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Bioinformatics Code

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21 Mar 2021
@telegram_1469876532:tchncs.deCarlo (Telegram)Ok I am going to check it11:43:33
@telegram_1469876532:tchncs.deCarlo (Telegram)270 is the sum of the number of residues present in the pdb structure (both chains)11:58:38
@telegram_1469876532:tchncs.deCarlo (Telegram)image.jpeg
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11:59:44
@telegram_1469876532:tchncs.deCarlo (Telegram)In red boxes you can see the residues missing in the crystallographic structure.11:59:44
@telegram_1469876532:tchncs.deCarlo (Telegram)The length of each one (including red boxes) is 175 (look at the numberings above the sequences)12:00:40
@telegram_1469876532:tchncs.deCarlo (Telegram)If you subtract to each one the red boxes you get 143 for chain A and 127 for chain B, and 143+127=27012:02:50
@telegram_1437907806:tchncs.dePR Sinha (Telegram)
In reply to Carlo (Telegram)
In red boxes you can see the residues missing in the crystallographic structure.
Ohh..I get it now
12:05:35
@telegram_1437907806:tchncs.dePR Sinha (Telegram)Thanks a lot12:05:54
@telegram_1469876532:tchncs.deCarlo (Telegram)
In reply to Carlo (Telegram)
In red boxes you can see the residues missing in the crystallographic structure.
Pay attention now to the numberings aside: they tells you the position of a specific aminoacid in the original sequence... As you can see in chain A the first available residue in the structure is the 25th (an H). In the chain B the first is the 28th (an A)
12:06:16
@telegram_1437907806:tchncs.dePR Sinha (Telegram)
In reply to Carlo (Telegram)
Pay attention now to the numberings aside: they tells you the position of a specific aminoacid in the original sequence... As you can see in chain A the first available residue in the structure is the 25th (an H). In the chain B the first is the 28th (an A)
Yes
12:07:06
@telegram_1469876532:tchncs.deCarlo (Telegram)This numeration is probably referred to the protein sequence expected from the cloning...and it is probably same or similar in the uniprotKB...☺️12:07:23
@telegram_1469876532:tchncs.deCarlo (Telegram)You're welcome12:07:28
@telegram_1437907806:tchncs.dePR Sinha (Telegram)So in any case, total length will be equal to or greater than residue count, right?12:10:32
@telegram_1437907806:tchncs.dePR Sinha (Telegram)
In reply to Carlo (Telegram)
This numeration is probably referred to the protein sequence expected from the cloning...and it is probably same or similar in the uniprotKB...☺️
U mean seq length (here 175) ?
12:12:59
@telegram_1469876532:tchncs.deCarlo (Telegram)image.jpeg
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12:17:22
@telegram_1469876532:tchncs.deCarlo (Telegram)The missing serine is the 24th residue in the original length... Was just saying this12:17:22
@telegram_1437907806:tchncs.dePR Sinha (Telegram)
In reply to Carlo (Telegram)
The missing serine is the 24th residue in the original length... Was just saying this
Ok
12:18:20
@telegram_1469876532:tchncs.deCarlo (Telegram)And it's the 1st in the structure (sincerely don't know why it counts if it misses also in the pdb...🙌)12:18:43
@telegram_1469876532:tchncs.deCarlo (Telegram)Just to warn you if you want to align it with the original one, they crystallized (or find the electron density map) for only a part of the protein12:20:00
@telegram_1437907806:tchncs.dePR Sinha (Telegram)
In reply to Carlo (Telegram)
Just to warn you if you want to align it with the original one, they crystallized (or find the electron density map) for only a part of the protein
Okay, sure
12:48:07
@telegram_1437907806:tchncs.dePR Sinha (Telegram)
In reply to Carlo (Telegram)
In red boxes you can see the residues missing in the crystallographic structure.
Are u visualizing the files on chimera?
12:57:53
@telegram_1469876532:tchncs.deCarlo (Telegram)Yep12:58:13
@telegram_1437907806:tchncs.dePR Sinha (Telegram)Okk12:59:44
24 Mar 2021
@telegram_791623181:tchncs.deSeema Soni. (Telegram) changed their display name from SRS (Telegram) to Seema Soni. (Telegram).12:40:01
25 Mar 2021
@a-27m:matrix.orgOlexiy Myronenko joined the room.12:00:53
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28 Mar 2021
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30 Mar 2021
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31 Mar 2021
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