How to decide on scut value in cmap function?

[santosh chaudhary]

Hi, I have a little confusion. How do be decide on scut values (0-3) for cmap? I was doing network analysis considering all heavy atom (using grpby) and each scut value gives little different result for network and thus node betweenness. Please suggest me.

thanks santosh

[Xinqiu Yao]

Hi,

It really depends on what purpose your study is and there is no absolute answer for what value is the best. You can use any value 0-3 as long as you understand what it means. If the results have only minor difference, then it doesn't matter which value you choose. If the difference is large, you need to dig into your data to find out why it is so different and which is the best suitable for your project.

Btw, this forum is mainly for asking questions directly related to the bio3d package. Generic scientific questions like above are probably not suitable here.

[santosh chaudhary]

Hi Xin, Thank you for the reply and sorry for this generic question. Probably i am not able to fully understand scut function. It would be very helpful if you please elaborate a liile bit more about scut function.

thanks santosh

[Xinqiu Yao]

Hi Santosh,

"Scut" is to mask contact between sequentially neighboring residues. For example, with scut=0 or 1, you will calculate contact for every residue pairs. With scut=3, residue pairs i/i+1 and i/i+2 will be excluded from the calculation (i.e. residues must be separated by at least 3 residues in sequence). Conventionally, scut=3/4 has been used to calculate e.g. native contact for protein folding problem. But it is not necessary the case for your problem. For example, you might want consider all residues in contact to calculate the network. scut=0 might be the choice. Hope it will help.

[santosh chaudhary]

Hi Xin,

Thank you very much. It was really helpful.

regards santosh