pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] g: cgo label orientation

[Robert C. <rl...@k2...>]

* de...@ia... <de...@ia...> [2002-08-20 07:03] wrote:
> On Sat, Aug 17, 2002 at 10:23:46PM +0200, Bartholomeus Kuettner wrote:
> > Hello there!
> > 
> > I followed mailing list instructions to create cgo based labels via a python
> > script. Unfortunately, the labels are not in plane but more like
> > perpendicular. So is there a way to alter the orientation of such cgo
> > labels. I think one could apply pymol's "set_view" matrix to the labels to
> > get them in plane. Wrong idea? Anyway, how one can rotate the cgo labels
> > without rotating the remaining molecule?
> 
> I don't have an answer ready-made for you, but there is a brief mention[1]
> of this problem in the pages Kristian Rother gave a link to several days
> ago.[2]
> 
> [1] http://www.rubor.de/bioinf/pymol_tips.html#cgolabels

That would be my response to a CGO label question back in May.

You could use the cmd.rotate and cmd.translate to position the labels,
but it is likely to be somewhat painful. If I'm not mistaken, the
rotation will always be about and axis through the origin and so you may
need to translate the label into the correct position.

Thus if you have your label in an object called 'text', you could do,

  cmd.rotate(axis='x',angle=20.,object='text')

and repeat this with different angles, until you get the orientation
correct.  Then use:

  cmd.translate(vector='[1.,2.,3.]',object='text')

(using the appropriate vector, of course!) to position the label.

Not ideal, but if it is sufficiently important, it can be done!

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] Secondary structure assignments

[<de...@ia...>]

On Mon, Jul 29, 2002 at 01:12:40PM -0400, Nathaniel Echols wrote:

> How hard would it be to incorporate the DSSP algorithm?  I was looking at
> the source for RasMol, which has a complete implementation.  My feeling is
> that this could be ported without too much misery.  However, RasMol's
> license terms are different, and I suspect even a complete translation
> into Python with the ChemPy API  would still be considered a "derivative
> work", meaning it wouldn't be able to be part of the main distribution,
> and meaning someone would still have to code DSSP from scratch.  (I have
> utterly no idea how it works, but RasMol's code seems clear enough despite
> lack of comments)

I am not a lawyer, just a scientist who happens to be interested
in these sorts of 'intellectual property' problems, so weigh the following
accordingly:

Copyright and the idea of derivative works applies to very specific
expressions of an idea.  So, unless the DSSP algorithym is patented, a
complete re-expression in a language like Python (instead of C or C++ or
whatever RasMol is written in) could probably be made different enough so as
to be an original work, distinct from RasMol's implementation.  This is what
the the Gnu project did with Unix command-line utilities for
example--rewrote them, added features, and so forth.

The best way to avoid "derivative work" concern is to code in a "clean room"
fashion, without reference to someone else's code.  In principle, this could
be done working from the original paper(s) that describe an algorithm.

Not that I'm volunteering ;-)  Just that I would hate to see someone who was
willing and interested in implementing secondary structure code for PyMol to
be frightened off the job if, indeed, it could be done in a way that respects
others' rights.

--Joe

Re: [PyMOL] g: cgo label orientation

[<de...@ia...>]

On Sat, Aug 17, 2002 at 10:23:46PM +0200, Bartholomeus Kuettner wrote:
> Hello there!
> 
> I followed mailing list instructions to create cgo based labels via a python
> script. Unfortunately, the labels are not in plane but more like
> perpendicular. So is there a way to alter the orientation of such cgo
> labels. I think one could apply pymol's "set_view" matrix to the labels to
> get them in plane. Wrong idea? Anyway, how one can rotate the cgo labels
> without rotating the remaining molecule?

I don't have an answer ready-made for you, but there is a brief mention[1]
of this problem in the pages Kristian Rother gave a link to several days
ago.[2]

[1] http://www.rubor.de/bioinf/pymol_tips.html#cgolabels
[2] http://www.geocrawler.com/lists/3/SourceForge/16586/0/9285265/

--Joe

[PyMOL] Transparent spheres

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

Dear PyMOL users,

Does anybody know of a way to either

  i) Change the radius of a specified atom, or
 ii) Make a CGO sphere semi-transparent?

Basically what I want is to be able to place a semi-transparent sphere
of a given radius, at a given point in space.

Thanks in anticipation for any suggestions, 

Gareth

-- 
-----------------------------------------------------------------------------
 Gareth Stockwell
 PhD student, Thornton Group
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                        
ga...@eb...
 Tel 01223 492548            Personal homepage:
http://www.ebi.ac.uk/~gareth

[PyMOL] g: cgo label orientation

[Bartholomeus K. <bku...@ep...>]

Hello there!

I followed mailing list instructions to create cgo based labels via a python
script. Unfortunately, the labels are not in plane but more like
perpendicular. So is there a way to alter the orientation of such cgo
labels. I think one could apply pymol's "set_view" matrix to the labels to
get them in plane. Wrong idea? Anyway, how one can rotate the cgo labels
without rotating the remaining molecule?

Thank you!

Greetings,
Bartholomeus

[PyMOL] q: dash options, transparency, global setting vs.local settings

[Bartholomeus K. <bku...@ep...>]

Dear all!

I've encountered several questions while playing aroung with PyMOL. Maybe
there is someone who could provide some help?

1. dash options

It seems that all the "dash" settings (e.g. "dash_length", "dash_with",
"dash_radius") are global modifiers and cannot be assigned to specific
interactions in a way like "set dash_gap=0.7, dist1". A different dash_gap
would prevent a situation where interactions perpendicular to the plane
become near solid lines while interactions in plane are looking fine.

2. transparency, sphere_transparency

Is it still the case in version 0.82 of PyMOL that transparency setting only
applies to surface or spheres (using sphere_transparency)?

3. global settings vs. local settings

I'm little bit wondering why some of the PyMOL settings one can assign to
different objects (e.g. cartoon_smooth_loops) while others seem to be
incompatible and work for the hole scene (e.g. dash_gap).

Thank you!

Greetings,
Bartholomeus

[PyMOL] Bug in Ray.c resulting in left-handed images with Povray

[Robert C. <rl...@k2...>]

Hi folks,

I found a bug in the povray output from PyMOL, when using the
orthographic perspective (the perspective projection is ok):

I had been playing around with using povray to make fancy images from
PyMOL output, but I noticed (actually somebody else did, I was too busy
admiring the special effects that I could create!) that the povray
output file that I created from pymol gives a mirror image. I simply
create my povray input file with:

	(header,data) = cmd.get_povray()
	povfile=open(file,'w')
	povfile.write(header)
	povfile.write(data)
	povfile.close()

The header looks something like:

camera {orthographic location <0.0 , 0.0 , 146.8305816650>
look_at  <0.0 , 0.0 , -1.0> right 64.2756500244*x up 65.9462890625*y}
#default { finish{phong    0.800 ambient    0.120 diffuse    1.080
phong_size 25.000000}}
light_source{<4000.0001,4000.0001,9853.1694>  rgb<1.0,1.0,1.0>}
plane{z , -236.2687 
 pigment{color rgb<1.0000,1.0000,1.0000>}
 finish{phong 0 specular 0 diffuse 0 ambient 1.0}}

The second line contains the information that describes the view.
To correct the image, I had to change the sign of
the X-axis (the "right" parameter). Thus changing:

   look_at  <0.0 , 0.0 , -1.0> right 64.2756500244*x up 65.9462890625*y}

 to:

   look_at  <0.0 , 0.0 , -1.0> right -64.2756500244*x up 65.9462890625*y}

Since it would be a pain to have to edit the povray file all the time,
I went looking for the word "look_at" in the sournce and I found the
offending lines in layer1/Ray.c (line 508). The diff to my correction
looks like:

*** ./Ray.c.orig        Fri Aug 16 14:35:05 2002
--- Ray.c       Fri Aug 16 13:46:33 2002
***************
*** 507,509 ****
      sprintf(buffer,"camera {orthographic location <0.0 , 0.0 , %12.10f>\nlook_at  <0.0 , 0.0 , -1.0> right %12.10f*x up %12.10f*y}\n",
!             front,I->Range[0],I->Range[1]);
    }
--- 507,509 ----
      sprintf(buffer,"camera {orthographic location <0.0 , 0.0 , %12.10f>\nlook_at  <0.0 , 0.0 , -1.0> right %12.10f*x up %12.10f*y}\n",
!             front,-1*I->Range[0],I->Range[1]);
    }

That is, I simply multiplied I->Range[0] by -1 to swap the hand of the
resulting image.

Hope this helps any confused povray-ers out there,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] Segmentation Fault

[Michael T. <tal...@ho...>]

Dear PyMOL Users,

This may have been answered before but I haven't found the answer yet. I 
have a script that has to iterate over a very large selection of atoms and 
when it runs it comes to a point where pymol shuts down and I recieve the 
message "Segmentation Fault" in my terminal window. I'm looking at trying to 
find out what this problem is and how do I go abot trying to correct it?

Thanks for all your help,
Michael Tallhamer
Undergraduate Researcher
Cleveland State University

_________________________________________________________________
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[PyMOL] manipulating maps

[David v. d. S. <sp...@xr...>]

Hi,

Could someone give me a hint on where to start when I want to manipulate
electron density maps? Where is the class definition for the map class?



-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
sp...@xr...	sp...@gr...   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

[PyMOL] Colour by object

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

Dear PyMOL-ers,

Apologies for not thinking about this question a bit more before mailing
the list - I have now written a script (attached) which does the job.

> Is there a simple way to colour each object currently loaded, with a
> different colour (in the same way that you can colour each chain in a
> molecule differently)?  This would be really useful in visualising a
> set of superposed structures.

The script is also available at

  http://www.ebi.ac.uk/~gareth/misc

Gareth


-- 
-----------------------------------------------------------------------------
 Gareth Stockwell
 PhD student, Thornton Group
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                        
ga...@eb...
 Tel 01223 492548            Personal homepage:
http://www.ebi.ac.uk/~gareth

[PyMOL] surfaces

[Jason M. <ja...@bi...>]

Hello:

Okay, I got the surface from Grasp read in by ungrasping it in
Raster3d.  Now the read in surface loses its electrostatic potential
colouring - is there any way to fix this?

Cheers,
JTM

*************************
Jason Thomas Maynes
MD/PhD Program
Faculty of Medicine
University of Alberta
ja...@bi...
*************************

[PyMOL] grasp surfaces

[Jason M. <ja...@bi...>]

Hello:

This might have been asked before but is there anyway to load an
electrostatic surface from grasp into pymol?

Cheers,
JTM

*************************
Jason Thomas Maynes
MD/PhD Program
Faculty of Medicine
University of Alberta
ja...@bi...
*************************

[PyMOL] Colour by object

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

Is there a simple way to colour each object currently loaded, with a
different colour (in the same way that you can colour each chain in a
molecule differently)?  This would be really useful in visualising a set
of superposed structures.

Gareth


-- 
-----------------------------------------------------------------------------
 Gareth Stockwell
 PhD student, Thornton Group
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                        
ga...@eb...
 Tel 01223 492548            Personal homepage:
http://www.ebi.ac.uk/~gareth

RE: [PyMOL] byres, around, expand etc

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

layer4/Selector.c

http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/pymol/pymol/layer3/Selecto=
r.c

search for SELE_ARD_ and SELE_EXP_ in "SelectorModulate1" in=20

and SELE_BYR1 in "SelectorLogic1"

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



> -----Original Message-----
> From: Michael Tallhamer [mailto:tal...@ho...]
> Sent: Tuesday, August 13, 2002 6:49 PM
> To: pym...@li...
> Subject: [PyMOL] byres, around, expand etc
>=20
>=20
> I would like to take a look at the code for these selection keywords:
>=20
> (byres, around, expand ... etc)
>=20
> Does anyone know where to find it?
>=20
> Thanks,
>=20
> Michael Tallhamer
> Undergraduate Researcher
> Cleveland State University
> E-mail: tal...@ho...
>=20
> _________________________________________________________________
> MSN Photos is the easiest way to share and print your photos:=20
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>=20
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] byres, around, expand etc

[Michael T. <tal...@ho...>]

I would like to take a look at the code for these selection keywords:

(byres, around, expand ... etc)

Does anyone know where to find it?

Thanks,

Michael Tallhamer
Undergraduate Researcher
Cleveland State University
E-mail: tal...@ho...

_________________________________________________________________
MSN Photos is the easiest way to share and print your photos: 
http://photos.msn.com/support/worldwide.aspx

[PyMOL] rTools and Movie for PyMOL released

[Kristian R. <kri...@be...>]

Dear fellows,

We would like to present some effort we have made to integrate some
structure analysis tools into PyMOL. I won't go into detail much, feel 
free to test it out.

Additionally, i have written a script that provides PyMOL commands 
making creation of smooth animations fairly easy.

All the stuff can be found on:
    http://www.rubor.de/bioinf

Authors  : K. Rother, C. Froemmel et al.,
Institute: Protein Structure Theory Group, Charite Berlin
            http://www.charite.de/bioinf

I am very curious to hear bug reports.

Kristian

Re: [PyMOL] cartoon_smooth_loops

[Jason M. <ja...@bi...>]

Hello:

You can create more than one object of the same protein, make one
smooth loops and display only a small section of that one.

Cheers,
JTM

On Sat, 10 Aug 2002, Bartholomeus Kuettner wrote:

> Hello there!
> 
> Is it possible to assign "cartoon_smooth_loops" to specific residues of a
> protein? Let's say, you want to draw cartoons for only one loop directly
> through the CA positions (set ...=0) but want to show smoothed loops
> (set...=1) for the remaining molecule.
> It seems to be a global modifier since an local assigment (set ...=0,
> "residues xyz") does not work.
> 
> Thank you!
> 
> Greetings,
> Bartholomeus Kuettner
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
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> _______________________________________________
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> 

*************************
Jason Thomas Maynes
MD/PhD Program
Faculty of Medicine
University of Alberta
ja...@bi...
*************************

[PyMOL] cartoon_smooth_loops

[Bartholomeus K. <bku...@ep...>]

Hello there!

Is it possible to assign "cartoon_smooth_loops" to specific residues of a
protein? Let's say, you want to draw cartoons for only one loop directly
through the CA positions (set ...=0) but want to show smoothed loops
(set...=1) for the remaining molecule.
It seems to be a global modifier since an local assigment (set ...=0,
"residues xyz") does not work.

Thank you!

Greetings,
Bartholomeus Kuettner

RE: [PyMOL] How to ouput a PDB file with transformed coordinates?

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

No, not a stupid question.  PyMOL doesn't currently provide a means for =
doing this -- I'll put it on the list...

Cheers,
Warren

> -----Original Message-----
> From: Luca Jovine [mailto:luc...@ma...]
> Sent: Thursday, August 08, 2002 4:41 PM
> To: Mailing List PyMol
> Subject: [PyMOL] How to ouput a PDB file with transformed coordinates?
>=20
>=20
> Hello PyMolers,
>=20
> This is probably a really stupid question, but, is there a=20
> simple way to=20
> create a PDB file with *transformed* coordinates? The "save" command=20
> always seems to save the original coordinates, even after=20
> altering the=20
> view with set_view etc...
> I apologize in advance if this is obvious,
>=20
> Thanks Luca
>=20
> --------------------------------------------------------
> Luca Jovine, Ph.D.
> Department of Molecular, Cell & Developmental Biology
> Mount Sinai School of Medicine
> Annenberg Building, Room 25-18
> One Gustave L. Levy Place, New York, NY 10029-6574, USA
> Voice: +1.212.241-8620  FAX: +1.509.356-2832
> E-Mail: luc...@ma...
> W3: http://www.mssm.edu/students/jovinl02
> --------------------------------------------------------
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>=20
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> This sf.net email is sponsored by:ThinkGeek
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> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] How to ouput a PDB file with transformed coordinates?

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

Hello PyMolers,

This is probably a really stupid question, but, is there a simple way to 
create a PDB file with *transformed* coordinates? The "save" command 
always seems to save the original coordinates, even after altering the 
view with set_view etc...
I apologize in advance if this is obvious,

Thanks Luca

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

Re: [PyMOL] Problem with Seleno-Cysteine

[<jo...@al...>]

Am Dienstag, 6. August 2002 18:33 schrieben Sie:
> The problem is that, by default, PyMOL doesn't create ribbons for HETATMs
> (typically ligands and solvent).  With the above command, you're converting
> selenocysteine residues into regular atoms and sorting them into place so
> that they can be included in the ribbon.

Ok, thanks. That does well for now, but wouldn't it be nicer to include this 
"alter" setting as default for pymol, e.g. for ESY and MSE (Seleno- 
Methionine), so that the user does not have to set it himself every time
they appear? Just an idea, because I have seen those rather often in 
metallo-enzymes; but this was the first time I searched for the reason of the 
broken backbone...

joerg

[PyMOL] how do you retrieve stored data

[Michael T. <tal...@ho...>]

I am new to pymol and I would like to retrieve residue id, name, atom name 
...etc for a given selection to use in a wizard. The manual only states that 
the iterate command can access them but I don't know how to put them into 
variables in a wizard. Any suggestions would be greatly appreciated. Thanks

Thanks
Michael Tallhamer
Undergraduate Researcher
Cleveland State University
tal...@ho...



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Re: [PyMOL] secondary structure again

[Kadmon <ka...@wa...>]

I made a mistake giving the URL in my last post, the correct DSSP page is
now http://www.cmbi.kun.nl/gv/dssp/index.html
Sorry for this.

Virgile ADAM

Re: [PyMOL] secondary structure again

[Kadmon <ka...@wa...>]

Dear Marco,
you can find DSSP at http://www.embl-heidelberg.de/dssp/ or could prefer use
Procheck from the CCP4 series (http://www.ccp4.ac.uk/) and run it on your
pdb file by the "procheck [pdbfile] [chain number] [resolution]" command.
You will obtain 10 postscript files in which you can find drawn in the 6th
one the secondary predicted structures that you can write in your helix and
sheets part in your pdb.

Hoping that it could help you

See ya

Virgile ADAM

[PyMOL] secondary structure again

[Marco F. <ma...@pr...>]

I have a problem to load secondary structure.

I read the previous mail and I do not have DSSP.

Any other way to load the secondary structure information into pymol?

thank you

marco