pymol-users Mailing List for PyMOL Molecular Graphics System

One should emphasize that this alignment is a *sequence* alignment in 
case of the "align" command.

Cheers,
   Thomas

On 11/30/2011 11:19 AM, Tsjerk Wassenaar wrote:
> Hi Martin,
>
> It does an alignment, finding matching pairs of atoms, removing
> outliers and calculating the RMSD over the remaining matches.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger<ma...@bl...>  wrote:
>> How does PyMOL calculate the RMSD between two structures where the
>> number of atoms is different?
>> Martin

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi Martin,

It does an alignment, finding matching pairs of atoms, removing
outliers and calculating the RMSD over the remaining matches.

Cheers,

Tsjerk

On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger <ma...@bl...> wrote:
> How does PyMOL calculate the RMSD between two structures where the
> number of atoms is different?
> Martin
>
>
>
>
>
>
> Am 11.11.11 14:59, schrieb Thomas Holder:
>> Hi Martin,
>>
>> is it the transform=0 argument what you are looking for?
>>
>> http://pymolwiki.org/index.php/Align#PYMOL_API
>>
>> x = cmd.align('foo', 'bar', transform=0)
>> print 'RMSD:', x[0]
>>
>> About the "some kind of refinement": There are arguments "cutoff" and
>> "cycles" that control this behaviour.
>>
>> Cheers,
>>   Thomas
>>
>> On 11/11/2011 02:46 PM, Martin Hediger wrote:
>>> Dear List.
>>> When aligning two structures using the PyMOL align command, one gets a
>>> final RMS value indicating some kind of "convergence" i would say. Can I
>>> somehow access the function for calculating this value directly from the
>>> pymol prompt without aligning?
>>>
>>> Thanks for hints
>>> Martin
>>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

How does PyMOL calculate the RMSD between two structures where the 
number of atoms is different?
Martin






Am 11.11.11 14:59, schrieb Thomas Holder:
> Hi Martin,
>
> is it the transform=0 argument what you are looking for?
>
> http://pymolwiki.org/index.php/Align#PYMOL_API
>
> x = cmd.align('foo', 'bar', transform=0)
> print 'RMSD:', x[0]
>
> About the "some kind of refinement": There are arguments "cutoff" and 
> "cycles" that control this behaviour.
>
> Cheers,
>   Thomas
>
> On 11/11/2011 02:46 PM, Martin Hediger wrote:
>> Dear List.
>> When aligning two structures using the PyMOL align command, one gets a
>> final RMS value indicating some kind of "convergence" i would say. Can I
>> somehow access the function for calculating this value directly from the
>> pymol prompt without aligning?
>>
>> Thanks for hints
>> Martin
>

Thanks Jason.

It works quite well in case of not very compliated ligands ( e.g bonds
beetween aa-tRNA and the  aa-tRNA syntase were correct ) but in the
sugar-bound enzyme there were some mistakes in representation of the
H-bonds netween water/ligand/active center ( some water also partisipate in
the ligand binding but in case where water and some residues of the active
sites were positioned iclosely the bonds were incorect ). So a I understood
I can fix this mistakes only manually ?

By the way, on what assumptions helix elements of my proteins were colored
after representation of the ligand binding with the cartoons ?

Finally how I could represent ionic contacts in the ion-binding proteins ?
E.g now I'm studing calmodulin wich has Ef-hand Ca-binding motifs. I've
tried to represent bonds beetwen some polar residues of the active site
with the ligand but failed :(



Thanks again,


James

2011/11/29 Jason Vertrees <jas...@sc...>

> James,
>
> > Is there any semi-avtomated way to find ligand binding pocket and do all
> > such things ?
>
> For your given object, click A > preset > ligands sites > cartoon. Try
> other options under that menu.
>
> Cheers,
>
> -- Jason
>
>
> > 2011/11/28 Thomas Holder <sp...@us...>
> >>
> >> Hi James,
> >>
> >> most trivial manner:
> >>
> >> as cartoon
> >> show sticks, resn LEU+ILE+VAL
> >> set cartoon_side_chain_helper
> >>
> >> and eventually something like this:
> >>
> >> show spheres, resn LEU+ILE+VAL and not name N+O+C
> >> set sphere_transparency, 0.5
> >>
> >>
> >> Cheers,
> >>  Thomas
> >>
> >> On 11/28/2011 02:58 PM, James Starlight wrote:
> >>>
> >>> Another question also linked with the non-covalent interaction.
> >>>
> >>> In particular I wounder to know how i Could represent all hydrophobic (
> >>> Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
> >>> like to represent the hydrophobic core of the proteins made from those
> >>> residues.
> >>>
> >>> Thanks,
> >>>
> >>> James
> >>
> >> --
> >> Thomas Holder
> >> MPI for Developmental Biology
> >> Spemannstr. 35
> >> D-72076 Tübingen
> >
> >
> >
> ------------------------------------------------------------------------------
> > All the data continuously generated in your IT infrastructure
> > contains a definitive record of customers, application performance,
> > security threats, fraudulent activity, and more. Splunk takes this
> > data and makes sense of it. IT sense. And common sense.
> > http://p.sf.net/sfu/splunk-novd2d
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>

Hi David,

> Since I happen to be playing with volumes right now, I tried that and
> it causes my sticks to pop out of the volumes (see attached).  This is
> on a build of the latest open source code in SVN.

You have found the reason why this isn't turned on by default. There
are still some problems with calculating depth that we haven't yet
fixed.

The way around this is to use the "draw" command with a very large
image size that you can scale down later to high-res.

Cheers,

-- Jason


> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
> <jas...@sc...> wrote:
>> Hi Lina,
>>
>> set ray_volume, on
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Nov 29, 2011 at 10:27 AM, lina <lin...@gm...> wrote:
>>> Hi,
>>>
>>> a quick question, how to keep the volume during ray.
>>>
>>> the volume is here,
>>>
>>> but after ray,
>>>
>>> it's gone,
>>>
>>> what's kinda of special settings I need to take care?
>>>
>>> Thanks with best regards,
>>>
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hey guys,

I am trying to calculate electrostatics with a ligand bound to my molecule using ABPS.  I am not having success.  Everything I've read seems to say that this is a normal limitation with APBS, and I've tried other programs to no avail.  I have not been able to rebuild my molecule in the "correct format" either.  Any help here is greatly appreciated.

Andrew
UMass Med School, Worcester, MA

On Wed, Nov 30, 2011 at 12:25 AM, Jason Vertrees
<jas...@sc...> wrote:
> Hi David,
>
> Are your data and color ramp points correct? If you send me the data,
> I can double-check what we've done.

I am also confusing how to put the quasi-center of volume on some certain atom.

Even I only chose one atom, but the volume still shifted away from
this certain atom,

The way I tried based on this page:
 http://www.pymolwiki.org/index.php/Isomesh

might I understand volume totally wrong.

Thanks ahead for pointing out.

p.s frankly speaking, I am interested in "volumn" simply cause the
representation looks fantastic.
>
> Cheers,
>
> -- Jason
>
> On Tue, Nov 29, 2011 at 10:56 AM, David Hall <li...@co...> wrote:
>> Since I happen to be playing with volumes right now, I tried that and
>> it causes my sticks to pop out of the volumes (see attached).  This is
>> on a build of the latest open source code in SVN.
>>
>> Thanks,
>> David
>>
>> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
>> <jas...@sc...> wrote:
>>> Hi Lina,
>>>
>>> set ray_volume, on
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>> On Tue, Nov 29, 2011 at 10:27 AM, lina <lin...@gm...> wrote:
>>>> Hi,
>>>>
>>>> a quick question, how to keep the volume during ray.
>>>>
>>>> the volume is here,
>>>>
>>>> but after ray,
>>>>
>>>> it's gone,
>>>>
>>>> what's kinda of special settings I need to take care?
>>>>
>>>> Thanks with best regards,
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All the data continuously generated in your IT infrastructure
>>>> contains a definitive record of customers, application performance,
>>>> security threats, fraudulent activity, and more. Splunk takes this
>>>> data and makes sense of it. IT sense. And common sense.
>>>> http://p.sf.net/sfu/splunk-novd2d
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>>
>>>
>>>
>>>
>>> --
>>> Jason Vertrees, PhD
>>> PyMOL Product Manager
>>> Schrodinger, LLC
>>>
>>> (e) Jas...@sc...
>>> (o) +1 (603) 374-7120
>>>
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi David,

Are your data and color ramp points correct? If you send me the data,
I can double-check what we've done.

Cheers,

-- Jason

On Tue, Nov 29, 2011 at 10:56 AM, David Hall <li...@co...> wrote:
> Since I happen to be playing with volumes right now, I tried that and
> it causes my sticks to pop out of the volumes (see attached).  This is
> on a build of the latest open source code in SVN.
>
> Thanks,
> David
>
> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
> <jas...@sc...> wrote:
>> Hi Lina,
>>
>> set ray_volume, on
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Nov 29, 2011 at 10:27 AM, lina <lin...@gm...> wrote:
>>> Hi,
>>>
>>> a quick question, how to keep the volume during ray.
>>>
>>> the volume is here,
>>>
>>> but after ray,
>>>
>>> it's gone,
>>>
>>> what's kinda of special settings I need to take care?
>>>
>>> Thanks with best regards,
>>>
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

On Tue, Nov 29, 2011 at 11:56 PM, David Hall <li...@co...> wrote:
> Since I happen to be playing with volumes right now, I tried that and
> it causes my sticks to pop out of the volumes (see attached).  This is
> on a build of the latest open source code in SVN.

Thanks for confirmation.

There are some unmet dependencies on my box, so I have to stick to 1.4
for a while and will try again in future.

Thanks and best regards,

>
> Thanks,
> David
>
> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
> <jas...@sc...> wrote:
>> Hi Lina,
>>
>> set ray_volume, on
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Nov 29, 2011 at 10:27 AM, lina <lin...@gm...> wrote:
>>> Hi,
>>>
>>> a quick question, how to keep the volume during ray.
>>>
>>> the volume is here,
>>>
>>> but after ray,
>>>
>>> it's gone,
>>>
>>> what's kinda of special settings I need to take care?
>>>
>>> Thanks with best regards,
>>>
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...

Hi Martin,

Here's a fourth option (and the technique worth noting :p ):

print len( set( [(i.chain,i.resi,i.resn) for i in
cmd.get_model(selection).atom] ) )

Cheers,

Tsjerk

On Tue, Nov 29, 2011 at 4:26 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi Martin,
>
> You get three options:
>
> (1) You can count alpha carbons:
>
> fetch 1rx1, async=0
>
> count_atoms n. CA
>
>
> (2) But, a protein could be missing alpha carbons then this is more
> complete (and the technique worth noting):
>
> n=0
> select qq, polymer
> select pp, None
> python
> while cmd.count_atoms("qq"):
>  cmd.select("pp", "br. first qq")
>  cmd.select("qq", "qq and not pp")
>  n+=1
> python end
> print "count_atoms: %d" % n
>
> If you put:
>
> select qq, *
>
> you'll get a higher count (160) because one atom in 1rx1's inorganic
> set is also named "CA".
>
>
> (3) The shorter version of (2) is:
>
> print len(cmd.get_model("poly").get_residues())
>
> Cheers,
>
> -- Jason
>
>
> On Tue, Nov 29, 2011 at 9:50 AM, Martin Hediger <ma...@bl...> wrote:
>> Dear List
>> How can I compute the numbers of residues in a model?
>>
>> Martin
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

On Tue, Nov 29, 2011 at 11:34 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi Lina,
>
> set ray_volume, on
Thanks,

is the ray_volume some new feature in latest version?

seems Version 1.4. no ray_volume feature.

Best regards,
>
> Cheers,
>
> -- Jason
>
> On Tue, Nov 29, 2011 at 10:27 AM, lina <lin...@gm...> wrote:
>> Hi,
>>
>> a quick question, how to keep the volume during ray.
>>
>> the volume is here,
>>
>> but after ray,
>>
>> it's gone,
>>
>> what's kinda of special settings I need to take care?
>>
>> Thanks with best regards,
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi Lina,

set ray_volume, on

Cheers,

-- Jason

On Tue, Nov 29, 2011 at 10:27 AM, lina <lin...@gm...> wrote:
> Hi,
>
> a quick question, how to keep the volume during ray.
>
> the volume is here,
>
> but after ray,
>
> it's gone,
>
> what's kinda of special settings I need to take care?
>
> Thanks with best regards,
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,

a quick question, how to keep the volume during ray.

the volume is here,

but after ray,

it's gone,

what's kinda of special settings I need to take care?

Thanks with best regards,

Hi Martin,

You get three options:

(1) You can count alpha carbons:

fetch 1rx1, async=0

count_atoms n. CA


(2) But, a protein could be missing alpha carbons then this is more
complete (and the technique worth noting):

n=0
select qq, polymer
select pp, None
python
while cmd.count_atoms("qq"):
  cmd.select("pp", "br. first qq")
  cmd.select("qq", "qq and not pp")
  n+=1
python end
print "count_atoms: %d" % n

If you put:

select qq, *

you'll get a higher count (160) because one atom in 1rx1's inorganic
set is also named "CA".


(3) The shorter version of (2) is:

print len(cmd.get_model("poly").get_residues())

Cheers,

-- Jason


On Tue, Nov 29, 2011 at 9:50 AM, Martin Hediger <ma...@bl...> wrote:
> Dear List
> How can I compute the numbers of residues in a model?
>
> Martin
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Dear List
How can I compute the numbers of residues in a model?

Martin

James,

> Is there any semi-avtomated way to find ligand binding pocket and do all
> such things ?

For your given object, click A > preset > ligands sites > cartoon. Try
other options under that menu.

Cheers,

-- Jason


> 2011/11/28 Thomas Holder <sp...@us...>
>>
>> Hi James,
>>
>> most trivial manner:
>>
>> as cartoon
>> show sticks, resn LEU+ILE+VAL
>> set cartoon_side_chain_helper
>>
>> and eventually something like this:
>>
>> show spheres, resn LEU+ILE+VAL and not name N+O+C
>> set sphere_transparency, 0.5
>>
>>
>> Cheers,
>>  Thomas
>>
>> On 11/28/2011 02:58 PM, James Starlight wrote:
>>>
>>> Another question also linked with the non-covalent interaction.
>>>
>>> In particular I wounder to know how i Could represent all hydrophobic (
>>> Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
>>> like to represent the hydrophobic core of the proteins made from those
>>> residues.
>>>
>>> Thanks,
>>>
>>> James
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Thanks, Thomas, Jason

both of the methods are useable :)

By the way I've forced with the problem of the representation of the active
sites of different enzymes. I need to view all my protein as the cartoons
and the ligand as the shpere in the ligand binding pocket. Besides I need
to mark residues wich are contact with the ligand ( E.g I want to mark it
as the lines and with the individual colour ). Finally I want to represent
Hbonds between active site residues and the ligand.

I've done this manually but its very long if I want to study 20-30
different enzymes during evening :)
Also I've found such sollution wich could do all that i want
http://www.pymolwiki.org/index.php/PLoS#Case_2:_Ligand-binding_sites_.28.E2.89.A5_novice.2Fintermediate.29

 but this way also I need to rewrite script for specified enzyme ( e.g mark
the active site residues and the distances for Hbonds etc )

Is there any semi-avtomated way to find ligand binding pocket and do all
such things ?

James



2011/11/28 Thomas Holder <sp...@us...>

> Hi James,
>
> most trivial manner:
>
> as cartoon
> show sticks, resn LEU+ILE+VAL
> set cartoon_side_chain_helper
>
> and eventually something like this:
>
> show spheres, resn LEU+ILE+VAL and not name N+O+C
> set sphere_transparency, 0.5
>
>
> Cheers,
>  Thomas
>
>
> On 11/28/2011 02:58 PM, James Starlight wrote:
>
>> Another question also linked with the non-covalent interaction.
>>
>> In particular I wounder to know how i Could represent all hydrophobic (
>> Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
>> like to represent the hydrophobic core of the proteins made from those
>> residues.
>>
>> Thanks,
>>
>> James
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>

Hi Martin,

It should be RMSD indeed. Mind that the final RMSD from align is obtained
after optimizing the fit by leaving out outliers.

Cheers,

Tsjerk

On Nov 29, 2011 10:07 AM, "Martin Hediger" <ma...@bl...> wrote:

Is the RMS the same as RMSD? PyMOL writes "RMS" when using align.
Martin





Am 11.11.11 14:59, schrieb Thomas Holder:

> Hi Martin, > > is it the transform=0 argument what you are looking for? >
> http://pymolwiki.org/i...
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Is the RMS the same as RMSD? PyMOL writes "RMS" when using align.
Martin





Am 11.11.11 14:59, schrieb Thomas Holder:
> Hi Martin,
>
> is it the transform=0 argument what you are looking for?
>
> http://pymolwiki.org/index.php/Align#PYMOL_API
>
> x = cmd.align('foo', 'bar', transform=0)
> print 'RMSD:', x[0]
>
> About the "some kind of refinement": There are arguments "cutoff" and 
> "cycles" that control this behaviour.
>
> Cheers,
>   Thomas
>
> On 11/11/2011 02:46 PM, Martin Hediger wrote:
>> Dear List.
>> When aligning two structures using the PyMOL align command, one gets a
>> final RMS value indicating some kind of "convergence" i would say. Can I
>> somehow access the function for calculating this value directly from the
>> pymol prompt without aligning?
>>
>> Thanks for hints
>> Martin
>

Hi Christian,

> I have a two chain protein and I want translat and rotate it using the
> commands translate and rotate. It is complicate to choose the rigth angel,
> because I cannot see the rotation axis. Is there a way to draw the axis system
> for the objects to see around which axis and how much I must rotate every
> single object. Does every object have is own axis system or is there a common
> system for all objects?

See http://www.pymolwiki.org/index.php/Axes.

Each object has its own transformation matrix. Rotate and translate
can act upon that matrix. See
http://www.pymolwiki.org/index.php/Get_object_matrix.


> When I color my protein according to the B-values is it possible to include a
> kind of  a legend like for the elctrostatics when I use APBS to get an idea
> about the minimum and maximum value?

An easy way is the following, but has two problems: (1) you're not
ensured the correct 1-1 mapping; (2) when you adjust the ramp the
lines colors don't change. But, it does work:

# fetch an example protein

fetch 1foo, async=0

# color it by b-factor

spectrum b, rainbow

# get the list of b-factors

x = []

cmd.iterate("1foo", "x.append(b)", space={'x':x})

# create the ramp across the range

cmd.ramp_new("myRamp", "1foo", [min(x), max(x)], "rainbow")


If I can recall the other way of mapping the ramp color to the lines,
I'll let you know. Right now it escapes me.

Cheers,

-- Jason

> Thanks in advance and Best Regards
>
> Christian
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Dear all,

I have a two chain protein and I want translat and rotate it using the 
commands translate and rotate. It is complicate to choose the rigth angel, 
because I cannot see the rotation axis. Is there a way to draw the axis system 
for the objects to see around which axis and how much I must rotate every 
single object. Does every object have is own axis system or is there a common 
system for all objects?

When I color my protein according to the B-values is it possible to include a 
kind of  a legend like for the elctrostatics when I use APBS to get an idea 
about the minimum and maximum value?

Thanks in advance and Best Regards

Christian

 

Hi Martin,

The temporary namespace for an atom means that variables like 'resn'
can be used to refer to the attribute with that name on the atom
instance.

You are right that iterate is here used to iterate over a single atom.
That does seem a bit odd :p But it seems to be a more straightforward
way to get to the properties desired.

This is what I would do:

residues=set()
iterate all, residues.add((chain,resn,resi))
for res in residues: cmd.save("%s-%s-%s.pdb"%res,"chain %s and resn %s
and resi %s"%res)

Of course that could be easily forged into a nice function :)

Hope it helps,

Tsjerk
On Mon, Nov 28, 2011 at 3:57 PM, Martin Hediger <ma...@bl...> wrote:
> In this example below (from Thomas), the method 'iterate' is used. The
> function saves every amino acid of a structure to a separate file. First
> of all, I'm not sure of how to understand the docs:
>
> " "iterate" iterates over an expression within a temporary namespace for
> each atom."
>
> What does temporary namespace for each atom mean? Also, since 'iterate'
> is used within the while-loop, are we only iterating over the single
> amino acid? Its confusing me because I constantly think of iterate as
> somekind of short hand notation of a for-loop, but I guess thats not it.
> It would be great if somebody could explain the iterate function a bit
> more to me.
>
> Thanks for your feedback.
> Martin
>
> # *****************************************************************
> # import statements
> def seq(state, selection="name ca or resn hoh or resn lig"):
>      cmd.select("prot", selection)
>      while cmd.pop("_tmp", "prot"):
>          cmd.iterate("_tmp", "stored.x=(resn,resv)")
>          # Special case 1: Waters.
>          if stored.x[0] == 'HOH':
>              filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>          # Special case 2: Substrate.
>          elif stored.x[0] == 'LIG':
>              filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>          # Other: protein back-bone.
>          else:
>              filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(), stored.x[1], state)
>          cmd.save(filename, "byres _tmp")
>      cmd.delete('_tmp prot')
>
> cmd.extend('seq', seq)
> # -----------------------------------------------------------------
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

In this example below (from Thomas), the method 'iterate' is used. The 
function saves every amino acid of a structure to a separate file. First 
of all, I'm not sure of how to understand the docs:

" "iterate" iterates over an expression within a temporary namespace for 
each atom."

What does temporary namespace for each atom mean? Also, since 'iterate' 
is used within the while-loop, are we only iterating over the single 
amino acid? Its confusing me because I constantly think of iterate as 
somekind of short hand notation of a for-loop, but I guess thats not it. 
It would be great if somebody could explain the iterate function a bit 
more to me.

Thanks for your feedback.
Martin

# *****************************************************************
# import statements
def seq(state, selection="name ca or resn hoh or resn lig"):
      cmd.select("prot", selection)
      while cmd.pop("_tmp", "prot"):
          cmd.iterate("_tmp", "stored.x=(resn,resv)")
          # Special case 1: Waters.
          if stored.x[0] == 'HOH':
              filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
          # Special case 2: Substrate.
          elif stored.x[0] == 'LIG':
              filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
          # Other: protein back-bone.
          else:
              filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(), stored.x[1], state)
          cmd.save(filename, "byres _tmp")
      cmd.delete('_tmp prot')

cmd.extend('seq', seq)
# -----------------------------------------------------------------

Hi James,

most trivial manner:

as cartoon
show sticks, resn LEU+ILE+VAL
set cartoon_side_chain_helper

and eventually something like this:

show spheres, resn LEU+ILE+VAL and not name N+O+C
set sphere_transparency, 0.5


Cheers,
   Thomas

On 11/28/2011 02:58 PM, James Starlight wrote:
> Another question also linked with the non-covalent interaction.
>
> In particular I wounder to know how i Could represent all hydrophobic (
> Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
> like to represent the hydrophobic core of the proteins made from those
> residues.
>
> Thanks,
>
> James

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Another question also linked with the non-covalent interaction.

In particular I wounder to know how i Could represent all hydrophobic ( Ley
Ile Val etc) sidechains in my proteins in most trivial manner? I'd like to
represent the hydrophobic core of the proteins made from those residues.


Thanks,

James

2011/11/27 Edward A. Berry <Be...@up...>

> Yes i think the strongest H-bonds are single acceptor and straight
> (angle at H = 180*). but these other bonds have significant
> strength also.
> Sorry, I'm a complete beginner at pymol. I have no idea how to
> do these things.
>
> ed
>
>
> James Starlight wrote:
>
>> Thanks Edward
>>
>> but recently I've studied generation of the Hbond in the water crystalls
>> ( ice ) where H
>> could be as the donor of only one H-bond. It seems that I need to refresh
>> my protein
>> physics course again :)
>>
>> By the way as I understtod the mode=2 way shows not only H-bonds but also
>> others
>> electrostatic bonds ( e.g as the salt bridges)
>> 1- Is there any way to make clear difference betwen two distinguished
>> electostatic contacts?
>>
>> 2- Also I'm looking for the most trivial way to show S-S bonds ( between
>> 2 Cys resiudes)
>> in the specified chain as well as between differen chains ( as in the
>> inslulin for instance ).
>>
>>
>> Thanks again,
>>
>> James
>>
>> 2011/11/26 Edward A. Berry <Be...@up... <mailto:Be...@up...
>> >>
>>
>>
>>    While the single acceptor H-bond is most common, bifurcated (or
>> three-centred) H-bods
>>    are not uncommon in crystal structures, as described starting page 22
>> of GA Jeffrey's
>>    book:
>>    http://www.amazon.com/__**Introduction-Hydrogen-Bonding-**
>> __Physical-Chemistry/dp/__**0195095499/ref=sr_1_2?ie=UTF8&**
>> __qid=1322331503&sr=8-2<" rel="nofollow">http://www.amazon.com/__Introduction-Hydrogen-Bonding-__Physical-Chemistry/dp/__0195095499/ref=sr_1_2?ie=UTF8&__qid=1322331503&sr=8-2>
>>
>>    <http://www.amazon.com/**Introduction-Hydrogen-Bonding-**
>> Physical-Chemistry/dp/**0195095499/ref=sr_1_2?ie=UTF8&**
>> qid=1322331503&sr=8-2<" rel="nofollow">http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8&qid=1322331503&sr=8-2>
>> >
>>
>>    James Starlight wrote:
>>
>>        Thomas, thank you for so detailed explanation.
>>
>>        This way works good but I'd like to ask you about possibe Hbonds
>> in the protein chain.
>>
>>        As I remember for protein physics courses the H atom is always
>> donor for only ONE
>>        H-bond (
>>        and O or N atoms could be akceptors for 1 or 2 Hbonds)
>>
>>        But In my case there are some cases where H atom ( white ) is
>> donor for the 2
>>        Hbonds.  By
>>        the way I found the same on the picture in WIKI too.
>>
>>        How it could be explaned ?
>>
>>        James
>>
>>
>>        ------------------------------**__----------------------------**
>> --__------------------
>>
>>        All the data continuously generated in your IT infrastructure
>>        contains a definitive record of customers, application performance,
>>        security threats, fraudulent activity, and more. Splunk takes this
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>> http://p.sf.net/sfu/splunk-**novd2d <>" rel="nofollow">http://p.sf.net/sfu/splunk-novd2d>>
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>>
>>
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