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Overlay abi initio with crystal structure

Posted: 2020.03.03 17:12
by han yin
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.

SASpy

Posted: 2020.03.09 10:41
by AL
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.

Re: SASpy

Posted: 2020.03.17 13:48
by han yin
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.

Assuming you are a Windows user...

Posted: 2020.03.18 15:50
by AL
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