-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, Most of the websites of our group use Jmol for visualizing pdb's but I've found a little problem: Jmol seems to remove from visualization those residues which have an insertion code. For example, we have the pdb with id 1nmb:
... ATOM 697 N VAL N 169 84.638 76.903 35.261 1.00 3.87 1NMB 939 ATOM 698 CA VAL N 169 86.045 76.864 35.607 1.00 2.00 1NMB 940 ATOM 699 C VAL N 169 86.289 77.821 36.731 1.00 3.24 1NMB 941 ATOM 700 O VAL N 169 87.039 77.504 37.668 1.00 6.94 1NMB 942 ATOM 701 CB VAL N 169 86.949 77.395 34.479 1.00 2.00 1NMB 943 ATOM 702 CG1 VAL N 169 88.390 77.105 34.826 1.00 2.00 1NMB 944 ATOM 703 CG2 VAL N 169 86.566 76.843 33.117 1.00 2.00 1NMB 945 ATOM 704 N TYR N 169A 85.648 78.992 36.633 1.00 2.00 1NMB 946 ATOM 705 CA TYR N 169A 85.844 80.069 37.589 1.00 2.00 1NMB 947 ATOM 706 C TYR N 169A 85.157 79.926 38.911 1.00 2.00 1NMB 948 ATOM 707 O TYR N 169A 85.416 80.733 39.790 1.00 6.18 1NMB 949 ATOM 708 CB TYR N 169A 85.466 81.434 37.002 1.00 2.00 1NMB 950 ATOM 709 CG TYR N 169A 85.988 81.716 35.622 1.00 4.48 1NMB 951 ATOM 710 CD1 TYR N 169A 87.359 81.803 35.370 1.00 2.00 1NMB 952 ATOM 711 CD2 TYR N 169A 85.107 81.813 34.539 1.00 2.00 1NMB 953 ATOM 712 CE1 TYR N 169A 87.844 81.964 34.060 1.00 2.00 1NMB 954 ATOM 713 CE2 TYR N 169A 85.574 81.971 33.243 1.00 2.59 1NMB 955 ATOM 714 CZ TYR N 169A 86.952 82.043 33.002 1.00 4.27 1NMB 956 ATOM 715 OH TYR N 169A 87.424 82.164 31.697 1.00 2.00 1NMB 957 ATOM 716 N ASN N 170 84.262 78.961 39.070 1.00 2.00 1NMB 958 ATOM 717 CA ASN N 170 83.585 78.815 40.362 1.00 5.18 1NMB 959 ATOM 718 C ASN N 170 83.673 77.422 40.965 1.00 3.52 1NMB 960 ATOM 719 O ASN N 170 83.342 77.214 42.132 1.00 2.72 1NMB 961 ATOM 720 CB ASN N 170 82.117 79.284 40.290 1.00 5.26 1NMB 962 ATOM 721 CG ASN N 170 81.202 78.280 39.586 1.00 11.79 1NMB 963 ATOM 722 OD1 ASN N 170 81.657 77.492 38.744 1.00 10.10 1NMB 964 ATOM 723 ND2 ASN N 170 79.893 78.355 39.873 1.00 4.35 1NMB 965 .... As you can see it has an inserted residue int he position 169 (you have the residue 169 & the residue 169A), and Jmol decides to remove residue 169A. This is a big problem for us, so I was wondering if you are aware of that and if it will be corrected in new versions. Perhaps I'm doing something wrong... If nobody is working on that, I could try to fix it (I've not had a look to the code yet and I'm really busy so I cannot promise it). Regards, - -- - ------------------------------------------------ Iván Párraga García Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinformática Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: [EMAIL PROTECTED] group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFEgA+gLWwmlDjmrRYRAg47AJ4+/Ae6QkFSofYbsKNZMOnb+9eeKgCgpY26 RaDLXNqtS9kPP1SJ7kO4vh0= =nrEG -----END PGP SIGNATURE----- _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
