Should phenix.refine be able to handle OXT? I find it is moving the OXT atom ~2A from where it should be. Do I need to rename it or add a separate definition to the refinement? Thanks, Chris
Should phenix.refine be able to handle OXT?
Yes.
I find it is moving the OXT atom ~2A from where it should be.
This shouldn't happen unless the atoms the OXT is bonded to are missing and it is floating around in isolation. Could you check the OXT bonds in the .geo file? (I hope it is obvious.) If you send me the fragment of our PDB file with the terminus and maybe a few residues before that I'll take a look. Ralf
Okay, I think I found the problem. After my first round of refinement the pdb file looked like this: ATOM 1903 N ALA A 124 -4.693 50.930 27.375 1.00 72.40 A N ANISOU 1903 N ALA A 124 9503 9688 8319 1028 520 1111 A N ATOM 1904 CA ALA A 124 -4.940 50.799 25.947 1.00 75.89 A C ANISOU 1904 CA ALA A 124 10040 10319 8474 1166 544 1164 A C ATOM 1905 CB ALA A 124 -5.775 51.970 25.467 1.00 77.30 A C ANISOU 1905 CB ALA A 124 10130 10588 8653 1211 479 1305 A C ATOM 1906 C ALA A 124 -3.615 50.754 25.196 1.00 75.91 A C ANISOU 1906 C ALA A 124 10074 10346 8421 1311 739 1335 A C ATOM 1907 O ALA A 124 -2.627 51.332 25.645 1.00 75.34 A O ANISOU 1907 O ALA A 124 9892 10148 8588 1315 850 1493 A O TER Then after manual rebuilding in coot, it became: ATOM 967 N ALA A 124 -4.693 50.930 27.375 1.00 72.40 A N ANISOU 967 N ALA A 124 9503 9688 8319 1028 520 1111 A N ATOM 968 CA ALA A 124 -4.940 50.799 25.947 1.00 75.89 A C ANISOU 968 CA ALA A 124 10040 10319 8474 1166 544 1164 A C ATOM 969 CB ALA A 124 -5.775 51.970 25.467 1.00 77.30 A C ANISOU 969 CB ALA A 124 10130 10588 8653 1211 479 1305 A C ATOM 970 C ALA A 124 -3.615 50.754 25.196 1.00 75.91 A C ANISOU 970 C ALA A 124 10074 10346 8421 1311 739 1335 A C ATOM 971 O ALA A 124 -2.627 51.332 25.645 1.00 75.35 A O ANISOU 971 O ALA A 124 9892 10148 8588 1315 850 1493 A O TER 972 ALA A 124 ATOM 973 OXT ALA A 124 -3.513 50.141 24.133 1.00 30.00 O So I'm guessing that phenix got confused by the OXT happening after the TER card. Everything looked okay in the .geo file. I will try the next round without the extra TER lines and see if that helps... Thanks, Chris -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Friday, May 23, 2008 9:28 AM To: [email protected] Subject: Re: [phenixbb] OXT
Should phenix.refine be able to handle OXT?
Yes.
I find it is moving the OXT atom ~2A from where it should be.
This shouldn't happen unless the atoms the OXT is bonded to are missing and it is floating around in isolation. Could you check the OXT bonds in the .geo file? (I hope it is obvious.) If you send me the fragment of our PDB file with the terminus and maybe a few residues before that I'll take a look. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Chris, yes, the TER card is definitely a problem. I'm sure the problem is resolved if you move the TER card one line down (the phenix pdb interpretation doesn't care about the extra stuff after the "TER "). Ralf
participants (2)
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Ralf W. Grosse-Kunstleve -
Rife, Christopher L