pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Warren:
	If you're not already saturated with volunteers, please count
me in.  I've got everything on hand that you're looking for below,
with the only note being that I've got the standard QT 6.4 installed
but not the pro version.  That being said, I'm game!

Sincerely,
Kevin

On Saturday, Nov 29, 2003, at 22:25 US/Central, 
pym...@li... wrote:

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> Today's Topics:
>
>    1. A Few Good Mac PyMOL OS X Beta Testers (Warren L. DeLano)
>
> --__--__--
>
> Message: 1
> From: "Warren L. DeLano" <wa...@de...>
> To: "'pymol'" <pym...@li...>
> Date: Sat, 29 Nov 2003 16:59:30 -0800
> Subject: [PyMOL] A Few Good Mac PyMOL OS X Beta Testers
>
> Mac Users:
>
> I have something new in the works for OS X/Aqua and need some beta
> testers for the next couple of months.
>
> Specifically, I am looking for users who:
>
> 1) have experience with full PyMOL (under Fink, X11, or Windows).
> 2) are current PyMOL sponsors/subscribers.
> 3) are running OS X 10.2.8 or 10.3.
> 4) have QuickTime 6.4 installed.
> 5) would value a Mac-enhanced PyMOL derivative.
> 6) don't mind closed-source software.
>
> If you meet all of these qualifications, please email me.  If you 
> don't,
> then please sit tight for now -- more information will be forthcoming 
> in
> January.
>
> Thanks,
> Warren
>
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax   (650)-593-4020
>
>
>
>
>
>
> --__--__--
>
> _______________________________________________
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> PyM...@li...
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> End of PyMOL-users Digest
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--
**********************************************************************
Kevin Gardner, Ph.D.                  Kev...@ut...
Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center
214-648-8916/FAX: -8947                      http://freedom7.swmed.edu

Mac Users:

I have something new in the works for OS X/Aqua and need some beta
testers for the next couple of months.

Specifically, I am looking for users who:

1) have experience with full PyMOL (under Fink, X11, or Windows).
2) are current PyMOL sponsors/subscribers.
3) are running OS X 10.2.8 or 10.3.
4) have QuickTime 6.4 installed.
5) would value a Mac-enhanced PyMOL derivative.
6) don't mind closed-source software.

If you meet all of these qualifications, please email me.  If you don't,
then please sit tight for now -- more information will be forthcoming in
January.

Thanks,
Warren

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

Hi all,

In the PyMOL of new version 0.93, the setting ribbon_sampling seems not
working to me. The ribbon representation is always the CA-trace, which
means ribbon_sampling is fixed at 1. The CA-trace does not change to
smooth curve after setting ribbon_sampling to other values. Do we get
some new settings to control ribbon? 

Thanks.
-- 
Keqiong Ye, PhD
Sloan Kettering Institute
411 E 67TH Street, RRL 269
New York, NY 10021, USA
Tel: (212) 639-7986 Fax: (212) 717-3066

Igor is right.  However, there is a new command in recent versions
 
map_double map-name

that will cut the map spacing in half by interpolating a new map via
trilinear interpolation.  This will generate a map with 2^3 = 8-fold
more grid points (and require 8X more RAM!)

load map1.ccp4
map_double map1
isomesh mesh1, map1, 1.0

will generate a mesh with half the spacing of the original map.

Note that map_double can usually only be used once on a given map before
averaging artifacts appear.

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:pymol-users-
> ad...@li...] On Behalf Of Igor Pechersky
> Sent: Tuesday, November 25, 2003 7:23 AM
> To: mwilke
> Cc: pym...@li...
> Subject: Re: [PyMOL] electron density settings
> 
>  mwilke <mw...@in...>:
> > Does anyone know how to alter the isomesh settings?  I'm trying to
> prepare
> > a figure with pretty electron density and would like to be able to
> decrease
> > the gap size of the mesh.  I found the variables that seem to make
sense
> > like "mesh_quality" and "min_mesh_spacing", but changing these
variables
> > doesn't seem to do anything.  "mesh_width" and "mesh_radius" only
> control
> > the thickness of the mesh lines.
> 
> Mark,
> you are correct, saying that "mesh_quality" and "min_mesh_spacing"
have
> nothing with
> isomesh. They are used only for surface maps (RepMesh). For map-based
> mesh, PyMOL uses
> dimension from the density map itself, without "smoothing
interpolations".
> So, to
> increase "visual toughness" of your isomesh, you should just load more
> fine-grained
> density map...
> As a "visualization trick", one might try to play with the set of
> isomeshes, based on
> the same density map and slightly differentiated by level, like this:
> 
> isomesh mesh1, map1, 1.0
> isomesh mesh2, map1, 1.25
> isomesh mesh3, map1, 1.50
> isomesh mesh4, map1, 1.75
> isomesh mesh5, map1, 2.0
> 
> and then color them differently.
> 
> 
> BTW, even with RepMesh you can't decrease gap size (via
min_mesh_spacing)
> less than
> some "hard lower threshold" - roughly, it is equivalent to 80 lines
per
> maximal
> dimension of the surrounding box for the underlying object.
> mesh_quality deals rather with the level of icosahedron approximations
for
> spheres...
> 
> 
> 
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 mwilke <mw...@in...>:
> Does anyone know how to alter the isomesh settings?  I'm trying to prepare
> a figure with pretty electron density and would like to be able to decrease
> the gap size of the mesh.  I found the variables that seem to make sense
> like "mesh_quality" and "min_mesh_spacing", but changing these variables
> doesn't seem to do anything.  "mesh_width" and "mesh_radius" only control
> the thickness of the mesh lines.

Mark,
you are correct, saying that "mesh_quality" and "min_mesh_spacing" have nothing with 
isomesh. They are used only for surface maps (RepMesh). For map-based mesh, PyMOL uses 
dimension from the density map itself, without "smoothing interpolations". So, to 
increase "visual toughness" of your isomesh, you should just load more fine-grained 
density map...
As a "visualization trick", one might try to play with the set of isomeshes, based on 
the same density map and slightly differentiated by level, like this:

isomesh mesh1, map1, 1.0
isomesh mesh2, map1, 1.25
isomesh mesh3, map1, 1.50
isomesh mesh4, map1, 1.75
isomesh mesh5, map1, 2.0

and then color them differently.


BTW, even with RepMesh you can't decrease gap size (via min_mesh_spacing) less than 
some "hard lower threshold" - roughly, it is equivalent to 80 lines per maximal 
dimension of the surrounding box for the underlying object. 
mesh_quality deals rather with the level of icosahedron approximations for spheres...

Nat et al:

1. For fortran, there is also an f2py interface:

http://cens.ioc.ee/projects/f2py2e/

2. Some things just seem far easier in perl, like is there a one line 
python-equivalent for this:

perl -pi -e 's/old/new/g' myfile.txt

?

3.  There is now a python-objective C bridge if you want to use python 
to program OS X aqua interfaces:

http://pyobjc.sourceforge.net/


Bill

Dear PyMol users,

I still have the problem, that rather frequently the hardware stereo is 
inverted on my linux box (RedHat 9.0/XFree86 4.3.0/Nvidia Quadro4 980 XGL 
with Nvidia driver 1.0-4496). I thought that I have solved the problem by 
setting and exporting the environment variable __GL_SYNC_TO_VBLANK in my 
.bashrc file, but this rather annoying problem still persists. So, has 
anybody else experienced this and maybe found a solution?

Best regards,

Dirk.

-- 

"Make everthing as simple as possible,
 but not simpler." Albert Einstein

****************************************
Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: 	+41-56-310-4722
Fax: 	+41-56-310-5288
E-mail:	dir...@ps...
http://sb.web.psi.ch
****************************************

Does anyone know how to alter the isomesh settings?  I'm trying to prepare a figure with pretty electron density and would like to be able to decrease the gap size of the mesh.  I found the variables that seem to make sense like "mesh_quality" and "min_mesh_spacing", but changing these variables doesn't seem to do anything.  "mesh_width" and "mesh_radius" only control the thickness of the mesh lines.

Thanks for the help with the loop radius and variable list.  It was just what I wanted.

- Mark Wilke

> I am not suggesting at all that users should now start coding for PyMOL
> in BASIC - naturally, the best way to extend PyMOL remains to write
> additional program modules in Python. Nevertheless, for people who
> already write code in languages other than Python, the above strategy
> might represent a useful alternative (well, until they learn Python
> anyway!)

Alternately, those of us who know Python can probably convert Perl code in
a fairly short time - a far easier task than writing the script from
scratch.  I've done similar stuff before; it's not too difficult once you
remember where to use the accursed dollar signs.

I completely sympathize with your use of Perl; I've grown to hate it, but
it's always the quickest solution even if I regret it months later.
However, I've decided that next time I need to write something large I'm
going to spend the extra time to master Python or Java.

It'd be wonderful if people would similarly wean themselves off Fortran
77. . . it's already a decade too late.

Just another little tip:

At the pymol GUI click at the "setting" menu and then "edit all".
There you will find all the variables you can set with very obvious names.

Hope it helps.

Mario Sanches

Luca Jovine wrote:
> Hi Mark,
>=20
>> (1) Does anyone know how to adjust the radius of the cartoon loops?
>=20
>=20
> set cartoon_loop_radius =3D <value>
>=20
>> (2) Is there a comprehensive list of these variable somewhere on-line =
or
>> in the program files that I can access?  I can't find these kind of
>> details in the on-line manual/reference and I feel stupid asking this=20
>> kind
>> of basic question to everyone.
>=20
>=20
> You can define a new function "setting_list" in a .py file (for example=
=20
> "setting_list.py"):
>=20
> def setting_list():
>     list =3D setting.get_name_list()
>     for name in list:
>         print "%s =3D> %s" % (name, setting.get_setting_text(name))
> cmd.extend('setting_list',setting_list)
>=20
> then simply type the following from within PyMOL:
>=20
>     PyMOL> run setting_list.py
>     PyMOL> setting_list
>=20
>=20
> Hope this helps - Luca
>=20
> --------------------------------------------------------
> 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
> --------------------------------------------------------
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive?  Does it
> help you create better code?  SHARE THE LOVE, and help us help
> YOU!  Click Here: http://sourceforge.net/donate/
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

--=20
Mario Sanches,  PhD Student
Protein Crystallography Group
S=E3o Paulo University, S=E3o Carlos Physics Institute
Phone:  +55 (16) 273 9868
sa...@if...

Hi Mark,

> (1) Does anyone know how to adjust the radius of the cartoon loops?

set cartoon_loop_radius = <value>

> (2) Is there a comprehensive list of these variable somewhere on-line 
> or
> in the program files that I can access?  I can't find these kind of
> details in the on-line manual/reference and I feel stupid asking this 
> kind
> of basic question to everyone.

You can define a new function "setting_list" in a .py file (for example 
"setting_list.py"):

def setting_list():
	list = setting.get_name_list()
	for name in list:
		print "%s => %s" % (name, setting.get_setting_text(name))
cmd.extend('setting_list',setting_list)

then simply type the following from within PyMOL:

	PyMOL> run setting_list.py
	PyMOL> setting_list


Hope this helps - 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
--------------------------------------------------------

(1) Does anyone know how to adjust the radius of the cartoon loops?

(2) Is there a comprehensive list of these variable somewhere on-line or
in the program files that I can access?  I can't find these kind of
details in the on-line manual/reference and I feel stupid asking this kind
of basic question to everyone.

Thanks in advance.

- Mark Wilke

Dear PyMOL users,

Following my previous posting of today about nuccyl, there's a general 
comment I'd like to make. I apologize in advance if it will seem 
trivial, but I don't recall reading anything about this on the mailing 
list, so here it goes.

Somewhat unorthodoxically for a PyMOL-related piece of code, the nuccyl 
program happens to be written in Perl and not in Python. The reason for 
this has nothing to do with the relative merits of the two languages, 
but simply with the fact that I know the former much better (blush).

However, the point I want to make is that, because nuccyl communicates 
with PyMOL by outputting standard coordinate (.pdb) and PyMOL command 
(.pml) files, it doesn't really matter in which language it was 
written. In fact, by outputting a list of PyMOL commands, any 
programming language could in principle be used to extend PyMOL's 
functionality.

I am not suggesting at all that users should now start coding for PyMOL 
in BASIC - naturally, the best way to extend PyMOL remains to write 
additional program modules in Python. Nevertheless, for people who 
already write code in languages other than Python, the above strategy 
might represent a useful alternative (well, until they learn Python 
anyway!)

Just a thought...

Ciao, 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
--------------------------------------------------------

Dear PyMOL users,

Following a useful suggestion by Tassos Perrakis, I added support for 
3DNA (http://rutchem.rutgers.edu/~xiangjun/3DNA/) to the program 
nuccyl, which can be used to generate Ribbons-style nucleic acid 
representations within PyMOL.

In practical terms, this means that nuccyl can now automatically output 
coordinates of cylinders representing nucleotides not only for RNA 
molecules (this was already implemented through RNAView), but also for 
DNA ones.

You can read about the program and download it from this site:

	 http://www.mssm.edu/students/jovinl02/research/nuccyl.html

I hope you find nuccyl useful; please let me know should you have any 
question or comment.

With best regards - 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
--------------------------------------------------------

I'm still not sure about all this 'cool' stuff - Python looks to me 
like the illegitimate spawn of C and BASIC, but then I used to program 
in 6502 machine code so what do I know .....

Below is a variant of camera_travel (as Pythonised by Lieven Buts) 
which takes an explicit final view matrix as an argument rather than a 
PyMol selection as in the original version. This allows you to specify 
the exact view you want, rather than relying on the combination of 
PyMol 'orient' and 'zoom' command to generate it for you. This is 
particularly useful for defining a base view to which you can return.

For those with tricky E-mail clients the routine is also attached as a 
text file.

Cheers,

Laurence



def camera_view_travel(first,nframes=30,new_view=(\
      1.000000000,    0.000000000,    0.000000000,\
      0.000000000,    1.000000000,    0.000000000,\
      0.000000000,    0.000000000,    1.000000000,\
      0.000000000,    0.000000000,  -50.000000000,\
      0.000000000,    0.000000000,    0.000000000,\
     40.000000000,  100.000000000,    0.000000000 )):
	"""
	Generate progressive view matrices to move the camera smoothly
	from the current view to a new view provided as an argument.

         first   - start frame
         nframes - duration
         new_view  - PyMol view matrix that defines the view at the end 
of the sequence
	"""

	try:
         	first=int(first)
	except:
		print "camera_travel: first frame must be an integer"
		return -1
	
	try:
         	nframes=int(nframes)
	except:
		print "camera_travel: number of frames"

	ff=float(1.0/nframes)

         old_view = cmd.get_view(2)

#       print ( "view : (" + "%8.3f, "*17 + "%8.3f)" ) % (old_view)
#       print "oldtran : %8.3f %8.3f %8.3f" % (old_view[12], 
old_view[13], old_view[14])

#       capture new zoom/clip parameters
         ozc1 = new_view[11]
         ozc2 = new_view[15]
         ozc3 = new_view[16]

#       calculate shift in zoom/clip parameters
         dzc1 = (ozc1 - old_view[11]) * ff
         dzc2 = (ozc2 - old_view[15]) * ff
         dzc3 = (ozc3 - old_view[16]) * ff

         ozc1 = old_view[11]
         ozc2 = old_view[15]
         ozc3 = old_view[16]

#       capture new translation vector component
         ox = new_view[12]
         oy = new_view[13]
         oz = new_view[14]

#       calculate shift vector
         dx = ox - old_view[12]
         dy = oy - old_view[13]
         dz = oz - old_view[14]

         dx = dx*ff
         dy = dy*ff
         dz = dz*ff

         ox = old_view[12]
         oy = old_view[13]
         oz = old_view[14]


#       capture old and new rotation matrix components in quaternion 
form

#       m[0][0] = v[0]  m[0][1] = v[1]  m[0][2] = v[2]
#       m[1][0] = v[3]  m[1][1] = v[4]  m[1][2] = v[5]
#       m[2][0] = v[6]  m[2][1] = v[7]  m[2][2] = v[8]

	qx1,qy1,qz1,qw1 = quaternion(old_view)
	qx2,qy2,qz2,qw2 = quaternion(new_view)

#       calc cosine
         cosom = qx1 * qx2 + qy1 * qy2 + qz1 * qz2 + qw1 * qw2

	limit = 0.001
	if cosom>1.0+limit:
		raise ValueError,"Cosine of omega way out of range (positive)"
	elif cosom>1.0:
		print "Warning: cosom corrected from ",cosom,"to",
		cosom = 1.0
		print cosom

	if cosom<-1.0-limit:
		raise ValueError,"Cosine of omega way out of range (negative)"
	elif cosom<-1.0:
		print "Warning: cosom corrected from ",cosom,"to",
		cosom = 1.0
		print cosom

#       adjust signs
         if (cosom < 0.0):
                 cosom = -cosom
                 to0 = -qx2
                 to1 = -qy2
                 to2 = -qz2
                 to3 = -qw2
         else:
                 to0 = qx2
                 to1 = qy2
                 to2 = qz2
                 to3 = qw2

#       calc coefficients
         omega = acos(cosom)
         sinom = sin(omega)
	if sinom==0.0:
		sinom=limit
		print "Warning: sinom corrected!"

#       restore old view
         cmd.set_view( ("%8.3f, " * 17 + "%8.3f") % tuple(old_view) )

#       loop interpolating over nframes generating interpolated 
quaternion
	for a in range(nframes+1):
                 scale0 = sin((1.0 - float(a*ff)) * omega) / sinom
                 scale1 = sin(float(a*ff) * omega) / sinom
                 rx = scale0 * qx1 + scale1 * to0;
                 ry = scale0 * qy1 + scale1 * to1;
                 rz = scale0 * qz1 + scale1 * to2;
                 rw = scale0 * qw1 + scale1 * to3;

		# convert back to matrix
                 x2 = rx + rx
                 y2 = ry + ry
                 z2 = rz + rz
                 xx = rx * x2
                 xy = rx * y2
                 xz = rx * z2
                 yy = ry * y2
                 yz = ry * z2
                 zz = rz * z2
                 wx = rw * x2
                 wy = rw * y2
                 wz = rw * z2

                 nv0 = 1.0 - (yy + zz)
                 nv3 = xy - wz
                 nv6 = xz + wy

                 nv1 = xy + wz
                 nv4 = 1.0 - (xx + zz)
                 nv7 = yz - wx

                 nv2 = xz - wy
                 nv5 = yz + wx
                 nv8 = 1.0 - (xx + yy)

		# update translation vector
                 ox = ox + dx
                 oy = oy + dy
                 oz = oz + dz

		# update zoom/clip parameters

                 ozc1 = ozc1 + dzc1
                 ozc2 = ozc2 + dzc2
                 ozc3 = ozc3 + dzc3

                 cmd.mdo("%d" % (first), ("set_view (" + "%8.3f, "*17 + 
"%8.3f)") %
                       
(nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1,
		       ox,oy,oz,ozc2,ozc3,old_view[17]))
                 first += 1

         cmd.set_view( ("%8.3f, "*17 + "%8.3f") %
                    
(nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1,
		    ox,oy,oz,ozc2,ozc3,old_view[17]))

On Monday 17 November 2003 14:06, Laurence Pearl wrote:
> I should add that I don't  actually know
> how to program in python and have no idea how its 'tuples' work, so
> this is a very FORTRAN-like routine - feel free to improve it.

I have attached a "Pythonized" version of the code. It uses docstrings
for the functions, try...except blocks to check some of the parameters,
and things like ("%8.3f" * 17) to save some repetition of format 
specifiers. Python is cool!

I have also changed the script to add two commands to PyMol using
cmd.extend: "camtrav first,nframes,selection,zoom,buffer" and 
"seqfly object,firstres,lastres". Usage examples:

#---------------------------------
load protein.pdb
run camera_travel.py
mset 1 x150
zoom all
camtrav 1,100,(resi 50),1,4
mplay

# This will zoom in from the complete molecule to residue 50.
#---------------------------------

#---------------------------------
load protein.pdb
run camera_travel.py
mset 1 x150
seqfly protein,1,8
mplay

# This will visit the sequence from residue 1 to 8
#---------------------------------

Finally, I ran into some trouble in a lysozyme structure (PDB 103L). At 
residue 139, cosom becomes slightly larger than 1 (1.0008 or so) and 
acos(cosom) fails. Also, omega and sinom become zero in this case, so 
the divisions by sinom fail. I added some checks to normalize this 
situation and stop the code from crashing, but we should look into 
what's causing this.

-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel

Hi Warren,

I am trying to use the Numeric module from within my PyMOL "pluggin" 
but I can not get it to work. It complains while importing Numeric. The 
message is:

ImportError: /usr/lib/python2.2/site-packages/Numeric/multiarray.so: 
undefined sybmol: _Py_NoneStruct

I had to change the PYTHONPATH variable in PyMOL 9.3 to get it to see 
Numeric since in 9.3 it seems like PyMOL uses ext as PYTHONPATH. In any 
case I dont think the problem is with changing the PYTHONPATH.  Have 
you been able to import Numeric to PyMOL? Please do let me know and any 
suggestions would be appreciated.

Regards,

Kaushik.

Jack,

* Jack Howarth <ho...@br...> [2003-11-11 11:17] wrote:
>       What exactly is the recommended approach for installing
> and maintaining custom pymol python scripts? While I have seen
> messages describing custom pymol scripts, their installation isn't
> described. Should I put them in the python directory tree or in
> the pymol directory tree with the rest of pymol's own python scripts?
> Or is there a way to have a system wide or local user directory
> that python will check for scripts?                

For myself, I keep the scripts in a directory (~/prog/python) that is
included in my PYTHONPATH environment variable.  The script that starts
pymol then appends to this path what it needs for itself.  I then also
automatically load the scripts via my .pymolrc file:

run /home/rlc/prog/python/load_models.py
run /home/rlc/prog/python/load_sep.py
run /home/rlc/prog/python/color_b.py
run /home/rlc/prog/python/stride_ss.py
run /home/rlc/prog/python/color_by_restype.py
run /home/rlc/prog/python/color_by_attype.py
run /home/rlc/prog/python/draw_cell.py
run /home/rlc/prog/python/draw_symops_cctbx.py
run /home/rlc/prog/python/data2bfactor.py

There is probably a better way, especially for a system-wide approach.

>       I am looking for an approach that will not require me
> to reinstall all of my custom pymol python scripts everytime
> I upgrade python and/or pymol. Thanks in advance for any
> hints.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Dera PyMol users,

it seems that I've "solved" the stereo inversion issue: I've errornously set 
and exported __GL_SYNC_TO_VBLANK environment variable in my .bash_profile 
(assuming it will be inherited to all sub-shells). Setting and exporting it 
in my .bashrc solved this stereo inversion problem. 

Good luck,

Dirk Kostrewa.

-- 

"Make everthing as simple as possible,
 but not simpler." Albert Einstein

****************************************
Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: 	+41-56-310-4722
Fax: 	+41-56-310-5288
E-mail:	dir...@ps...
http://sb.web.psi.ch
****************************************

Well even this late in my career I still aspire to be cool, so here it  
is much as requested, a python routine to make the camera travel from  
place to place in your molecule.

The arguments to the routine are :

FIRST:		frame number for start of the sequence
NFRAMES :	number of frames the sequence takes
SEL :		a valid PyMol atom selection, encased in quotes, which defines  
the view at the end of the sequence
ZFLAG :		a flag to indicate whether the final view should be 'zoomed'  
or not.
ZLEVEL :		the degree of zoom - exactly the same as the 'buffer'  
parameter in PyMol cmd.zoom

The routine generates view matrices that interpolate between the  
current view and the view specified by the atom selection, updating the  
view as it finishes so it can be applied iteratively to travel from  
way-point to way-point.

I've also included a little routine which applies camera_travel  
sequentially to each residue along a polypeptide chain - the movie is  
quite large, and when running fast on a Mac G5 can make you a little  
sea-sick, but it does illustrate the power of the routine. The major  
technical problem comes from the need to interpolate general rotation  
matrices, which is solved by using a quaternion representation. The  
code for this is adapted from an article in a magazine called  
GameDeveloper by Nick Bobick. I should add that I don't  actually know  
how to program in python and have no idea how its 'tuples' work, so  
this is a very FORTRAN-like routine - feel free to improve it.


# camera_travel - Laurence Pearl, November 2003

import cmd
import math

def camera_travel(first,nframes=30,sel='(all)',zflag=0,zlevel=2):

#	first	- start frame
#	nframes	- duration
#	sel	- atom selection that defines the orientation at the end of the  
sequence

	new_view = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
	old_view = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
	nxt = [1,2,0]
	q = [0,0,0,1]
	first=int(first)
	nframes=int(nframes)
	ff=float(1.0/nframes)

	old_view = cmd.get_view(2)

#	print "view : (%8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f,  
%8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f,  
%8.3f)" % (old_view)
#	print "oldtran : %8.3f %8.3f %8.3f" % (old_view[12], old_view[13],  
old_view[14])

#	do orient operation on selection


	cmd.orient(sel,0)

#	if zoom to selection is required add this into view matrix

	if zflag != 0:
		cmd.zoom(sel,zlevel,0,1)

#	get new view

	new_view = cmd.get_view()

#	capture new zoom/clip parameters

	ozc1 = new_view[11]
	ozc2 = new_view[15]
	ozc3 = new_view[16]

#	calculate shift in zoom/clip parameters

	dzc1 = (ozc1 - old_view[11]) * ff
	dzc2 = (ozc2 - old_view[15]) * ff
	dzc3 = (ozc3 - old_view[16]) * ff

	ozc1 = old_view[11]
	ozc2 = old_view[15]
	ozc3 = old_view[16]

#	capture new translation vector component

	ox = new_view[12]
	oy = new_view[13]
	oz = new_view[14]

#	calculate shift vector

	dx = ox - old_view[12]
	dy = oy - old_view[13]
	dz = oz - old_view[14]

	dx = dx*ff
	dy = dy*ff
	dz = dz*ff
	ox = old_view[12]
	oy = old_view[13]
	oz = old_view[14]


#	capture old rotation matrix component

#	m[0][0] = v[0]	m[0][1] = v[1]	m[0][2] = v[2]
#	m[1][0] = v[3]	m[1][1] = v[4]	m[1][2] = v[5]
#	m[2][0] = v[6]	m[2][1] = v[7]	m[2][2] = v[8]

#	convert to quaternion form

	tr = old_view[0]+old_view[4]+old_view[8]

	if tr > 0.0 :
		s = math.sqrt(tr + 1.0)
		qw1 = s / 2.0
		s = 0.5 / s
		qx1 = (old_view[5] - old_view[7]) * s
		qy1 = (old_view[6] - old_view[2]) * s
		qz1 = (old_view[1] - old_view[3]) * s
	else :
		i = 0
		if (old_view[4] > old_view[0]):
			i = 1
		if (old_view[8] > old_view[i+3*i]):
			i = 2
		j = nxt[i]
		k = nxt[j]
		s = math.sqrt ((old_view[i+i*3] - (old_view[j+j*3] +  
old_view[k+k*3])) + 1.0)
		q[i] = s * 0.5
		if (s != 0.0):
			s = 0.5 / s
		q[3] = (old_view[k+3*j] - old_view[j+3*k]) * s
		q[j] = (old_view[j+3*i] + old_view[i+3*j]) * s
		q[k] = (old_view[k+3*i] + old_view[i+3*k]) * s
		qx1 = q[0]
		qy1 = q[1]
		qz1 = q[2]
		qw1 = q[3]


#	capture new rotation matrix component

#	m[0][0] = v[0]	m[0][1] = v[1]	m[0][2] = v[2]
#	m[1][0] = v[3]	m[1][1] = v[4]	m[1][2] = v[5]
#	m[2][0] = v[6]	m[2][1] = v[7]	m[2][2] = v[8]

#	convert to quaternion form

	tr = new_view[0]+ new_view[4]+ new_view[8]

	if tr > 0.0 :
		s = math.sqrt(tr + 1.0)
		qw2 = s / 2.0
		s = 0.5 / s
		qx2 = (new_view[5] - new_view[7]) * s
		qy2 = (new_view[6] - new_view[2]) * s
		qz2 = (new_view[1] - new_view[3]) * s
	else :
		i = 0
		if (new_view[4] > new_view[0]):
			i = 1
		if (new_view[8] > new_view[i+3*i]):
			i = 2
		j = nxt[i]
		k = nxt[j]
		s = math.sqrt ((new_view[i+i*3] - (new_view[j+j*3] +  
new_view[k+k*3])) + 1.0)
		q[i] = s * 0.5
		if (s != 0.0):
			s = 0.5 / s
		q[3] = (new_view[k+3*j] - new_view[j+3*k]) * s
		q[j] = (new_view[j+3*i] + new_view[i+3*j]) * s
		q[k] = (new_view[k+3*i] + new_view[i+3*k]) * s
		qx2 = q[0]
		qy2 = q[1]
		qz2 = q[2]
		qw2 = q[3]

#	calc cosine

	cosom = qx1 * qx2 + qy1 * qy2 + qz1 * qz2 + qw1 * qw2
	
#	adjust signs

	if (cosom < 0.0):
		cosom = -cosom
		to0 = -qx2
		to1 = -qy2
		to2 = -qz2
		to3 = -qw2
	else:
		to0 = qx2
		to1 = qy2
		to2 = qz2
		to3 = qw2

#	calc coefficients

	omega = math.acos(cosom)
	sinom = math.sin(omega)

#	restore old view

	cmd.set_view("%8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f,  
%8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f" %  
(old_view[0],old_view[1],old_view[2],old_view[3],old_view[4],old_view[5] 
,old_view[6],old_view[7],old_view[8],old_view[9],old_view[10],old_view[1 
1],old_view[12],old_view[13],old_view[14],old_view[15],old_view[16],old_ 
view[17]) )

#	loop interpolating over nframes generating interpolated quaternion

	a = 0
	while a  <  (nframes+1) :
		scale0 = math.sin((1.0 - float(a*ff)) * omega) / sinom
		scale1 = math.sin(float(a*ff) * omega) / sinom
		rx = scale0 * qx1 + scale1 * to0;
		ry = scale0 * qy1 + scale1 * to1;
         	rz = scale0 * qz1 + scale1 * to2;
         	rw = scale0 * qw1 + scale1 * to3;

#	convert back to matrix

		x2 = rx + rx
		y2 = ry + ry
		z2 = rz + rz
		xx = rx * x2
		xy = rx * y2
		xz = rx * z2
		yy = ry * y2
		yz = ry * z2
		zz = rz * z2
		wx = rw * x2
		wy = rw * y2
		wz = rw * z2		

		nv0 = 1.0 - (yy + zz)
		nv3 = xy - wz
		nv6 = xz + wy

		nv1 = xy + wz
		nv4 = 1.0 - (xx + zz)
		nv7 = yz - wx

		nv2 = xz - wy
		nv5 = yz + wx
		nv8 = 1.0 - (xx + yy)

#	update translation vector

		ox = ox + dx
		oy = oy + dy
		oz = oz + dz

#	update zoom/clip parameters if required

		if zflag != 0:
			ozc1 = ozc1 + dzc1
			ozc2 = ozc2 + dzc2
			ozc3 = ozc3 + dzc3


		cmd.mdo("%d" % (first),"set_view (%8.3f, %8.3f, %8.3f, %8.3f, %8.3f,  
%8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f,  
%8.3f, %8.3f, %8.3f)" %  
(nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1,ox,oy 
,oz,ozc2,ozc3,old_view[17]))
		a = a + 1
		first = first + 1

	cmd.set_view("%8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f,  
%8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f, %8.3f" %  
(nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1,ox,oy 
,oz,ozc2,ozc3,old_view[17]))



# SEQUENCE VISITOR
ires = 1
fr=1
res=" "
while ires < 215:
	res = "resi %d" % (ires)
	camera_travel(fr,9,res,1,2)
	cmd.mdo("%d" % (fr+10),"show sticks,(resi %d and not n;c,n,o)" %  
(ires))
	fr = fr + 15
	ires = ires + 1






On Thursday, November 13, 2003, at 09:24 PM, classen wrote:

> When making a movie It would be cool if you could set way-points to  
> create a
> sophisticated "tour"
> of your molecule.
>
> Each way-point would be a different view of your molecule.
>
> Then you could specify the number of frames between any two way-points
> (views). Each frame
> would be a specified amount of time and by changing the number of  
> frames you
> would change the
> timing for that particular section of the movie.
>
> Press the play button and voila your tour begins.... zooming in,  
> rotating,
> zooming back out, etc.
>
> Would this be difficult to implement?
>
> Regards,
> Scott Classen
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Scott Classen, Ph.D.
>    ACS Postdoctoral Fellow
>    Department of Molecular & Cell Biology
>    University of California, Berkeley
>    237 Hildebrand Hall #3206
>    Berkeley, CA 94720-3206
>    LAB 510.643.9491
>    FAX 510.643.9290
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
> -------------------------------------------------------
> This SF.Net email sponsored by: ApacheCon 2003,
> 16-19 November in Las Vegas. Learn firsthand the latest
> developments in Apache, PHP, Perl, XML, Java, MySQL,
> WebDAV, and more! http://www.apachecon.com/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
------------------------------------------------------------------------ 
--
   Laurence H. Pearl

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

   Phone +44-207-970 6045 : Secretary +44-207-970 6046
   FAX   +44-207-970 6051 : E-Mail Lau...@ic...
------------------------------------------------------------------------ 
--
   " Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin
------------------------------------------------------------------------ 
--

      What exactly is the recommended approach for installing
and maintaining custom pymol python scripts? While I have seen
messages describing custom pymol scripts, their installation isn't
described. Should I put them in the python directory tree or in
the pymol directory tree with the rest of pymol's own python scripts?
Or is there a way to have a system wide or local user directory
that python will check for scripts?                
      I am looking for an approach that will not require me
to reinstall all of my custom pymol python scripts everytime
I upgrade python and/or pymol. Thanks in advance for any
hints.
                            Jack

There is one other convenient format:  ".pkl", that works like PDB, but
is a Pickled copy of the PyMOL Model Class.  The main advantage this has
over .pdb is that it saves and restores extra properties such as
secondary structure code, atom types, van der waals radii, formal and
partial charges, etc.  

load myprot.pdb
dss
show cartoon
alter 100-110/, ss='H'
alter 65-67,ss='L'
save myprot.pkl

... quit program, complete your PhD, take a vacation, and come back...

load myprot.pkl
show cartoon

will work.

".pkl" has the additional advantage of being a simple molecular object
useful in straight Python, outside of PyMOL.  All you need to do is have
a copy of PyMOL's "chempy" module available in your PYTHONPATH

from chempy import io

model = io.pkl.fromFile("myprot.pkl")
for atom in model.atom:
   print atom.name
   
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 
> Igor Pechersky
> Sent: Friday, November 14, 2003 3:07 AM
> To: an...@bi...; Andreas Foerster
> Cc: pymol
> Subject: Re: [PyMOL] dss & ribbon representation
> 
> 
>  Andreas Foerster <an...@bi...>:
> 
> > - The dss algorithm is great, a very quick way to assign secondary 
> > structure. Is there a way of conserving the information when saving 
> > the pdb?
> There are at least 3 ways to store SS assignments from PyMOL. 
> Depends on your needs:
> 
> 1. Save PyMOL session (*.pse). Atom properties, including 
> "ss", will be restorable by 
> PyMOL.
> 
> 2. Print SS in "PHD-like" format. So, assuming that unfamous 
> 1tii.pdb is loaded
> PyMOL>import pymol
> PyMOL>stored.ss = []
> PyMOL>iterate 1tii//a//ca, stored.ss.append(string.ljust(ss,1))
> PyMOL>print string.join(stored.ss,"")
> 
> will print single string like 
> LSSSSSSLLLHHHHHHHLLLLLLLLLLLLLLLLLLLLLHHHHHHLLLLLLLLLLLSSSSSLL
> HHHHHHHHHHHHLLLLSSSSSSSSLLL
> LSSSHHHHHLLLLLLHHHLLSSSSLLLLHHHLSSSSSSSLLLLLLLLLLLLLLLHHHHLLLL
> LLLHHHHHHHLLLLLLLHHHHLLHHHH
> HLLHHHLL
> 
> 3. Wait for Warren to vivify cSetting_save_pdb_ss :)
> 
> 
> > Sometimes it's nice to edit the assignment.
> I haven't understood your question. You might edit dss 
> assignment just by
> PyMOL>alter pk1, ss='S'
> 
> Is it sufficient? 
> 
> -igor
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by: ApacheCon 2003,
> 16-19 November in Las Vegas. Learn firsthand the latest 
> developments in Apache, PHP, Perl, XML, Java, MySQL, WebDAV, 
> and more! http://www.apachecon.com/ 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li... 
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

 Andreas Foerster <an...@bi...>:

> - The dss algorithm is great, a very quick way to assign secondary
> structure. Is there a way of conserving the information when saving the
> pdb? 
There are at least 3 ways to store SS assignments from PyMOL. Depends on your needs:

1. Save PyMOL session (*.pse). Atom properties, including "ss", will be restorable by 
PyMOL.

2. Print SS in "PHD-like" format. So, assuming that unfamous 1tii.pdb is loaded
PyMOL>import pymol
PyMOL>stored.ss = []
PyMOL>iterate 1tii//a//ca, stored.ss.append(string.ljust(ss,1))
PyMOL>print string.join(stored.ss,"")

will print single string like
LSSSSSSLLLHHHHHHHLLLLLLLLLLLLLLLLLLLLLHHHHHHLLLLLLLLLLLSSSSSLLHHHHHHHHHHHHLLLLSSSSSSSSLLL
LSSSHHHHHLLLLLLHHHLLSSSSLLLLHHHLSSSSSSSLLLLLLLLLLLLLLLHHHHLLLLLLLHHHHHHHLLLLLLLHHHHLLHHHH
HLLHHHLL

3. Wait for Warren to vivify cSetting_save_pdb_ss :)


> Sometimes it's nice to edit the assignment.
I haven't understood your question. You might edit dss assignment just by
PyMOL>alter pk1, ss='S'

Is it sufficient? 

-igor

Hi pymol community. Two questions.

- The dss algorithm is great, a very quick way to assign secondary
structure. Is there a way of conserving the information when saving the
pdb? Sometimes it's nice to edit the assignment.

- In contrast to versions 0.9 and earlier, version 0.93 connects the CA
with straight lines in ribbon representation. It looks conspicuously
like O. Is there a way of smoothing the ribbon?
   set ribbon_smooth, 1 doesn't do the trick.


Thanks a bunch


Andreas


-- 
                    Andreas Förster
Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg.
Salt Lake City, UT 84132, phone: 001.801.585.3919
home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529
        http://www.biochem.utah.edu/~andreas

 sl...@ma...:
> does anyone know how to color only the ribbon of a polypeptide, while
> not coloring the CA atoms when using spheres?
>
duplicate your polypeptide, show the ribbon of one instance and atoms of another one

-igor