amino acid frame triplet side chain

[biochunan]

Hello, thanks for open sourcing your project.

I was wondering if I train ScanNet from scratch, should I modify line 170 to use Nitrogen atom of the current amino acid atom_coordinate instead of the previous aimo acid i.e. atom_coordinates[l-1]. I noticed in your comment that it was due to a previou issue. So just to confirm if I retrain the network, my understanding is I should replace line 169-175 line 182-188, is that correct?

ScanNet/preprocessing/protein_frames.py

Lines 166 to 188 in 77d8510

	#'''
	#TO CHANGE FOR NEXT NETWORK ITERATION... I used the wrong nitrogen when I rewrote the function...
	if l>0:
	if (0 in atom_id) & (1 in atom_id) & (17 in atom_ids[l-1]): # If C,N,Calpha are here, place virtual CoM
	sidechain_CoM = 3 * atom_coordinate[atom_id.index(1)] - atom_coordinates[l-1][atom_ids[l-1].index(17)] - \
	atom_coordinate[atom_id.index(0)]
	else:
	if verbose:
	print('Warning, pathological amino acid missing side chain and backbone', l)
	sidechain_CoM = atom_coordinate[-1]
	else:
	if verbose:
	print('Warning, pathological amino acid missing side chain and backbone', l)
	sidechain_CoM = atom_coordinate[-1]
	#'''
	# if (0 in atom_id) & (1 in atom_id) & (17 in atom_id): # If C,N,Calpha are here, place virtual CoM
	# sidechain_CoM = 3 * atom_coordinate[atom_id.index(1)] - atom_coordinate[atom_id.index(17)] - \
	# atom_coordinate[atom_id.index(0)]
	# else:
	# if verbose:
	# print('Warning, pathological amino acid missing side chain and backbone', l)
	# sidechain_CoM = atom_coordinate[-1]

[jertubiana]

Hi,
Thanks for your interest in our research.
Regarding protein_frames.py, please leave as it is, the change was already made.
However, if you retrain, you can comment l427 of file preprocessing/protein_chemistry.py and uncomment l428.
This is a bug regarding histidine parsing that I only noticed recently.
Best regards,
Jérôme

[biochunan]

Thansk for your reply! Though I am still confused about line 169-171 in protein_frames.py

For examle, a Glycine (residue index l), as in line 169-171 you are calculating its virtual side-chain CoM using the glycine's C and Cα atom coordinates and the Nitrogen atom of its preceding residue (l-1) if I understand correctly. In your paper, the side chain CoM was defined using Cα, C, N atom vector coordinates of the residue. So, why using nitrogen from preceding residue atom_coordinates[l-1][atom_ids[l-1].index(17)] rather than the glycine its own nitrogen atom e.g. atom_coordinate[atom.index(17)]?

[jertubiana]

Hi, sorry for the belated reply and the confusion. After double checking the situation, you are correct. You should indeed comment out 169-171). I thought I had already made the correction but had actually not. Thanks for pointing out the issue, and best of luck for your future research. Best, Jérôme

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On 18 Oct 2022, at 17:09, ChuNan Liu ***@***.***> wrote: Thansk for your reply! Though I am still confused about line 169-171 in protein_frames.py For examle, a Glycine (residue index l), as in line 169-171 you are calculating its virtual side-chain CoM using the glycine's C and Cα atom coordinates and the Nitrogen atom of its preceding residue (l-1) if I understand correctly. In your paper, the side chain CoM was defined using Cα, C, N atom vector coordinates of the residue. So, why using nitrogen from preceding residue atom_coordinates[l-1][atom_ids[l-1].index(17)] rather than the glycine its own nitrogen atom e.g. atom_coordinate[atom.index(17)]? — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACHSPJV6K6QEKP33PFGOUNLWD2VTHANCNFSM6AAAAAARHJNS3Y>. You are receiving this because you modified the open/close state.