I wrote:

> Hi Buz,
> 
> On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow <bu...@ma...> wrote:
> 
> > Does anyone know of a script that is capable of displaying the  
> > surfaces identified by msms in pymol?
> 
> I have a script called msms_cgo.py that you can download from:
> 
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
> 
> Download it and run it. You can get some usage information by doing:
> 
>   PyMOL>msms_cgo ?
>   Usage: msms_cgo file_name [, obj_name [, surfcolor ]]

Unfortunately I had forgotten to add it to the web page itself, although
the file was there.  This is now fixed.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hi Buz,

On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow <bu...@ma...> wrote:

> Does anyone know of a script that is capable of displaying the  
> surfaces identified by msms in pymol?

I have a script called msms_cgo.py that you can download from:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Download it and run it. You can get some usage information by doing:

  PyMOL>msms_cgo ?
  Usage: msms_cgo file_name [, obj_name [, surfcolor ]]

or

  PyMOL>help msms_cgo
  msms_cgo file_name, [obj_name ] , surfcolor
        default surfcolor is white (1.,1.,1.) 
 
So only a file name is required (and you can omit the ".face" or
".vert").  You can just give it a file name (e.g. your surfaces are in
my_mol.vert and my_mol.face:

  msms_cgo my_mol

It will create an object called "my_mol_msms" and colour it white.  If you
want a different colour and object name, then do:

  msms_cgo my_mol, my_surf, surfcolor=(.5,.5,.5)

to make it gray.

Unfortunately it can only do one colour at the moment.  I haven't tried to
modify it to colour the surface according to the atom, although that
shouldn't be too hard to do.

Remember that if the cavities are enclosed, interior surfaces, then they
likely have inward pointing normals and the outside of the cavity will not
be lit unless you select "Two Sided Lighting" from the Display menu.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hi All,

Does anyone know of a script that is capable of displaying the  
surfaces identified by msms in pymol?

It would be nice to have a program that could read in existing .vert   
and .face files. I've included small starting sections of these .face  
and .vert files as examples:

# MSMS solvent excluded surface vertices for protein.xyzr
#vertex #sphere density probe_r
     282    1296  1.00  1.20
    26.022     6.472     7.936    -0.226     0.027    -0.974        
0     607  2
    24.564     6.680     6.807     0.989    -0.147    -0.033        
0     655  2
    25.071     7.472     6.969     0.567    -0.807    -0.168        
0     657  2
    24.499     6.386     6.838     0.956    -0.293    -0.018        
0     655  2
    25.956     6.178     7.966    -0.259    -0.120    -0.958        
0     607  2
    25.398     5.470     7.845     0.206     0.471    -0.858        
0     608  2
    25.738     5.204     7.835     0.376     0.338    -0.863        
0     608  2


# MSMS solvent excluded surface faces for protein.xyzr
#faces  #sphere density probe_r
     560    1296  1.00  1.20
      1      5    195  3      3
    195      5    196  3      3
    195    196      2  3      3
      2    196      4  3      3
      5      8      6  3      5
      6      8      7  3      5
      8     11      9  3      7
      9     11     10  3      7


Thanks! and all the best,

--Buz

Hi Jason,

Thanks a lot for this! I was able to code up a very simple solution to  
my problem using Tsjerk's suggestion.

In my problem I have a series of very similar structures, and I wanted  
to calculate the principal axes of a section of these structures and  
then align the principal axes of another section of the structure with  
those principal axes:

while i < len(eigVectors0001_1):
	# the m matrix is a matrix of the principal axes of segment 1 of  
structure 1
	m = array([eigVectors0001_1[1], eigVectors0001_2[1],  
eigVectors0001_3[1]])
	m = transpose(m)	

	# The n matrix is a matrix of the principal axes of segment of  
structure i
	n = array([eigVectors0001_1[i], eigVectors0001_2[i],  
eigVectors0001_3[i]])
	n = transpose(n)	

	# r is the rotation matrix to rotate the n axes onto the m axes
	r = dot(m,inverse(n))

	# p is a matrix of the principal axes of segment 2 in structure i
	p = array([eigVectors0002_1[i], eigVectors0002_2[i],  
eigVectors0002_3[i]])
	p = transpose(p)

	# q are the rotated principal axes of segment 2 in structure i
	q = dot(r,p)

	i+=1

Thanks again! and all the best,

--Buz


On Jan 29, 2008, at 8:31 AM, Jason Vertrees wrote:

> Buz,
>
> Tsjerk's answer is right on.  This has already been implemented for  
> PyMOL as a
> plugin.  See Kabsch/optAlign from "cealign," here:
>  http://www.pymolwiki.org/index.php/Kabsch
> The code is open-source and so can be applied elsewhere.
>
> Another simple method is to simply calculate the SVD of the  
> correlation
> matrix.  Then multiply the right and left singular vectors by each  
> other --
> that will yield the DxD rotation matrix (where D is the dimension of  
> your
> vector sets).  (This is how Kabsch/optAlign works.)
>
> -- Jason
>
> On Monday 28 January 2008 10:48:29 pm
> pym...@li... wrote:
>> ------------------------------
>>
>> Message: 3
>> Date: Sat, 26 Jan 2008 10:04:06 +0100
>> From: "Tsjerk Wassenaar" <ts...@gm...>
>> Subject: Re: [PyMOL] Algorithm to Rotate One Set of Vectors onto
>>         Another
>> To: "Buz Barstow" <bu...@ma...>
>> Cc: pym...@li...
>> Message-ID:
>>         <8ff...@ma...>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi Buz,
>>
>> To my opinion, this is not the best place for your question. Pymol is
>> a molecular viewer...
>> But the question itself is basically trivial from the linear algebra
>> point of view.
>>
>> If X is your source set of orthogonal vectors and Y is the target,
>> then you should have some sort of matrix R to satisfy
>>
>> Y = RX
>>
>> But, since it should only be a rotation, you'll first have to
>> transform X and Y to their orthonormal counterparts N and M:
>>
>> M = RN
>>
>> Then
>>
>> MN^-1=RNN^-1
>>
>> such that
>>
>> R = MN^-1
>>
>> If both sets are of equal dimensions (and full rank), there's an  
>> exact
>> solution. Otherwise, there's a bit more trouble...
>>
>> So, taking your favourite language with the proper linear algebra
>> package, it comes down to:
>>
>> normalize X -> N
>> normalize Y -> M
>> invert N
>> multiply M with the inverse of N
>>
>> By the way, you're probably dealing with 3x3 matrices here (molecules
>> in cartesian space), in which case the routines are simple enough to
>> write down yourself (I believe these were even in the array.py I
>> posted like two days ago).
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Jan 25, 2008 10:55 PM, Buz Barstow <bu...@ma...> wrote:
>>> Dear All,
>>>
>>> I'm looking for an algorithm that will allow me to derive a
>>> transformation matrix that superimposes one set of orthogonal  
>>> vectors
>>> onto another set of orthogonal vectors, that I can then use to
>>> transform another set of orthogonal vectors.
>>>
>>> Thanks! and all the best,
>>>
>>> --Buz
>
>
>
> -- 
>
> Jason Vertrees (jav...@ut...)
> Doctoral Candidate
> Biophysical, Structural & Computational Biology Program
> University of Texas Medical Branch
> Galveston, Texas
>
> http://www.best.utmb.edu/
> http://www.pymolwiki.org/
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Buz,

Tsjerk's answer is right on.  This has already been implemented for PyMOL a=
s a=20
plugin.  See Kabsch/optAlign from "cealign," here:  =20
  http://www.pymolwiki.org/index.php/Kabsch
The code is open-source and so can be applied elsewhere.

Another simple method is to simply calculate the SVD of the correlation=20
matrix.  Then multiply the right and left singular vectors by each other --=
=20
that will yield the DxD rotation matrix (where D is the dimension of your=20
vector sets).  (This is how Kabsch/optAlign works.)

=2D- Jason

On Monday 28 January 2008 10:48:29 pm=20
pym...@li... wrote:
> ------------------------------
>
> Message: 3
> Date: Sat, 26 Jan 2008 10:04:06 +0100
> From: "Tsjerk Wassenaar" <ts...@gm...>
> Subject: Re: [PyMOL] Algorithm to Rotate One Set of Vectors onto
> =A0=A0=A0=A0=A0=A0=A0=A0Another
> To: "Buz Barstow" <bu...@ma...>
> Cc: pym...@li...
> Message-ID:
> =A0=A0=A0=A0=A0=A0=A0=A0<8ff898150801260104k4902e5f0tcb94e8ebbbf1e027@mai=
l.gmail.com>
> Content-Type: text/plain; charset=3DISO-8859-1
>
> Hi Buz,
>
> To my opinion, this is not the best place for your question. Pymol is
> a molecular viewer...
> But the question itself is basically trivial from the linear algebra
> point of view.
>
> If X is your source set of orthogonal vectors and Y is the target,
> then you should have some sort of matrix R to satisfy
>
> Y =3D RX
>
> But, since it should only be a rotation, you'll first have to
> transform X and Y to their orthonormal counterparts N and M:
>
> M =3D RN
>
> Then
>
> MN^-1=3DRNN^-1
>
> such that
>
> R =3D MN^-1
>
> If both sets are of equal dimensions (and full rank), there's an exact
> solution. Otherwise, there's a bit more trouble...
>
> So, taking your favourite language with the proper linear algebra
> package, it comes down to:
>
> normalize X -> N
> normalize Y -> M
> invert N
> multiply M with the inverse of N
>
> By the way, you're probably dealing with 3x3 matrices here (molecules
> in cartesian space), in which case the routines are simple enough to
> write down yourself (I believe these were even in the array.py I
> posted like two days ago).
>
> Hope it helps,
>
> Tsjerk
>
> On Jan 25, 2008 10:55 PM, Buz Barstow <bu...@ma...> wrote:
> > Dear All,
> >
> > I'm looking for an algorithm that will allow me to derive a
> > transformation matrix that superimposes one set of orthogonal vectors
> > onto another set of orthogonal vectors, that I can then use to
> > transform another set of orthogonal vectors.
> >
> > Thanks! and all the best,
> >
> > --Buz



=2D-=20

Jason Vertrees (jav...@ut...)
Doctoral Candidate
Biophysical, Structural & Computational Biology Program
University of Texas Medical Branch=20
Galveston, Texas

http://www.best.utmb.edu/
http://www.pymolwiki.org/

Chris,

Thanks -- fixed.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Chris Want
> Sent: Monday, January 28, 2008 9:04 AM
> To: pym...@li...
> Subject: [PyMOL] Small VRML export bug
> 
> 
> Hi Warren,
> 
> In the current SVN sources, line 1214 of layer1/Ray.c sets 
> "shininess" equal to 8 for exported VRML files. The VRML97 
> specification, however, wants shininess to be between 0.0 and 1.0.
> So, I would recommend changing the shininess to 0.8.
> 
> Cheers,
> Chris
> 
> --
>   ____________________________________________________________________
> ( Chris Want                                                         )
> ( Research Computing Support                                         )
> ( Academic Information and Communication Technologies (AICT)         )
> ( University of Alberta                                              )
> ( Tel: 1-780-492-9418                                                )
>   --------------------------------------------------------------------
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi Warren,

In the current SVN sources, line 1214 of layer1/Ray.c sets
"shininess" equal to 8 for exported VRML files. The VRML97
specification, however, wants shininess to be between 0.0 and 1.0.
So, I would recommend changing the shininess to 0.8.

Cheers,
Chris

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

Dear Warren,

Does the algorithm support flexible alignment? Thanks a lot!

Best regards,
Linda

DeLano Scientific wrote:
> Linda,
>
> It is not a published algorithm except in the sense that the implementation
> is open-source.  In a nutsheel:
>
> "align" does a BLAST-like BLOSUM62-weighted dynamic programming sequence
> alignment followed by a series of refinement cycles intended to improve the
> fit by eliminating pairing with high relative variability (e.g. >2 standard
> deviations from the cycle's mean deviance).
>
> "super" does a sequence-independent structure-based dynamic programming
> alignment followed by that same 3D refinement strategy.  
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de...
>  
>
>   
>> -----Original Message-----
>> From: pym...@li... 
>> [mailto:pym...@li...] On Behalf Of Lu Lin
>> Sent: Friday, January 25, 2008 4:29 AM
>> To: pym...@li...
>> Subject: [PyMOL] algorithm for alignment
>>
>> Hi all,
>>
>> Anyone know which algorithm PyMOL uses to align or super of 
>> two structures?
>>
>> Thanks a lot!
>>
>> Best,
>> Linda
>>
>>
>>
>> --------------------------------------------------------------
>> -----------
>> This SF.net email is sponsored by: Microsoft Defy all 
>> challenges. Microsoft(R) Visual Studio 2008.
>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>     
>
>   

Hi,

'save' will save all atoms by default, not only the visible ones.
cat in Linux will surely be more efficient than loading in Pymol and
saving, but the question related to alignment. cat doesn't do that for
you. So the procedure would be:

load A.pdb,A
load B.pdb,B
align A,B
save AB-aligned.pdb

Just one addition, Pymol may reorder the atoms. If this is okay (it
won't matter for subsequent displaying), don't bother. Otherwise,
before saving you might want to 'set retain_order,on'

Cheers,

Tsjerk

On Jan 26, 2008 11:11 AM, Martin H=F6fling <mar...@gm...> wrote:
> Am Samstag, 26. Januar 2008 schrieb Lu Lin:
> > Hi, Abhi,
> > You mean save them separately? Is there some way to save them into one
> > file? Thanks!!
>
> By default, the save command should save all (visible?) atoms. Should be =
in
> documentation of save. Any way you can also make a selection of your two
> molecules and save the selection to one file.
>
> Even if you have two files, "cat" will produce a single file quicker than
> loading them into pymol ;-)
>
> Best
>         Martin
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



--=20
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Am Samstag, 26. Januar 2008 schrieb Lu Lin:
> Hi, Abhi,
> You mean save them separately? Is there some way to save them into one
> file? Thanks!!

By default, the save command should save all (visible?) atoms. Should be in 
documentation of save. Any way you can also make a selection of your two 
molecules and save the selection to one file.

Even if you have two files, "cat" will produce a single file quicker than 
loading them into pymol ;-)

Best
	Martin

Hi Buz,

To my opinion, this is not the best place for your question. Pymol is
a molecular viewer...
But the question itself is basically trivial from the linear algebra
point of view.

If X is your source set of orthogonal vectors and Y is the target,
then you should have some sort of matrix R to satisfy

Y = RX

But, since it should only be a rotation, you'll first have to
transform X and Y to their orthonormal counterparts N and M:

M = RN

Then

MN^-1=RNN^-1

such that

R = MN^-1

If both sets are of equal dimensions (and full rank), there's an exact
solution. Otherwise, there's a bit more trouble...

So, taking your favourite language with the proper linear algebra
package, it comes down to:

normalize X -> N
normalize Y -> M
invert N
multiply M with the inverse of N

By the way, you're probably dealing with 3x3 matrices here (molecules
in cartesian space), in which case the routines are simple enough to
write down yourself (I believe these were even in the array.py I
posted like two days ago).

Hope it helps,

Tsjerk


On Jan 25, 2008 10:55 PM, Buz Barstow <bu...@ma...> wrote:
> Dear All,
>
> I'm looking for an algorithm that will allow me to derive a
> transformation matrix that superimposes one set of orthogonal vectors
> onto another set of orthogonal vectors, that I can then use to
> transform another set of orthogonal vectors.
>
> Thanks! and all the best,
>
> --Buz
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi, Abhi,
You mean save them separately? Is there some way to save them into one 
file? Thanks!!
Best,
Linda

Abhinav Verma wrote:
> there is something on the menu, file->save->molecule
> after the alignment, choose the molecule you want to save and just 
> save. pymol saves the pdb with new coordinates.
>
> cheers,
> Abhi
>
> On Jan 25, 2008 10:29 PM, Lu Lin <ll...@cs... 
> <mailto:ll...@cs...>> wrote:
>
>     Hi Hally,
>     Thank you for your reply! Could you tell me how to save the alignment
>     result to a new .pdb file?
>     Thanks again!
>
>     Best,
>     Linda
>
>     Hally Shaffer wrote:
>     > Linda,
>     >
>     > To align two proteins, they have to have the same number of
>     atoms. You can
>     > manipulate the pdb files to delete part of one protein or remove
>     a small
>     > molecule ligand if need be. You will need to save the
>     "corrected" pdb files to
>     > load for the alignment.
>     >
>     > Attached is a picture of two proteins I aligned (one is in the
>     apo form and the
>     > other is the ligand-bound holo form of the protein). The major
>     difference
>     > between the two is indicated in red. I had to load my two pdb
>     files and then the
>     > ligand (rea) as a separate pdb file. The commands are below.
>     >
>     > load 1LBDm.pdb, 1LBD
>     > load 1FBYm.pdb, 1FBY
>     > load REA.pdb, rea
>     >
>     > align 1LBD, 1FBY
>     >
>     >
>     > Good luck,
>     > Hally
>     > --
>     > Hally Shaffer
>     > <>< Graduate Student
>     > Georgia Institute of Technology
>     > School of Chemistry and Biochemistry
>     > gt...@ma... <mailto:gt...@ma...>
>     >
>     >
>     > Quoting Lu Lin <ll...@cs... <mailto:ll...@cs...>>:
>     >
>     >
>     >> Hi all,
>     >>
>     >> Anyone know which algorithm PyMOL uses to align or super of two
>     structures?
>     >>
>     >> Thanks a lot!
>     >>
>     >> Best,
>     >> Linda
>     >>
>     >>
>     >>
>     >>
>     -------------------------------------------------------------------------
>     >> This SF.net email is sponsored by: Microsoft
>     >> Defy all challenges. Microsoft(R) Visual Studio 2008.
>     >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>     >> _______________________________________________
>     >> PyMOL-users mailing list
>     >> PyM...@li...
>     <mailto:PyM...@li...>
>     >> https://lists.sourceforge.net/lists/listinfo/pymol-users
>     >>
>     >>
>     >>
>     >>
>     ------------------------------------------------------------------------
>     >>
>
>
>     -------------------------------------------------------------------------
>     This SF.net email is sponsored by: Microsoft
>     Defy all challenges. Microsoft(R) Visual Studio 2008.
>     http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>     _______________________________________________
>     PyMOL-users mailing list
>     PyM...@li...
>     <mailto:PyM...@li...>
>     https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

Dear Warren,
Thank you for your reply!
Besides, sometimes when I align two structures by their ca atoms, one of 
them keeps trembling, do you know why?

Thanks again!

Best regards,
Linda

DeLano Scientific wrote:
> Linda,
>
> It is not a published algorithm except in the sense that the implementation
> is open-source.  In a nutsheel:
>
> "align" does a BLAST-like BLOSUM62-weighted dynamic programming sequence
> alignment followed by a series of refinement cycles intended to improve the
> fit by eliminating pairing with high relative variability (e.g. >2 standard
> deviations from the cycle's mean deviance).
>
> "super" does a sequence-independent structure-based dynamic programming
> alignment followed by that same 3D refinement strategy.  
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de...
>  
>
>   
>> -----Original Message-----
>> From: pym...@li... 
>> [mailto:pym...@li...] On Behalf Of Lu Lin
>> Sent: Friday, January 25, 2008 4:29 AM
>> To: pym...@li...
>> Subject: [PyMOL] algorithm for alignment
>>
>> Hi all,
>>
>> Anyone know which algorithm PyMOL uses to align or super of 
>> two structures?
>>
>> Thanks a lot!
>>
>> Best,
>> Linda
>>
>>
>>
>> --------------------------------------------------------------
>> -----------
>> This SF.net email is sponsored by: Microsoft Defy all 
>> challenges. Microsoft(R) Visual Studio 2008.
>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>     
>
>   

there is something on the menu, file->save->molecule
after the alignment, choose the molecule you want to save and just save.
pymol saves the pdb with new coordinates.

cheers,
Abhi

On Jan 25, 2008 10:29 PM, Lu Lin <ll...@cs...> wrote:

> Hi Hally,
> Thank you for your reply! Could you tell me how to save the alignment
> result to a new .pdb file?
> Thanks again!
>
> Best,
> Linda
>
> Hally Shaffer wrote:
> > Linda,
> >
> > To align two proteins, they have to have the same number of atoms. You
> can
> > manipulate the pdb files to delete part of one protein or remove a small
> > molecule ligand if need be. You will need to save the "corrected" pdb
> files to
> > load for the alignment.
> >
> > Attached is a picture of two proteins I aligned (one is in the apo form
> and the
> > other is the ligand-bound holo form of the protein). The major
> difference
> > between the two is indicated in red. I had to load my two pdb files and
> then the
> > ligand (rea) as a separate pdb file. The commands are below.
> >
> > load 1LBDm.pdb, 1LBD
> > load 1FBYm.pdb, 1FBY
> > load REA.pdb, rea
> >
> > align 1LBD, 1FBY
> >
> >
> > Good luck,
> > Hally
> > --
> > Hally Shaffer
> > <>< Graduate Student
> > Georgia Institute of Technology
> > School of Chemistry and Biochemistry
> > gt...@ma...
> >
> >
> > Quoting Lu Lin <ll...@cs...>:
> >
> >
> >> Hi all,
> >>
> >> Anyone know which algorithm PyMOL uses to align or super of two
> structures?
> >>
> >> Thanks a lot!
> >>
> >> Best,
> >> Linda
> >>
> >>
> >>
> >>
> -------------------------------------------------------------------------
> >> This SF.net email is sponsored by: Microsoft
> >> Defy all challenges. Microsoft(R) Visual Studio 2008.
> >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------
> >>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Hi Hally,
Thank you for your reply! Could you tell me how to save the alignment 
result to a new .pdb file?
Thanks again!

Best,
Linda

Hally Shaffer wrote:
> Linda,
>
> To align two proteins, they have to have the same number of atoms. You can
> manipulate the pdb files to delete part of one protein or remove a small
> molecule ligand if need be. You will need to save the "corrected" pdb files to
> load for the alignment.
>
> Attached is a picture of two proteins I aligned (one is in the apo form and the
> other is the ligand-bound holo form of the protein). The major difference
> between the two is indicated in red. I had to load my two pdb files and then the
> ligand (rea) as a separate pdb file. The commands are below.
>
> load 1LBDm.pdb, 1LBD
> load 1FBYm.pdb, 1FBY
> load REA.pdb, rea
>
> align 1LBD, 1FBY
>
>
> Good luck,
> Hally
> --
> Hally Shaffer
> <>< Graduate Student
> Georgia Institute of Technology
> School of Chemistry and Biochemistry
> gt...@ma...
>
>
> Quoting Lu Lin <ll...@cs...>:
>
>   
>> Hi all,
>>
>> Anyone know which algorithm PyMOL uses to align or super of two structures?
>>
>> Thanks a lot!
>>
>> Best,
>> Linda
>>
>>
>>
>> -------------------------------------------------------------------------
>> This SF.net email is sponsored by: Microsoft
>> Defy all challenges. Microsoft(R) Visual Studio 2008.
>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>     
>>
>> ------------------------------------------------------------------------
>>

Dear All,

I'm looking for an algorithm that will allow me to derive a  
transformation matrix that superimposes one set of orthogonal vectors  
onto another set of orthogonal vectors, that I can then use to  
transform another set of orthogonal vectors.

Thanks! and all the best,

--Buz

Linda,

It is not a published algorithm except in the sense that the implementation
is open-source.  In a nutsheel:

"align" does a BLAST-like BLOSUM62-weighted dynamic programming sequence
alignment followed by a series of refinement cycles intended to improve the
fit by eliminating pairing with high relative variability (e.g. >2 standard
deviations from the cycle's mean deviance).

"super" does a sequence-independent structure-based dynamic programming
alignment followed by that same 3D refinement strategy.  

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of Lu Lin
> Sent: Friday, January 25, 2008 4:29 AM
> To: pym...@li...
> Subject: [PyMOL] algorithm for alignment
> 
> Hi all,
> 
> Anyone know which algorithm PyMOL uses to align or super of 
> two structures?
> 
> Thanks a lot!
> 
> Best,
> Linda
> 
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Microsoft Defy all 
> challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi all,

Anyone know which algorithm PyMOL uses to align or super of two structures?

Thanks a lot!

Best,
Linda

## (: Python proof E-mail :) ##

# Hi Jo=E3o,
#
# It indeed appears that the attachments are not preserved for the
list (or that one at least)
# You can save the text of this mail as arrow.py and run it instead.
#
# Best,
#
# Tsjerk

from pymol import cmd
from pymol.cgo import *
from math import *

#
# Some functions to allow drawing arrows (vectors) in Pymol
# In need of proper documentation...
#
# Please don't distribute (parts of) this file, without credits
#
# (c)2006 Tsjerk A. Wassenaar, PhD, University of Utrecht
#
# t s j e r k w .at. g m a i l .dot. c o m
# http://nmr.chem.uu.nl/~tsjerk/
#

def t( X ):
    if not X: return X
    Y =3D []
    for i in range( len( X[0] ) ):
        Y.append( [] )
        for j in X:
            Y[i].append( j[i] )
    return Y

def v_add( a, b ):   return ( a[0]+b[0], a[1]+b[1], a[2]+b[2] )
def v_sub( a, b ):   return ( a[0]-b[0], a[1]-b[1], a[2]-b[2] )
def vecprod( a, b ): return ( a[1]*b[2]-a[2]*b[1],
a[2]*b[0]-a[0]*b[2], a[0]*b[1]-a[1]*b[0] )
def inprod( a, b=3DNone ):
    if b: return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]
    else: return a[0]*a[0] + a[1]*a[1] + a[2]*a[2]
def svmult( s, a ):  return ( s*a[0], s*a[1], s*a[2] )
def norm( a ):       return svmult( 1/sqrt(inprod( a )), a )

def mvmult( R, x ):
    y =3D []
    for i in R: y.append( inprod( i, x ) )
    return tuple(y)

def mv_add( X, a ):
    Y =3D []
    for i in X:
        Y.append( v_add( i, a ) )
    return Y

def mmmult( R, X ):
    Y =3D []
    for i in X: Y.append( mvmult( R, i ) )
    return Y

def smatrix( v ): return [[ v[0], 0, 0 ], [ 0, v[1], 0 ], [ 0, 0, v[2] ]]
def rmatrix( v ):
    cosx, sinx =3D cos( v[0] ), sin( v[0] )
    cosy, siny =3D cos( v[1] ), sin( v[1] )
    cosz, sinz =3D cos( v[2] ), sin( v[2] )

    return mmmult( mmmult( [[1,0,0],[0,cosx,-sinx],[0,sinx,cosx]],
                          [[cosy,0,-siny],[0,1,0],[siny,0,cosy]] ),
                   [[cosz,-sinz,0],[sinz,cosz,0],[0,0,1]] )

def block( i, dphi ):
    ddphi =3D 0.25*dphi
    phi0  =3D i*dphi
    phi1  =3D phi0+ddphi
    phi2  =3D phi1+ddphi
    phi3  =3D phi2+ddphi
    phi4  =3D phi3+ddphi
    sqrt2 =3D sqrt(2)
    return [  (-0.5*sqrt2,-0.5*sqrt2*cos(phi2),0.5*sqrt2*sin(phi2)),
              (1,0,0),
              (0,cos(phi0),-sin(phi0)),
              (0,cos(phi1),-sin(phi1)),
              (0,cos(phi2),-sin(phi2)),
              (0,cos(phi3),-sin(phi3)),
              (0,cos(phi4),-sin(phi4))
           ]

def cgo_triangle_fan( X ):
    Y =3D []
    while ( X ):
        i =3D X.pop(0)
        Y.extend( [ NORMAL, i[0], i[1], i[2], ] )
        for i in range( 6 ):
            i =3D X.pop(0)
            Y.extend( [ VERTEX, i[0], i[1], i[2], ] )
    return Y

def cgo_arrow1( S, E, r=3D0.2, hr=3D0.4, hl=3D1.0 ):
    P0 =3D S
    D  =3D v_sub( E, S )
    DL =3D inprod( D, D )
    P1 =3D v_add( S, svmult( (DL-hl)/DL, D ) )
    P2 =3D E

    # Define a vector orthogonal to P1-P0
    V =3D v_sub( P1, P0 )
    V =3D norm( V )
    if V[2] !=3D 0:
        A =3D ( 1, 1, -(V[0]+V[1])/V[2] )
    elif V[1] !=3D 0:
        A =3D ( 1, -V[0]/V[1], 0 )
    else:
        A =3D ( 0, -V[0], 0 )
    A =3D norm( A )

    B =3D vecprod( V, A )
    print (inprod(V), inprod(B), inprod(A))
    R =3D t([ svmult( hl,V ), svmult( hr,A ), svmult( hr,B ) ])

    # Define the transformation matrix (scale and rotation)
    #C =3D v_sub( P2, P1 )
    #scale  =3D ( hl, hr, hr )
    #rotate =3D ( 0, acos( C[0]/sqrt(C[0]**2+C[2]**2) ), acos(
C[0]/sqrt(C[0]**2+C[1]**2) ) )
    #R =3D mmmult( smatrix( scale ), rmatrix( rotate ) )

    obj =3D [
      CYLINDER, S[0], S[1], S[2], P1[0], P1[1], P1[2], r, 1, 1, 1, 1, 1, 1,
      COLOR, 1, 0, 0,
      BEGIN, TRIANGLE_FAN ]

    N =3D 10
    dphi =3D 2*pi/N
    crds =3D []
    for i in range(N+1):
        crds.extend( block( i, dphi ) )
    crds =3D mv_add( mmmult( R, crds ), P1 )
    obj.extend( cgo_triangle_fan( crds ) )
    obj.extend( [ END, ] )

    return obj

def cgo_arrow( S, E, r=3D0.2, hr=3D0.4, hl=3D1.0, name=3D"arrow", state=3D1=
 ):
    obj =3D cgo_arrow1( S, E, r=3Dr, hr=3Dhr, hl=3Dhl )
    cmd.load_cgo( obj, name, state )

def cgo_arrows( X, r=3D0.2, hr=3D0.4, hl=3D1.0, name=3D"arrow", state=3D1 )=
:
    obj =3D []
    for i in X:
        obj.extend( cgo_arrow1( (i[0], i[1], i[2]), (i[3], i[4],
i[5]), r=3Dr, hr=3Dhr, hl=3Dhl ) )

    cmd.load_cgo( obj, name, state )


#--
# Tsjerk A. Wassenaar, Ph.D.
# Junior UD (post-doc)
# Biomolecular NMR, Bijvoet Center
# Utrecht University
# Padualaan 8
# 3584 CH Utrecht
# The Netherlands
# P: +31-30-2539931
# F: +31-30-2537623

Hi Hally,

It's worthwhile getting on terms with Linux. You mention you start a
"blank program" suggesting to me you're starting pymol without
anything to be loaded ("pymol"). It's not true that this can only be
done in the pymol directory. You can do it anywhere, as long as you've
got pymol in your PATH or you explicitly include the directory where
the pymol executable is. If you do it in the directory where you're
foo.pml file is, you can just do 'pymol foo.pml'. Otherwise you could
still do 'pymol /home/hally/somedirectory/foo.pml'.
The same goes if you've just started pymol. If you've started it in
the correct directory, you can just do @foo.pml. In any case you can
do @/home/hally/somedirectory/foo.pml. You could also, within pymol,
change directories to go to the place where you have the script, as
Lieven suggests. The thing is, you need to tell the computer where the
programs/scripts are. It can't know it by itself. It only 'knows'
which directory it was called from.

Cheers,

Tsjerk


On 1/23/08, Hally Shaffer <gt...@ma...> wrote:
> I installed pymol onto a linux system.  I can open the program, open the pdb
> file, and open a .pse file, but I cannot open the .pml file which contains the
> manipulations that I've already made. Any suggestions?
>
> --
> Hally Shaffer
> <>< Graduate Student
> Georgia Institute of Technology
> School of Chemistry and Biochemistry
> gt...@ma...
>
>
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi All,
=20
I am looking for a script to draw arrows.=20
I know this has been discussed before in the mailing list, but I can not do=
wnload the attachment "arrow.py" from this message:
http://sourceforge.net/mailarchive/message.php?
msg_id=3D8ff898150701110024y4b111ab2ic195813792c4b8d%40mail.gmail.com
=20
I get something like "File not found on server"
=20
Does anyone know how I can get this file?
Or maybe does anyone have similar script that could send me?
=20
Many Thanks
Joao
_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/=