Re: [PyMOL] How do you list H-bonds in pymol?

[Thomas Holder]

Hi Mina,

Badoo Mina wrote, On 04/05/13 16:49:
> This is my first post to the group. I hope it would be a great experience :)

I hope so too :)

> I am trying to compare the H-bonds in two NMR strcutures. So, I need to
> calculate H-bonds with a cutoff 2.5 and angle 35 angestrom that are
> availbale in 10 structures out of 20. I run list_hbonds.py as below:
> list_hb, selection1, cutoff=2.5, angle=35
> but it doesn not meet what I want.

Can you be more precise why it does not meet what you want? What result
do you get, and what result do you expect? I would use the hb_list
script like this:

PyMOL> fetch 2m1c, async=0
PyMOL> split_states 2m1c, prefix=s
PyMOL> list_hb s_0001, cutoff=2.5, angle=35, hb_list_name=hb1
PyMOL> list_hb s_0002, cutoff=2.5, angle=35, hb_list_name=hb2
PyMOL> list_hb s_0003, cutoff=2.5, angle=35, hb_list_name=hb3
...

> I want to look at inter and intra
> H-bonds (between two complexes of the protein and in each chain, too).
> How can I do that when I have splitted the ensemble to the 20 structures
> in pymol?

Actually I would be prefer PyMOL's distance command for such a job, it
works on all states at once, so you don't need to split states.

PyMOL> fetch 2m1c, async=0
PyMOL> set h_bond_max_angle, 35
PyMOL> distance hbAB, chain A, chain B, 2.5, mode=2
PyMOL> distance hbAA, chain A, chain A, 2.5, mode=2
PyMOL> distance hbBB, chain B, chain B, 2.5, mode=2

This doesn't print the H-bond pairs to the console output. If you need
that, use this script: http://pymolwiki.org/index.php/Get_raw_distances

See also: http://pymolwiki.org/index.php/Distance

Hope that helps.

Cheers,
  Thomas

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

--
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire 
the most talented Cisco Certified professionals. Visit the 
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] movie for morphing

[Thomas Holder]

Hi Jianghai,

if your morph has 30 states, this short script will y-rock at the
beginning, the middle, and the end or the morph:

mset 1 x51 -15 x61 -30 x51
movie.rock 1, 40
movie.rock 76, 115
movie.rock 151, 190

Instead of movie.rock, you can also use movie.nutate of course.

See also: http://pymolwiki.org/index.php/Mset

Cheers,
  Thomas

Jianghai Zhu wrote, On 04/05/13 20:59:
> Hi,
> 
> I have a pdb containing the morphing. I can play the movie with the 
> loaded pdb file. Now I want to start the movie with rocking the
> first state for a few seconds and end the movie with rocking the last
> state for a few seconds. How do I do that? Can I rock or nutate a
> state in the middle for a few seconds as well?
> 
> Thanks.
> 
> --Jianghai

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

--
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire 
the most talented Cisco Certified professionals. Visit the 
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net