PyMOL Molecular Graphics System

Tassos,

> 1. How do I make a cartoon passing through Ca's ? It refuses 
> to do that with default values like for a 'full' PDB file !

set cartoon_flat_sheets, off
set cartoon_smooth_loops, off

Also, the following command will reduce cartoon "jitter" during animations

set cartoon_refine_normals, off

> 2. I want to include another single molecule and have frames 
> where the second molecules 'stays the same'

This is actually the default behavior if you load a second PDB file that
contains only one state.  If it has multiple states, then you'll need to
specifically set a state for that object.  For example:

load animation1.pdb
load animation2.pdb
set state, 1, animation2
mplay

would freeze animation2 at state 1, while playing through animation 2

To change the default freezing behavior for single-state object, set
static_singletons, off

Cheers,
Warren


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

> -----Original Message-----
> From: pymol-users-admin@... 
> [mailto:pymol-users-admin@...] On Behalf Of 
> Anastassis Perrakis (NKI)
> Sent: Monday, September 27, 2004 2:05 AM
> To: pymol-users@...
> Cc: warren@...
> Subject: [PyMOL] Ca-only and multi-mol PDB
> 
> Dear Warren et al,
> 
> A couple of questions about PyMol:
> 
> When I open a multi-molecule PDB file, it nicely stores every 
> 'instance' of the PDB in a frame.
> This file is coming from the 'Dynamite' server of Martin 
> Noble and has only Ca's.
> 
> I have two problems:
> 1. How do I make a cartoon passing through Ca's ? It refuses 
> to do that with default values like for a 'full' PDB file !
> 2. I want to include another single molecule and have frames 
> where the second molecules 'stays the same'
> while the first one changes in each frame. Is that easy to do 
> ? Anyone has a script ?
> 
> Thanks in advance,
> 
> Tassos
> 
> 
> 
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Hi, A couple of things:

a) I've just installed the latest MacPymol (after having a major  
crash and having to re-install EVERYTHING), and my middle mouse  
button doesn't seem to work. I can't move things around on the  
screen.  The other buttons work fine, and the middle one scrolls OK,  
so I can slab - but I want to move things!!  I have played with the  
MouseWorks thing in System Prefs, and can change the middle button  
clicking to do what any of the other button clicks do, but there is  
no option for "middle button".  Is there a key combination I can put  
in that will let it move things?

b)I'm trying to make a surface and a cartoon of a CA-only structure.   
A search of my email archive tells me that by now Pymol should be  
able to create at least a ribbon from this sort of file, but I can't  
figure out how to do it.  Can someone please instruct me?

Ta

Bronwyn



Bronwyn Carlisle
Biochemistry Department
University of Otago
PO Box 56
710 Cumberland St
Dunedin

email: bronwyn.carlisle@...
tel: +64 (0)3 4797704

Hi Bronwyn,

Don't know about MacPymol, but with regards to the second issue, a
C-alpha trace, you can do it with:

set cartoon_trace,1
show cartoon

The surface will be tougher, you could play with setting the vanderwaals ra=
dius:

show surface
alter (all),vdw=3D4
rebuild

And you can repeat the last two commands for different values for the
vdwr to suit your needs. You could also play with setting the radius
for the solvent probe to determine the surface.

Hope it helps,

Tsjerk




On 8/17/05, Bronwyn Carlisle <bronwyn.carlisle@...> wrote:
> Hi, A couple of things:
>=20
> a) I've just installed the latest MacPymol (after having a major
> crash and having to re-install EVERYTHING), and my middle mouse
> button doesn't seem to work. I can't move things around on the
> screen.  The other buttons work fine, and the middle one scrolls OK,
> so I can slab - but I want to move things!!  I have played with the
> MouseWorks thing in System Prefs, and can change the middle button
> clicking to do what any of the other button clicks do, but there is
> no option for "middle button".  Is there a key combination I can put
> in that will let it move things?
>=20
> b)I'm trying to make a surface and a cartoon of a CA-only structure.
> A search of my email archive tells me that by now Pymol should be
> able to create at least a ribbon from this sort of file, but I can't
> figure out how to do it.  Can someone please instruct me?
>=20
> Ta
>=20
> Bronwyn
>=20
>=20
>=20
> Bronwyn Carlisle
> Biochemistry Department
> University of Otago
> PO Box 56
> 710 Cumberland St
> Dunedin
>=20
> email: bronwyn.carlisle@...
> tel: +64 (0)3 4797704
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic=
es
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q=
A
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

On Wednesday 17 August 2005 05:44, Bronwyn Carlisle wrote:
> b)I'm trying to make a surface and a cartoon of a CA-only structure.
> A search of my email archive tells me that by now Pymol should be
> able to create at least a ribbon from this sort of file, but I can't
> figure out how to do it.  Can someone please instruct me?

For the ribbon representation:

set ribbon_trace_atoms,1

I don't know about the surface representation, though.

-- 
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

Hi Bronwyn,

I had the same problem (using a Logitech MX310 under OS X 10.4.2). As 
somebody previously suggested, I just uninstalled the Logitech software, 
so the os treats the mouse as 'generic'. And now the middle button 
behaves as expected.

hope this helps,

Xavier

Bronwyn Carlisle wrote:

> Hi, A couple of things:
>
> a) I've just installed the latest MacPymol (after having a major  
> crash and having to re-install EVERYTHING), and my middle mouse  
> button doesn't seem to work. I can't move things around on the  
> screen.  The other buttons work fine, and the middle one scrolls OK,  
> so I can slab - but I want to move things!!  I have played with the  
> MouseWorks thing in System Prefs, and can change the middle button  
> clicking to do what any of the other button clicks do, but there is  
> no option for "middle button".  Is there a key combination I can put  
> in that will let it move things?
>
> b)I'm trying to make a surface and a cartoon of a CA-only structure.   
> A search of my email archive tells me that by now Pymol should be  
> able to create at least a ribbon from this sort of file, but I can't  
> figure out how to do it.  Can someone please instruct me?
>
> Ta
>
> Bronwyn
>
>
>
> Bronwyn Carlisle
> Biochemistry Department
> University of Otago
> PO Box 56
> 710 Cumberland St
> Dunedin
>
> email: bronwyn.carlisle@...
> tel: +64 (0)3 4797704
>
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

-- 
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)

E-mail: Xavier.Deupi@...
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021

Yes, I know the move command, but my mouse USED to translate things  
when you clicked the scroll wheel, it just doesn't since I had to re- 
install things.  I like using it rather than the command line.

Bronwyn


On 18/08/2005, at 8:14 AM, Peter Adrian Meyer wrote:

> Hi Bronwyn,
>
>
>> a) I've just installed the latest MacPymol (after having a major
>> crash and having to re-install EVERYTHING), and my middle mouse
>> button doesn't seem to work. I can't move things around on the
>> screen.  The other buttons work fine, and the middle one scrolls OK,
>> so I can slab - but I want to move things!!  I have played with the
>> MouseWorks thing in System Prefs, and can change the middle button
>> clicking to do what any of the other button clicks do, but there is
>> no option for "middle button".  Is there a key combination I can put
>> in that will let it move things?
>>
>
> move x,5.0; should work as far as translating the model.  With a
> three-button mouse (no scroll wheel), middle mouse translates and
> shift-right mouse moves the clipping planes (on unix, at least, but it
> might be of use for getting the system preferences configured).
>
>
>>
>> b)I'm trying to make a surface and a cartoon of a CA-only structure.
>> A search of my email archive tells me that by now Pymol should be
>> able to create at least a ribbon from this sort of file, but I can't
>> figure out how to do it.  Can someone please instruct me?
>>
>
> Can't help you here...I've been wondering about how to do a ca- 
> trace for a
> while (not sure what use a surface from a CA model would be,  
> though...).
>
> Hope this helps,
>
> Pete
>
>
>>
>> Ta
>>
>> Bronwyn
>>
>>
>>
>> Bronwyn Carlisle
>> Biochemistry Department
>> University of Otago
>> PO Box 56
>> 710 Cumberland St
>> Dunedin
>>
>> email: bronwyn.carlisle@...
>> tel: +64 (0)3 4797704
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>> Testing & QA
>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>> bsce5sf
>> _______________________________________________
>> PyMOL-users mailing list
>> PyMOL-users@...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>
>


Bronwyn Carlisle
Biochemistry Department
University of Otago
PO Box 56
710 Cumberland St
Dunedin

email: bronwyn.carlisle@...
tel: +64 (0)3 4797704

Thank-you, that worked beautifully.  Before the crash the MouseWorks  
software can't have been working properly.

Bronwyn

On 18/08/2005, at 10:01 AM, Xavier Deupi wrote:

> Hi Bronwyn,
>
> I had the same problem (using a Logitech MX310 under OS X 10.4.2).  
> As somebody previously suggested, I just uninstalled the Logitech  
> software, so the os treats the mouse as 'generic'. And now the  
> middle button behaves as expected.
>
> hope this helps,
>
> Xavier
>
> Bronwyn Carlisle wrote:
>
>
>> Hi, A couple of things:
>>
>> a) I've just installed the latest MacPymol (after having a major   
>> crash and having to re-install EVERYTHING), and my middle mouse   
>> button doesn't seem to work. I can't move things around on the   
>> screen.  The other buttons work fine, and the middle one scrolls  
>> OK,  so I can slab - but I want to move things!!  I have played  
>> with the  MouseWorks thing in System Prefs, and can change the  
>> middle button  clicking to do what any of the other button clicks  
>> do, but there is  no option for "middle button".  Is there a key  
>> combination I can put  in that will let it move things?
>>
>> b)I'm trying to make a surface and a cartoon of a CA-only  
>> structure.   A search of my email archive tells me that by now  
>> Pymol should be  able to create at least a ribbon from this sort  
>> of file, but I can't  figure out how to do it.  Can someone please  
>> instruct me?
>>
>> Ta
>>
>> Bronwyn
>>
>>
>>
>> Bronwyn Carlisle
>> Biochemistry Department
>> University of Otago
>> PO Box 56
>> 710 Cumberland St
>> Dunedin
>>
>> email: bronwyn.carlisle@...
>> tel: +64 (0)3 4797704
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>> Testing & QA
>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>> bsce5sf
>> _______________________________________________
>> PyMOL-users mailing list
>> PyMOL-users@...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
> -- 
> Xavier Deupi, Ph.D.
> Department of Molecular and Cellular Physiology
> Beckman Center for Molecular and Genetic Medicine (B161)
> 279 Campus Drive, Stanford University School of Medicine
> Stanford, CA 94305 (USA)
>
> E-mail: Xavier.Deupi@...
> Phone: +1 (650) 725-6497
> Fax : +1 (650) 725-8021
>
>


Bronwyn Carlisle
Biochemistry Department
University of Otago
PO Box 56
710 Cumberland St
Dunedin

email: bronwyn.carlisle@...
tel: +64 (0)3 4797704