pymol-users Mailing List for PyMOL Molecular Graphics System

Hello,
While I am in editing mode, there is a keyboard shortcut to display the
distance between to selected atoms, but I cant remember it. I would
appreciate if someone could refresh my memory. Another related question
would be where I can find a list of shortcuts currently available in Pymol?
And finally, I recall seeing a feature request related to displaying the
default values for all the available commands in Pymol, for example what is
default value for specular. Was this feature implemented?
Thank you.
Marius

Hello,

Possibly.

I have python code that attempts to parse dssp files. Add that to a
script to call dssp (not so hard) and then call the parsing code, then
annotate the structure with the result...

Maybe all this already exists somewhere?

gilleain

On Fri, Nov 28, 2008 at 1:39 PM, DimitryASuplatov <ge...@gm...> wrote:
> Hello,
> Is there a way to incorporate dssp into pymol for secondary structure
> annotation?
> Thank you.
> SDA
>
>
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Hello,
Is there a way to incorporate dssp into pymol for secondary structure
annotation?
Thank you.
SDA

Hi,

When you load in several pdb files in pymol, the objects get colored by 
a default color scheme, e.g. first green, second cyan, third magenta etc.

Where can I get a ordered list of these color names?

Thanks 
Abhinav 

Stanford Synchrotron Radiation Laboratory 
Joint Center for Structural Genomics 
Mail Stop 99 
Phone: (650) 926-2992 
Fax: (650) 926-3292 

Hi Carsten,

That did the trick! Thank you!

All the best,

--Buz


On Nov 24, 2008, at 3:10 PM, Schubert, Carsten [PRDUS] wrote:

> Buz your image size will automatically be limited by the separation  
> of two equal points in the respective images, which should be ~62 mm  
> apart. Let me know if you need more details.
>
> Carsten
>
> -----Original Message-----
> From: Buz Barstow [mailto:bu...@ma...]
> Sent: Monday, November 24, 2008 3:01 PM
> To: pym...@li...
> Subject: [PyMOL] Making Stereo Pair Graphics
>
>
> Dear All,
>
> I'd like to make a stereo pair graphic using pymol.
>
> I'd like to know what is an appropriate size for each image in the
> pair, and what their separation should be.
>
> Thanks! and all the best,
>
> --Buz
>
>
>
> -------------------------------------------------------------------------
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> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
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Buz your image size will automatically be limited by the separation of two equal points in the respective images, which should be ~62 mm apart. Let me know if you need more details.

Carsten

-----Original Message-----
From: Buz Barstow [mailto:bu...@ma...]
Sent: Monday, November 24, 2008 3:01 PM
To: pym...@li...
Subject: [PyMOL] Making Stereo Pair Graphics


Dear All,

I'd like to make a stereo pair graphic using pymol.

I'd like to know what is an appropriate size for each image in the  
pair, and what their separation should be.

Thanks! and all the best,

--Buz



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Dear All,

I'd like to make a stereo pair graphic using pymol.

I'd like to know what is an appropriate size for each image in the  
pair, and what their separation should be.

Thanks! and all the best,

--Buz

Have you ever tried to represent your protein as a “sausage”-style  
cartoon, with the tube diameter scaled by values in the B-factor  
column ? We present an array of useful PyMOL scripts links to solve  
your problem.
PyMOL scripts collection: http://rosettadesigngroup.com/blog/?p=10

Nir London.
Rosetta Design Group
http://rosettadesigngroup.com
http://rosettadesigngroup.com/blog/

Hello All,

I
am using PyMol program to identify and list all the surface residues on
a protein and write them to a file in pdb format. I am able to identify
them, I can see the program display the surface, but I am unable to
just list those residues and write them to a file. I am relatively new
to this program, any help would be greatly appreciated.

Thank You

Thiru



      

Attention Crystallographers:

DeLano Scientific LLC will be exhibiting at the 19th WCPCW meeting April 5-8
in Asilomar, California with our usual setup: laptop, LCD, and plenty of
time to talk PyMOL.

But in addition, we are also settin up a WCPCW PyMOL event: most likely a
2-3 hour workshop that will directly reflect what you tell us you would like
to see.

So if you decide to attend this meeting, then please let us know if you are
also likely to participate in the PyMOL event (so we can arrange space), and
whether or not you have any special requests.  Given 3 hours, we would
probably do something like this:

Hour 1: Introductory training (the basics, scenes, sessions, rendering,
etc.)

Hour 2: Open Q & A. (your questions)

Hour 3: Advanced training (scripting, movies, etc.)

The WCPCW announcement email is included below, the link is http://wcpcw.org
, and the early-registration deadline is January 9th.

We hope to see you in April!

Cheers,
Warren

mailto:su...@de...?subject=WCPCW

-----Original Message-----
From: 19th WCPCW 2009 [mailto:in...@wc...]
Sent: Wednesday, November 19, 2008 2:46 PM
Subject: 19th WCPCW Registration Now Open!

Greetings Fellow Crystallographers:

We are pleased to invite you and your lab to the 19th West Coast Protein
Crystallography Workshop (WCPCW), which is scheduled for April 5-8,
2009 and
will be held at the beautiful Asilomar Conference grounds in Pacific Grove,
CA.

The upcoming workshop promises to be an exceptional conference with
prominent keynote speakers, Brian Matthews and Flo Quiocho.

We have opened the website to start accepting registration (www.wcpcw.org ).
The deadline for the standard registration fees is January 8, 2009.
The late registration deadline is February 8, 2009.

Abstracts may also be submitted for the workshop through the website
(www.wcpcw.org).  The abstract deadline is February 8, 2009. While all
presentation topics are welcome, we encourage you to emphasize methods,
consistent with the idea that WCPCW is an instructional workshop. We also
welcome your ideas for session and open-discussion topics.

If you are interested in helping support the workshop by being a sponsor or
exhibitor, please e-mail us at: in...@wc....

Finally, please help us update our mailing list by sending e-mail addresses
of your current lab members and other interested parties to us at:
in...@wc...
.

Sincerely,
Conference Organizers
Enoch Baldwin
Andrew Fisher
David Wilson

Dimitry,

Thank you for the input.  For future reference, this is precisely the sort of feedback the issue Trackers on SourceForge are intended to accomodate, and everyone should feel welcome to use them as follows:  

Go to http://www.pymol.org and seek out the TRACKERS section about halfway down. Follow "bugs", "features", or "support" then click on "add new artifact", add your comment, and then click submit.  You don't need a SourceForge account, though having one will enable you to get feedback on your issue down the line.

As for this specific issue, that is a good suggestion.  Right now the interactive dihedral display is chemistry-centric in that it displays the dihedral between the 1-4 atoms of highest chemical precedence (first order).  It would make sense to have the option of a more protein-centric view that would preferentially display phi's, psi's, and chi's, and perhaps likewise for nucleic acids.

Cheers,
Warren


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


-----Original Message-----
From: DimitryASuplatov [mailto:ge...@gm...] 
Sent: Thursday, November 13, 2008 4:53 AM
To: pym...@li...
Subject: [PyMOL] Dihedrals: Not a bug, though might cause misunderstanding

Hello,
I have just noticed that the dihedral angle obtained by Ctrl-Click (in Edit mode) on Ca-C bond in protein backbone is not actually the psi dihedral (N-Ca-C-N) but rather the angle between N-Ca-C-O (shown in white on the attached picture)! 
"dihedral" command shows the right value for psi (shown in yellow on the picture).

This is not a bug though it is confusing because phi angle is calculated correctly in both cases. Furthermore the necessity of rerunning "dihedral" each time psi adjustment is needed and lack of "live-preview"
is not very comfortable.
It might be worth tweaking this issue.

SDA 

Hello,
I have just noticed that the dihedral angle obtained by Ctrl-Click (in
Edit mode) on Ca-C bond in protein backbone is not actually the psi
dihedral (N-Ca-C-N) but rather the angle between N-Ca-C-O (shown in
white on the attached picture)! 
"dihedral" command shows the right value for psi (shown in yellow on the
picture).

This is not a bug though it is confusing because phi angle is calculated
correctly in both cases. Furthermore the necessity of rerunning
"dihedral" each time psi adjustment is needed and lack of "live-preview"
is not very comfortable.
It might be worth tweaking this issue.

SDA 

Ah!  spectacular....

Thanks very much -- those two suggestions have just very likely saved me
HOURS of work!

-Tom 

-----Original Message-----
From: DeLano Scientific [mailto:de...@de...] 
Sent: Tuesday, November 11, 2008 6:15 PM
To: Thomas Stout
Cc: pym...@li...
Subject: RE: [PyMOL] another odd PyMOL question....

Tom,

label all, color

will display the numeric color identifiers which can be used in place of
color names.  You can also use "iterate" to fetch them back out as a
list:

stored.list = []
iterate all, stored.list.append(color)
print stored.list

Cheers,
Warren

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


-----Original Message-----
From: Thomas Stout [mailto:ts...@ex...]
Sent: Tuesday, November 11, 2008 3:35 PM
To: pym...@li...; Mat...@im...
Subject: Re: [PyMOL] another odd PyMOL question....


So, a follow up question becomes: is there a way to report what color
something is?

:)

-Tom 

-----Original Message-----
From: Mat...@im... [mailto:Mat...@im...]

Sent: Tuesday, November 11, 2008 1:52 PM
To: Thomas Stout
Cc: pym...@li...
Subject: Re: [PyMOL] another odd PyMOL question....



"Thomas Stout" <ts...@ex...> wrote on 11/11/2008 04:46:38 PM:

>
> Hi again everyone --
>
> I have another odd PyMOL question: does anyone know if it is possible 
> to make selections based on what color certain atoms are?
> I need to do some wholesale re-coloring of a series of complicated 
> figures and it would be extremely useful if I could just say something
like:
>
> "color  red, (everything that is currently blue)"
>
> Thanks,
> Tom
>


How about:

> color red, yourmolecule and (color blue)

Works for me.  Of course, you have to know the color name for the color
you're looking at - maybe there's a way of getting the RGB values for an
atom?

- Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


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Hi
When I display my model in pymol it shows a break, but I don't see such
breaks in Rasmol or Chimera. I know pymol uses a more restricted definition
of bond length and angle, but is there a way to hide these breaks.
Thanks
Ambrish

Tom,

label all, color

will display the numeric color identifiers which can be used in place of
color names.  You can also use "iterate" to fetch them back out as a list:

stored.list = []
iterate all, stored.list.append(color)
print stored.list

Cheers,
Warren

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


-----Original Message-----
From: Thomas Stout [mailto:ts...@ex...] 
Sent: Tuesday, November 11, 2008 3:35 PM
To: pym...@li...; Mat...@im...
Subject: Re: [PyMOL] another odd PyMOL question....


So, a follow up question becomes: is there a way to report what color
something is?

:)

-Tom 

-----Original Message-----
From: Mat...@im... [mailto:Mat...@im...]

Sent: Tuesday, November 11, 2008 1:52 PM
To: Thomas Stout
Cc: pym...@li...
Subject: Re: [PyMOL] another odd PyMOL question....



"Thomas Stout" <ts...@ex...> wrote on 11/11/2008 04:46:38 PM:

>
> Hi again everyone --
>
> I have another odd PyMOL question: does anyone know if it is possible 
> to make selections based on what color certain atoms are?
> I need to do some wholesale re-coloring of a series of complicated 
> figures and it would be extremely useful if I could just say something
like:
>
> "color  red, (everything that is currently blue)"
>
> Thanks,
> Tom
>


How about:

> color red, yourmolecule and (color blue)

Works for me.  Of course, you have to know the color name for the color
you're looking at - maybe there's a way of getting the RGB values for an
atom?

- Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.


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confidential and privileged and is for the sole use of the intended
recipient. Any review, reliance or distribution by others or forwarding
without express permission is strictly prohibited. If you are not the
intended recipient, please contact the sender and delete all copies.


Exelixis, Inc. reserves the right, to the extent and under circumstances
permitted by applicable law, to retain, monitor and intercept e-mail
messages to and from its systems.


-------------------------------------------------------------------------
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Build the coolest Linux based applications with Moblin SDK & win great
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So, a follow up question becomes: is there a way to report what color
something is?

:)

-Tom 

-----Original Message-----
From: Mat...@im... [mailto:Mat...@im...]

Sent: Tuesday, November 11, 2008 1:52 PM
To: Thomas Stout
Cc: pym...@li...
Subject: Re: [PyMOL] another odd PyMOL question....



"Thomas Stout" <ts...@ex...> wrote on 11/11/2008 04:46:38 PM:

>
> Hi again everyone --
>
> I have another odd PyMOL question: does anyone know if it is possible 
> to make selections based on what color certain atoms are?
> I need to do some wholesale re-coloring of a series of complicated 
> figures and it would be extremely useful if I could just say something
like:
>
> "color  red, (everything that is currently blue)"
>
> Thanks,
> Tom
>


How about:

> color red, yourmolecule and (color blue)

Works for me.  Of course, you have to know the color name for the color
you're looking at - maybe there's a way of getting the RGB values for an
atom?

- Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this
e-mail is not the intended recipient, or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that reading it is strictly prohibited.  If you have received
this e-mail in error, please immediately return it to the sender and
delete it from your system.  Thank you.


This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.


Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

"Thomas Stout" <ts...@ex...> wrote on 11/11/2008 04:46:38 PM:

>
> Hi again everyone --
>
> I have another odd PyMOL question: does anyone know if it is
> possible to make selections based on what color certain atoms are?
> I need to do some wholesale re-coloring of a series of complicated
> figures and it would be extremely useful if I could just say something
like:
>
> "color  red, (everything that is currently blue)"
>
> Thanks,
> Tom
>


How about:

> color red, yourmolecule and (color blue)

Works for me.  Of course, you have to know the color name for the color
you're looking at - maybe there's a way of getting the RGB values for an
atom?

- Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

 
Hi again everyone --
 
I have another odd PyMOL question: does anyone know if it is possible to
make selections based on what color certain atoms are?   I need to do
some wholesale re-coloring of a series of complicated figures and it
would be extremely useful if I could just say something like:
 
"color  red, (everything that is currently blue)"
 
Thanks,
Tom
 
PS - No, the original selections that were made to construct the figures
were not retained in the session file, just the completed "scenes" 


This email (including any attachments) may contain material
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the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.


Exelixis, Inc. reserves the right, to the extent and under
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and intercept e-mail messages to and from its systems.

QT,
 
No, unfortunately, it is more complicated than that...see the community
wiki:
 
http://pymolwiki.org/index.php/Get_View
 
Also, for sectioning, you may wish to disable depth_cue
 
unset depth_cue
 
Cheers,
Warren

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

 

  _____  

From: QT [mailto:rdi...@gm...] 
Sent: Tuesday, November 11, 2008 12:31 AM
To: DeLano Scientific
Cc: pym...@li...
Subject: Re: [PyMOL] Camera Orientation


Yup, thanks for your help that did it.  Although the script didn't spring
back to the default camera anchor point after it did the 360 degree rotation
about y-axis, I understand now.  So, to move the camera anchor point around,
you modify the parameter 9-11 of set_view(), which controls the x,y,z anchor
point of the camera.

Now I've come to understand that parameter 15 and 16 essentially define the
clipping plane.  How are these related to each other because I also want to
do sectioning of the ribosome tunnel from front to back in 10A increment.

Is the clipping plane static or can you also rotate the clipping plane to do
horizontal and diagonal sectioning, or is that accomplished by rotating the
structure about its axis?

By default the clipping plane sections from front to back or vertical
sections.

Quyen


On Tue, Nov 11, 2008 at 12:30 AM, DeLano Scientific <de...@de...>
wrote:


Ah ha, now I see what you're angling at!  What a great question -- I'm
amazed this hasn't come up before in ten years of usage and development.

The core problem is that PyMOL's camera has been designed from day one to
orbit around a specific point in space, not at a point.  To get the effect
you desire, I think you'll need to transiently back up the camera, rotate it
about its prior orgin and then move it back again.  Here's an example script
which does that:


load $TUT/1hpv.pdb

set field_of_view, 45

zoom organic
orient organic
show stick, polymer
show surface
set surface_color, white
set transparency, 0.5
clip slab, 30
set line_width, 5

cmd.move("z",-cmd.get_view()[11])

python

def spin():
   from pymol import cmd
   for x in range(360):
      cmd.move("z",cmd.get_view()[11])
      cmd.turn("y",1)
      cmd.move("z",-cmd.get_view()[11])
      cmd.refresh()

threading.Thread(target=spin).start()

python end

Cheers,
Warren



________________________________

From: QT [mailto:rdi...@gm...]

Sent: Monday, November 10, 2008 10:04 PM
To: DeLano Scientific
Cc: pym...@li...
Subject: Re: [PyMOL] Camera Orientation



Ah thank you Warren, that gave it a fish-eye effect that seems to work.  Is
there any other way to go about this problem?  Is there no way to move the
camera from looking in to looking out?  By default, the camera is anchored
outside the molecule, can the camera be anchored to a point inside the
molecule but not on any atom?

Quyen


On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <de...@de...>
wrote:


       Quyen,

       If clipping isn't the effect you want, the solution probably lies in
increasing the camera field of view angle which will enable PyMOL to better
"get of inside" spaces without having nearby elements appear to intersect
the camera surface (or front clipping plane).

       set field_of_view, 45

       Cheers,
       Warren
       --
       DeLano Scientific LLC
       Subscriber Support Services
       mailto:su...@de...


________________________________

       From: QT [mailto:rdi...@gm...]
       Sent: Monday, November 10, 2008 12:15 AM
       To: pym...@li...
       Subject: [PyMOL] Camera Orientation


       Hello everyone,

       I have a question regarding camera orientation.  I'm using pymol to
explore the surface of the peptide tunnel in the ribosome and would like to
change the camera orientation so that I can look around "in there" without
getting occluded.  Clipping plane is not useful because I don't want the
surface to disappear.  In a sense, I want to change the default camera
orientation of pymol from "looking in" to "looking out".  This is much like
standing in a room and looking around.  I think the answer lies in the 18
parameters of set_view, but which should I change and how are these
computed?

       Regards,
       Quyen Tran

       Department of Biochemistry
       University of Houston

Yup, thanks for your help that did it.  Although the script didn't spring
back to the default camera anchor point after it did the 360 degree rotation
about y-axis, I understand now.  So, to move the camera anchor point around,
you modify the parameter 9-11 of set_view(), which controls the x,y,z anchor
point of the camera.

Now I've come to understand that parameter 15 and 16 essentially define the
clipping plane.  How are these related to each other because I also want to
do sectioning of the ribosome tunnel from front to back in 10A increment.

Is the clipping plane static or can you also rotate the clipping plane to do
horizontal and diagonal sectioning, or is that accomplished by rotating the
structure about its axis?

By default the clipping plane sections from front to back or vertical
sections.

Quyen


On Tue, Nov 11, 2008 at 12:30 AM, DeLano Scientific <de...@de...>wrote:

> Ah ha, now I see what you're angling at!  What a great question -- I'm
> amazed this hasn't come up before in ten years of usage and development.
>
> The core problem is that PyMOL's camera has been designed from day one to
> orbit around a specific point in space, not at a point.  To get the effect
> you desire, I think you'll need to transiently back up the camera, rotate
> it
> about its prior orgin and then move it back again.  Here's an example
> script
> which does that:
>
>
> load $TUT/1hpv.pdb
> set field_of_view, 45
> zoom organic
> orient organic
> show stick, polymer
> show surface
> set surface_color, white
> set transparency, 0.5
> clip slab, 30
> set line_width, 5
>
> cmd.move("z",-cmd.get_view()[11])
>
> python
>
> def spin():
>    from pymol import cmd
>    for x in range(360):
>       cmd.move("z",cmd.get_view()[11])
>       cmd.turn("y",1)
>       cmd.move("z",-cmd.get_view()[11])
>       cmd.refresh()
>
> threading.Thread(target=spin).start()
>
> python end
>
> Cheers,
> Warren
>
>
> ________________________________
>
> From: QT [mailto:rdi...@gm...]
> Sent: Monday, November 10, 2008 10:04 PM
> To: DeLano Scientific
> Cc: pym...@li...
> Subject: Re: [PyMOL] Camera Orientation
>
>
> Ah thank you Warren, that gave it a fish-eye effect that seems to work.  Is
> there any other way to go about this problem?  Is there no way to move the
> camera from looking in to looking out?  By default, the camera is anchored
> outside the molecule, can the camera be anchored to a point inside the
> molecule but not on any atom?
>
> Quyen
>
>
> On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <de...@de...>
> wrote:
>
>
>        Quyen,
>
>        If clipping isn't the effect you want, the solution probably lies in
> increasing the camera field of view angle which will enable PyMOL to better
> "get of inside" spaces without having nearby elements appear to intersect
> the camera surface (or front clipping plane).
>
>        set field_of_view, 45
>
>        Cheers,
>        Warren
>        --
>        DeLano Scientific LLC
>        Subscriber Support Services
>        mailto:su...@de...
>
>
> ________________________________
>
>        From: QT [mailto:rdi...@gm...]
>        Sent: Monday, November 10, 2008 12:15 AM
>        To: pym...@li...
>        Subject: [PyMOL] Camera Orientation
>
>
>        Hello everyone,
>
>        I have a question regarding camera orientation.  I'm using pymol to
> explore the surface of the peptide tunnel in the ribosome and would like to
> change the camera orientation so that I can look around "in there" without
> getting occluded.  Clipping plane is not useful because I don't want the
> surface to disappear.  In a sense, I want to change the default camera
> orientation of pymol from "looking in" to "looking out".  This is much like
> standing in a room and looking around.  I think the answer lies in the 18
> parameters of set_view, but which should I change and how are these
> computed?
>
>        Regards,
>        Quyen Tran
>
>        Department of Biochemistry
>        University of Houston
>
>
>
>
>

Ah ha, now I see what you're angling at!  What a great question -- I'm
amazed this hasn't come up before in ten years of usage and development.
 
The core problem is that PyMOL's camera has been designed from day one to
orbit around a specific point in space, not at a point.  To get the effect
you desire, I think you'll need to transiently back up the camera, rotate it
about its prior orgin and then move it back again.  Here's an example script
which does that:

 
load $TUT/1hpv.pdb
set field_of_view, 45
zoom organic
orient organic
show stick, polymer
show surface
set surface_color, white
set transparency, 0.5
clip slab, 30
set line_width, 5

cmd.move("z",-cmd.get_view()[11])

python

def spin():
    from pymol import cmd
    for x in range(360):
       cmd.move("z",cmd.get_view()[11])
       cmd.turn("y",1)
       cmd.move("z",-cmd.get_view()[11])
       cmd.refresh()

threading.Thread(target=spin).start()

python end

Cheers,
Warren


________________________________

From: QT [mailto:rdi...@gm...] 
Sent: Monday, November 10, 2008 10:04 PM
To: DeLano Scientific
Cc: pym...@li...
Subject: Re: [PyMOL] Camera Orientation


Ah thank you Warren, that gave it a fish-eye effect that seems to work.  Is
there any other way to go about this problem?  Is there no way to move the
camera from looking in to looking out?  By default, the camera is anchored
outside the molecule, can the camera be anchored to a point inside the
molecule but not on any atom?

Quyen


On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <de...@de...>
wrote:


	Quyen,
	 
	If clipping isn't the effect you want, the solution probably lies in
increasing the camera field of view angle which will enable PyMOL to better
"get of inside" spaces without having nearby elements appear to intersect
the camera surface (or front clipping plane).
	 
	set field_of_view, 45
	 
	Cheers,
	Warren
	--
	DeLano Scientific LLC
	Subscriber Support Services
	mailto:su...@de...
	 

________________________________

	From: QT [mailto:rdi...@gm...] 
	Sent: Monday, November 10, 2008 12:15 AM
	To: pym...@li...
	Subject: [PyMOL] Camera Orientation
	
	
	Hello everyone,
	
	I have a question regarding camera orientation.  I'm using pymol to
explore the surface of the peptide tunnel in the ribosome and would like to
change the camera orientation so that I can look around "in there" without
getting occluded.  Clipping plane is not useful because I don't want the
surface to disappear.  In a sense, I want to change the default camera
orientation of pymol from "looking in" to "looking out".  This is much like
standing in a room and looking around.  I think the answer lies in the 18
parameters of set_view, but which should I change and how are these
computed?
	
	Regards,
	Quyen Tran
	
	Department of Biochemistry
	University of Houston
	

Ah thank you Warren, that gave it a fish-eye effect that seems to work.  Is
there any other way to go about this problem?  Is there no way to move the
camera from looking in to looking out?  By default, the camera is anchored
outside the molecule, can the camera be anchored to a point inside the
molecule but not on any atom?

Quyen

On Mon, Nov 10, 2008 at 11:15 PM, DeLano Scientific <de...@de...>wrote:

>  Quyen,
>
> If clipping isn't the effect you want, the solution probably lies in
> increasing the camera field of view angle which will enable PyMOL to better
> "get of inside" spaces without having nearby elements appear to intersect
> the camera surface (or front clipping plane).
>
> set field_of_view, 45
>
> Cheers,
> Warren
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:su...@de...
>
>
>  ------------------------------
> *From:* QT [mailto:rdi...@gm...]
> *Sent:* Monday, November 10, 2008 12:15 AM
> *To:* pym...@li...
> *Subject:* [PyMOL] Camera Orientation
>
> Hello everyone,
>
> I have a question regarding camera orientation.  I'm using pymol to explore
> the surface of the peptide tunnel in the ribosome and would like to change
> the camera orientation so that I can look around "in there" without getting
> occluded.  Clipping plane is not useful because I don't want the surface to
> disappear.  In a sense, I want to change the default camera orientation of
> pymol from "looking in" to "looking out".  This is much like standing in a
> room and looking around.  I think the answer lies in the 18 parameters of
> set_view, but which should I change and how are these computed?
>
> Regards,
> Quyen Tran
>
> Department of Biochemistry
> University of Houston
>

Quyen,
 
If clipping isn't the effect you want, the solution probably lies in
increasing the camera field of view angle which will enable PyMOL to better
"get of inside" spaces without having nearby elements appear to intersect
the camera surface (or front clipping plane).
 
set field_of_view, 45
 
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...
 

  _____  

From: QT [mailto:rdi...@gm...] 
Sent: Monday, November 10, 2008 12:15 AM
To: pym...@li...
Subject: [PyMOL] Camera Orientation


Hello everyone,

I have a question regarding camera orientation.  I'm using pymol to explore
the surface of the peptide tunnel in the ribosome and would like to change
the camera orientation so that I can look around "in there" without getting
occluded.  Clipping plane is not useful because I don't want the surface to
disappear.  In a sense, I want to change the default camera orientation of
pymol from "looking in" to "looking out".  This is much like standing in a
room and looking around.  I think the answer lies in the 18 parameters of
set_view, but which should I change and how are these computed?

Regards,
Quyen Tran

Department of Biochemistry
University of Houston

 
Ah Ha!  Yes, that does the trick....
Many thanks to all for that solution!

-Tom



-----Original Message-----
From: Mauricio Esguerra [mailto:esg...@rc...] 
Sent: Monday, November 10, 2008 1:23 PM
To: Thomas Stout
Cc: pym...@li...
Subject: Re: [PyMOL] rotating "maps" ??


Hi Thomas,

Try turn instead of rotate, that might work.

Good luck,

+++++++++++++++++++++++++++++++++++++++++++++++
+ Mauricio Esguerra Neira                     +
+ T.A. and Graduate Student                   +
+ Wilma K. Olson Group                        +
+ Chemistry and Chemical Biology Department   +
+ Rutgers, The State University of New Jersey +
+ Phone Number: 732-445-4619                  +
+ Email: esg...@ed...            +
+++++++++++++++++++++++++++++++++++++++++++++++


On Mon, 10 Nov 2008, Thomas Stout wrote:

>
> Hi All --
>
> I've just stumbled into an odd behavior that is either a bug, or more 
> likely my mis-understanding some aspect of how PyMOL works.  I've 
> created "low resolution" surfaces on a hetero-meric protein complex to

> illustrate the packing together of various protein chains.  I've made 
> these surfaces somewhat transparent so that the underlying protein 
> chain can still be seen.
>
> Here's how the gaussian maps are made (a la Warren DeLano's recent
> suggestions):
> pymol> alter /proteinA, b=120
> pymol> alter /proteinB, b=120
> pymol> (etc)
> pymol> alter /proteinA, q=1
> pymol> alter /proteinB, q=1
> pymol> (etc)
> pymol> set gaussian_resolution, 4
> pymol> map_new mapA, gaussian, 1, /proteinA map_new mapB, gaussian, 1,

> pymol> /proteinB
> pymol> (etc)
>
> Now, for the odd behavior.  After I've created figure one as above, I 
> want to rotate the complex by 90 degrees and create a figure viewing 
> down the orthogonal axis.  If I click and drag with the mouse, all 
> objects rotate as expected.  However, issuing:
> pymol> rotate x, 90
>
> results in the proteins rotating appropriately, but the gaussian maps 
> remain in place.  Is there some setting required to allow 
> transformations to be applied to maps from the command line?
>
> Thanks,
> Tom
>
>
>
>
> This email (including any attachments) may contain material that is 
> confidential and privileged and is for the sole use of the intended 
> recipient. Any review, reliance or distribution by others or 
> forwarding without express permission is strictly prohibited. If you 
> are not the intended recipient, please contact the sender and delete 
> all copies.
>
>
> Exelixis, Inc. reserves the right, to the extent and under 
> circumstances permitted by applicable law, to retain, monitor and 
> intercept e-mail messages to and from its systems.
>

This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.


Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

Hi Thomas,

Try turn instead of rotate, that might work.

Good luck,

+++++++++++++++++++++++++++++++++++++++++++++++
+ Mauricio Esguerra Neira                     +
+ T.A. and Graduate Student                   +
+ Wilma K. Olson Group                        +
+ Chemistry and Chemical Biology Department   +
+ Rutgers, The State University of New Jersey +
+ Phone Number: 732-445-4619                  +
+ Email: esg...@ed...            +
+++++++++++++++++++++++++++++++++++++++++++++++


On Mon, 10 Nov 2008, Thomas Stout wrote:

>
> Hi All --
>
> I've just stumbled into an odd behavior that is either a bug, or more
> likely my mis-understanding some aspect of how PyMOL works.  I've
> created "low resolution" surfaces on a hetero-meric protein complex to
> illustrate the packing together of various protein chains.  I've made
> these surfaces somewhat transparent so that the underlying protein chain
> can still be seen.
>
> Here's how the gaussian maps are made (a la Warren DeLano's recent
> suggestions):
> pymol> alter /proteinA, b=120
> pymol> alter /proteinB, b=120
> pymol> (etc)
> pymol> alter /proteinA, q=1
> pymol> alter /proteinB, q=1
> pymol> (etc)
> pymol> set gaussian_resolution, 4
> pymol> map_new mapA, gaussian, 1, /proteinA
> pymol> map_new mapB, gaussian, 1, /proteinB
> pymol> (etc)
>
> Now, for the odd behavior.  After I've created figure one as above, I
> want to rotate the complex by 90 degrees and create a figure viewing
> down the orthogonal axis.  If I click and drag with the mouse, all
> objects rotate as expected.  However, issuing:
> pymol> rotate x, 90
>
> results in the proteins rotating appropriately, but the gaussian maps
> remain in place.  Is there some setting required to allow
> transformations to be applied to maps from the command line?
>
> Thanks,
> Tom
>
>
>
>
> This email (including any attachments) may contain material
> that is confidential and privileged and is for the sole use of
> the intended recipient. Any review, reliance or distribution by
> others or forwarding without express permission is strictly
> prohibited. If you are not the intended recipient, please
> contact the sender and delete all copies.
>
>
> Exelixis, Inc. reserves the right, to the extent and under
> circumstances permitted by applicable law, to retain, monitor
> and intercept e-mail messages to and from its systems.
>