pymol-users

[PyMOL] rotate translate two different objects indpendently and legend

[Christian R. <chr...@bb...>]

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

 

Re: [PyMOL] rotate translate two different objects indpendently and legend

[Jason V. <jas...@sc...>]

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
> _______________________________________________
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>



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

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

[PyMOL] Get number of residues in model

[Martin H. <ma...@bl...>]

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

Martin

Re: [PyMOL] Get number of residues in model

[Jason V. <jas...@sc...>]

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

Re: [PyMOL] Get number of residues in model

[Tsjerk W. <ts...@gm...>]

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