Overlay abi initio with crystal structure

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
Post Reply
Message
Author
han yin
Member
Posts: 7
Joined: 2019.10.11 13:30

Overlay abi initio with crystal structure

#1 Post by han yin » 2020.03.03 17:12

Greetings

I am practicing abi initio modelling with ATSAS 3.0.1 and mono-disperse lysozyme sample.

I have a working model that i'd like to overlay with the crystal structure of lysozyme from PDB database. Anyone know how could you do this in Pymol?

Since the Abi initio only provides an "envelope" of the protein so to speak, the typical method from Pymol such as Super and Align doesnt work very well with the crystal structure.

Many thanks.

User avatar
AL
Administrator
Posts: 727
Joined: 2007.08.03 18:55
Location: EMBL Hamburg, Germany
Contact:

SASpy

#2 Post by AL » 2020.03.09 10:41

Please install the SASpy plugin.
Open your ab initio model and the crystal structure in PyMOL.
Open SASpy, switch to the 'supalm' tab. Under 'Model selection' choose the two models and click 'Execute'.
This will work well for globular models like lysozyme. If you have very elongated models it is better to use SUPCOMB from the command line.

han yin
Member
Posts: 7
Joined: 2019.10.11 13:30

Re: SASpy

#3 Post by han yin » 2020.03.17 13:48

AL wrote:
2020.03.09 10:41
Please install the SASpy plugin.
Open your ab initio model and the crystal structure in PyMOL.
Open SASpy, switch to the 'supalm' tab. Under 'Model selection' choose the two models and click 'Execute'.
This will work well for globular models like lysozyme. If you have very elongated models it is better to use SUPCOMB from the command line.
Thank you very much for the reply. The Damaver and Primus from 3.0.1 has been working great since the update, but i could not open the supcomb command function: the command prompt window opens then instantly closes. Could i ask what might the problem be?

Thanks again for your help and developing this software.

User avatar
AL
Administrator
Posts: 727
Joined: 2007.08.03 18:55
Location: EMBL Hamburg, Germany
Contact:

Assuming you are a Windows user...

#4 Post by AL » 2020.03.18 15:50

han yin wrote:
2020.03.17 13:48
...i could not open the supcomb command function: the command prompt window opens then instantly closes.
How to use the Windows command line
ATSAS: how to update/modify your PATH settings

Post Reply