Re: [PyMOL] aligned and cealign command

[Thomas Holder]

Hi Jiri,

Try this on the PyMOL command line:

# example structures (use your own here)
fetch 1ake, s1, async=0
fetch 4ake, s2, async=0

# import the "angle_between_domains" command
run 
https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py

# align on chain A
align s1 & chain A, s2 & chain A

# measure rotation and displacement of chain B
angle_between_domains s1 & chain B, s2 & chain B, method=cealign

For 1ake and 4ake, this reports:
 Angle: 21.70 deg, Displacement: 56.08 angstrom

See also:
https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10995.html
https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13015.html

Hope that helps.

Cheers,
  Thomas

On 15 Dec 2016, at 07:02, chemocev marker  wrote:

> Hi Pymol user
> I have a heterodimer protein and I wanted to compare it with homologous 
> structures. The chain B of both the structures can be align with align 
> command and in doing so, the chain A is misaligned and which can be only 
> align by the cealign command. The sequence similarity between chain A is very 
> low but the both chains have similar fold. I am interested to know, how much 
> degree the subunits move or rotate when we aligned the chain A with cealign 
> command.
> best
> Jiri

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] aligned and cealign command

[chemocev marker]

Hi Pymol user
I have a heterodimer protein and I wanted to compare it with homologous
structures. The chain B of both the structures can be align with align
command and in doing so, the chain A is misaligned and which can be only
align by the cealign command. The sequence similarity between chain A is
very low but the both chains have similar fold. I am interested to know,
how much degree the subunits move or rotate when we aligned the chain A
with cealign command.
best
Jiri
--
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engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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