Hi Robbie,
Oops, sorry, I used
CCP4 6.3: Refmac_5.7.0032 version 5.7.0032 : 05/09/12
(confirmed by the log file)
so I am using the current version and the problem still persists.
Thanks!
Markus
On 18/04/13 03:31 PM, Robbie Joosten wrote:
> Hi Markus,
>
> You could try changing your Refmac version. The version you are using is ancient. You may have an old version in your
> PATH next to the new one because your CCP4 seems up to date.
>
> AFAICT there is nothing wrong with the LINKR or the HETATM records
>
> Sent from my Windows Phone
> ------------------------------------------------------------------------------------------------------------------------
> From: Markus Meier
> Sent: 2013-04-18 22:19
> To: [log in to unmask]
> Subject: [ccp4bb] Alternate sugar conformations in refmac 5.5.0110
>
> Dear all,
>
> I am trying to refine a beta-D-N-Acetyl glucosamine moiety (NAG) linked
> to an asparagine (ASN) in Refmac.
> (version CCP4 6.3: Refmac_5.5.0110 version 5.5.0110 : 08/05/10)
>
> The sugar has two alternate conformations that occupy the same position in the electron
> density but are rotated 180° relative to each other. Even though I have
> defined two alternate conformations for the asparagine side chain, the
> sugar and the beta-link, Refmac pushes the two conformations apart, out of the electron
> density (while still honouring the link to Asn). So it seems that Refmac applies repulsive
> forces between the alternate conformations.
>
> Did anyone else experience this and/or can suggest a fix?
> All help is very much appreciated!
>
> My definitions for the alternate conformations in the PDB file are below:
>
> LINKR C1 ANAG E 1 ND2AASN A 116 NAG-ASN
> LINKR C1 BNAG E 1 ND2BASN A 116 NAG-ASN
> HETATM 125 C1 ANAG E 1 30.978 40.626 -25.446 0.50 98.96 E C
> HETATM 126 C2 ANAG E 1 30.428 41.897 -26.138 0.50100.81 E C
> HETATM 127 N2 ANAG E 1 29.783 41.751 -27.447 0.50 94.26 E N
> HETATM 128 C7 ANAG E 1 28.807 42.561 -27.924 0.50 89.45 E C
> HETATM 129 O7 ANAG E 1 28.325 42.377 -29.035 0.50 83.16 E O
> HETATM 130 C8 ANAG E 1 28.252 43.720 -27.128 0.50 87.63 E C
> HETATM 131 C3 ANAG E 1 31.618 42.847 -26.221 0.50102.77 E C
> HETATM 132 O3 ANAG E 1 31.420 43.888 -27.159 0.50102.25 E O
> HETATM 133 C4 ANAG E 1 31.840 43.369 -24.802 0.50103.37 E C
> HETATM 134 O4 ANAG E 1 32.969 44.217 -24.782 0.50104.91 E O
> HETATM 135 C5 ANAG E 1 32.040 42.223 -23.785 0.50 94.99 E C
> HETATM 136 C6 ANAG E 1 31.564 42.633 -22.381 0.50 86.60 E C
> HETATM 137 O6 ANAG E 1 32.632 42.591 -21.462 0.50 77.76 E O
> HETATM 138 O5 ANAG E 1 31.458 40.954 -24.130 0.50 99.19 E O
> HETATM 139 C1 BNAG E 1 30.271 40.925 -24.108 0.50 98.96 E C
> HETATM 140 C2 BNAG E 1 31.415 41.878 -23.684 0.50100.81 E C
> HETATM 141 N2 BNAG E 1 32.048 41.664 -22.378 0.50 94.26 E N
> HETATM 142 C7 BNAG E 1 33.331 41.981 -22.079 0.50 89.45 E C
> HETATM 143 O7 BNAG E 1 33.784 41.778 -20.959 0.50 83.16 E O
> HETATM 144 C8 BNAG E 1 34.276 42.586 -23.092 0.50 87.63 E C
> HETATM 145 C3 BNAG E 1 30.816 43.277 -23.775 0.50102.77 E C
> HETATM 146 O3 BNAG E 1 31.569 44.240 -23.061 0.50102.25 E O
> HETATM 147 C4 BNAG E 1 30.718 43.597 -25.266 0.50103.37 E C
> HETATM 148 O4 BNAG E 1 30.115 44.862 -25.440 0.50104.91 E O
> HETATM 149 C5 BNAG E 1 29.907 42.532 -26.038 0.50 94.99 E C
> HETATM 150 C6 BNAG E 1 30.373 42.426 -27.500 0.50 86.60 E C
> HETATM 151 O6 BNAG E 1 29.320 42.743 -28.381 0.50 77.76 E O
> HETATM 152 O5 BNAG E 1 29.866 41.216 -25.458 0.50 99.19 E O
> ATOM 745 N ASN A 116 27.207 36.475 -25.453 1.00 62.15 A N
> ATOM 746 CA AASN A 116 28.475 37.144 -25.135 0.50 61.77 A C
> ATOM 747 CB AASN A 116 28.182 38.336 -24.223 0.50 69.02 A C
> ATOM 748 CG AASN A 116 29.037 39.555 -24.495 0.50 79.45 A C
> ATOM 749 OD1AASN A 116 28.656 40.644 -24.047 0.50 83.18 A O
> ATOM 750 ND2AASN A 116 30.178 39.419 -25.218 0.50 87.72 A N
> ATOM 751 C ASN A 116 29.353 36.143 -24.389 1.00 53.28 A C
> ATOM 752 O ASN A 116 29.778 36.380 -23.266 1.00 48.83 A O
> ATOM 753 CA BASN A 116 28.575 37.144 -25.135 0.50 61.77 A C
> ATOM 754 CB BASN A 116 28.282 38.336 -24.223 0.50 69.02 A C
> ATOM 755 CG BASN A 116 29.487 39.201 -23.920 0.50 79.45 A C
> ATOM 756 OD1BASN A 116 30.611 38.710 -24.084 0.50 83.18 A O
> ATOM 757 ND2BASN A 116 29.299 40.471 -23.478 0.50 87.72 A N
>
> The Refmac log output shows that link description was recognized correctly for each conformation:
> WARNING : residue: NAG 1 chain:EE
> atom: "O1 " is absent in coord_file
> WARNING : link(spec):NAG-ASN is found dist = 1.466 ideal_dist= 1.439
> ch:EE res: 1 NAG at:C1 A->AA res: 116 ASN at:ND2 A
> WARNING : link(spec):NAG-ASN is found dist = 1.244 ideal_dist= 1.439
> ch:EE res: 1 NAG at:C1 B->AA res: 116 ASN at:ND2 B
>
>
> Best regards,
> Markus
>
> --
> Markus Meier, Ph.D.
> University of Manitoba
> Department of Chemistry
> 144 Dysart Road
--
Markus Meier, Ph.D.
University of Manitoba
Department of Chemistry
144 Dysart Road
Winnipeg, MB, R3T 2N2, Canada
Phone: +1 204 474 7172
Fax: +1 204 474 7608
E-mail: [log in to unmask]
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