Hi Thanx for your response. I was quite surprised to see such examples listed as outlier in the pdb validation report. The angles are deviating by 8-10 deg. Am I being so picky on this. Do you suggest me to ignore such warnings
Cheers PK ________________________________ From: Hinrichs, Winfried <winfried.hinri...@uni-greifswald.de> Sent: 16 November 2021 19:24 To: Prasun Kumar <prasun.ku...@bristol.ac.uk> Subject: Re: [ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues Dear PR, 0.1Angstrom is not a general disaster - you should talk to a chemist. Best, Winfried Hinrichs ---------------------------------------------------------------------- ---------------------------------------------------------------------- Am Dienstag, den 16-11-2021 um 19:56 schrieb Prasun Kumar: Hi Group I am refining one of the structures that has modified amino acid and it is not defined in the CCP4 dictionary. I got the restrains using ELBOW and used it for refinement. However, when I refine the structure using REFMAC, the bond length deviates significantly from the ideal/ given value in the restrains file. for example: BR-CZ bond length is 2.01 ang (observed), but the ideal value is 1.9 ang. Bond angle and torsional angles are also behaving in a similar way. Can you please suggest a method by which I can fix this issue. I am happy to provide any other information. Thank You PK ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
