Dear Leila, Here is the description of PDB format. http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ATOM
Looking at first lines of your pdb file, I think no segid defined in your pdb file. So, please try "/com.pdb//a/2/ca" or "com.pdb and chain a and resi 2 and name ca". Cheers, Keitaro 2011/4/16 leila karami <[email protected]>: > Dear pymol users > > I read in the tutorial: > > Atom Selection Macros > > /object-name/segi-identifier/ > chain-identifier/resi-identifier/name-identifier > > I don't understand segi-identifier > > I want to select a atom ca in residue 2 in chain a in com.pdb. > > object-name = com.pdb > segi-identifier = ? > chain-identifier = a > resi-identifier = 2 > name-identifier = ca > > when I used select active, /com.pdb/a/2/ca ---> > > Selector-Error: Invalid Selection Name. > ( ( com.pdb ) & s; A & c; 2 & r; CA ) > > when I used select active, /com/A/2/CA ---> Selector: selection "active" > defined with 0 atoms. > > I can't attach com.pdb to this e-mail. > > First lines of com.pdb is as follows: > > ATOM 1 N GLY A 1 45.630 41.790 34.260 1.00 0.00 > ATOM 2 H1 GLY A 1 46.390 41.270 33.830 1.00 0.00 > ATOM 3 H2 GLY A 1 45.740 41.840 35.260 1.00 0.00 > ATOM 4 H3 GLY A 1 44.740 41.370 34.040 1.00 0.00 > ATOM 5 CA GLY A 1 45.580 43.190 33.840 1.00 0.00 > ATOM 6 HA1 GLY A 1 46.610 43.520 33.710 1.00 0.00 > ATOM 7 HA2 GLY A 1 45.050 43.760 34.610 1.00 0.00 > ATOM 8 C GLY A 1 44.660 43.310 32.640 1.00 0.00 > ATOM 9 O GLY A 1 43.950 42.320 32.420 1.00 0.00 > ATOM 10 N LYS A 2 44.740 44.420 31.910 1.00 0.00 > ATOM 11 H LYS A 2 45.260 45.170 32.340 1.00 0.00 > ATOM 12 CA LYS A 2 44.070 44.610 30.630 1.00 0.00 > ATOM 13 HA LYS A 2 44.200 43.700 30.050 1.00 0.00 > ATOM 14 CB LYS A 2 44.820 45.700 29.870 1.00 0.00 > ATOM 15 HB1 LYS A 2 44.600 46.580 30.480 1.00 0.00 > ATOM 16 HB2 LYS A 2 44.400 45.770 28.870 1.00 0.00 > > what is segi-identifier in com.pdb? > > please guide me about that. > > best wishes. > > > -- > > Leila Karami > Ph.D. student of Physical Chemistry > > K.N. Toosi University of Technology > Theoretical Physical Chemistry Group > > ------------------------------------------------------------------------------ > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] > ------------------------------------------------------------------------------ Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
