Hey Folks, It is a relatively new feature to be able to read SDF compound structure files in Chimera. (I have release 2350 for Windows - I will be upgrading to the new snapshot that I just saw while looking around the site) Anyway - I tried with a compound sdf file that I got from PubChem (enclosed) - but seemed to have problems. At first it gave an error shown in the first lines below - and then seemed to say that it opened the files - but no atoms were displayed and no new model ID was generated and put into the Model Panel . Opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Error reading C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf: Unexpected end of file (parser state: post header 1) in MOL/SDF file 'C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf' Done opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Error reading C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf: Unexpected end of file (parser state: post header 1) in MOL/SDF file 'C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf' Done opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf I tried various atom selections and displaying all - but it seems obvious that it has not read in atoms and bonds. I have browsed around the documentation and only found a link to the sdf file formats. (I checked this out and tried editing out two of the header lines - ) It seems the error is unexpected end of file past the header. When checking the sdf file format information it seems that the $$$$ should be the only end of file mark - and there is only one at the end of my file. I also tried the whole procedure with a different sdf file from PubChem. Can anyone recognize what is causing the error in the enclosed file? Beyond that - are there other instructions on sdf file use in chimera that I did not see in searching the documentation? Thanks in advance, Mark -- Mark Andrake, Ph.D. Research Associate Fox Chase Cancer Center ICR428 7701 Burholme Ave. Philadelphia, PA 19111 215-728-3654 mark.andrake@fccc.edu 16048627 -OEChem-05040716572D 113118 0 0 0 0 0 0 0999 V2000 3.4030 4.5407 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -2.2663 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2.5369 5.0407 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9030 5.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9030 3.6746 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -3.2663 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 10.7288 -2.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.7288 -2.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1864 -3.2991 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1265 4.0641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8972 -2.1423 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 16.7693 2.3693 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6424 -5.4263 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0223 -3.0754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 18.7407 5.5226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 18.0148 2.0782 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9473 2.7359 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 11.5196 1.7056 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.5185 -4.0434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 18.1050 3.8579 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.9473 4.3454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1258 0.9008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5309 3.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5309 1.8086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 4.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8628 0.2337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 3.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 0.7337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7573 4.9318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6399 5.2970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2579 1.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4553 0.1588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2129 1.3091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1874 2.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5309 3.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0309 2.6746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 4.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8628 -0.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5901 1.0411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.1659 2.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 2.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.5948 0.2337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0309 2.6746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 4.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -1.2663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 3.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9007 0.0906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.5948 -0.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8338 2.9879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2329 -0.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.8123 2.7817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5436 -1.6042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.4801 3.5260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8757 -2.3485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4586 3.3198 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7281 -5.0211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5238 -3.9406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.8470 4.5283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.5133 2.9450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8630 -5.5226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1187 -4.8548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.7139 4.0298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.5076 3.0513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1208 4.4296 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2595 5.2953 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3937 5.4340 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2299 5.4876 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4493 5.8870 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0499 5.1064 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8048 2.0774 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6405 1.2975 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9953 0.5745 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0397 -0.3012 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9154 -0.2568 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4661 1.8751 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6470 1.5623 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9598 0.7432 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 11.6611 2.7775 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 12.4187 3.0251 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8409 4.0776 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3409 3.2116 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 5.1607 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3258 -1.0763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0432 0.7491 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2075 1.5290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 12.9347 1.6684 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.6923 1.9160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 1.9207 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1318 0.5437 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7209 2.1377 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7321 2.7307 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2833 -0.3973 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4477 0.3826 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1318 -1.0763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.0650 3.5632 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.3074 3.3156 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6860 -0.9457 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8503 -0.1658 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 15.3386 2.4541 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.5810 2.2065 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9261 -2.0921 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0905 -1.3122 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 15.7114 4.1013 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.9538 3.8537 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 4.7307 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4029 -5.9383 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2283 -6.0236 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5812 -4.5457 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7551 -5.3570 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9651 4.5966 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3038 3.8392 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1244 2.9876 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5087 2.4313 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 1 4 2 0 0 0 0 1 5 2 0 0 0 0 1 44 1 0 0 0 0 2 6 1 0 0 0 0 2 7 2 0 0 0 0 2 8 2 0 0 0 0 2 45 1 0 0 0 0 3105 1 0 0 0 0 9 19 1 0 0 0 0 9 54 1 0 0 0 0 10 20 1 0 0 0 0 10 55 1 0 0 0 0 11 54 2 0 0 0 0 12 55 2 0 0 0 0 13 56 2 0 0 0 0 14 57 2 0 0 0 0 15 58 2 0 0 0 0 16 59 2 0 0 0 0 17 23 2 0 0 0 0 17 27 1 0 0 0 0 17 31 1 0 0 0 0 18 24 1 0 0 0 0 18 28 1 0 0 0 0 18 34 1 0 0 0 0 19 56 1 0 0 0 0 19 57 1 0 0 0 0 20 58 1 0 0 0 0 20 59 1 0 0 0 0 21 23 1 0 0 0 0 21 25 1 0 0 0 0 21 29 1 0 0 0 0 21 30 1 0 0 0 0 22 24 1 0 0 0 0 22 26 1 0 0 0 0 22 32 1 0 0 0 0 22 33 1 0 0 0 0 23 35 1 0 0 0 0 24 36 2 0 0 0 0 25 27 2 0 0 0 0 25 37 1 0 0 0 0 26 28 2 0 0 0 0 26 38 1 0 0 0 0 27 41 1 0 0 0 0 28 42 1 0 0 0 0 29 64 1 0 0 0 0 29 65 1 0 0 0 0 29 66 1 0 0 0 0 30 67 1 0 0 0 0 30 68 1 0 0 0 0 30 69 1 0 0 0 0 31 39 1 0 0 0 0 31 70 1 0 0 0 0 31 71 1 0 0 0 0 32 72 1 0 0 0 0 32 73 1 0 0 0 0 32 74 1 0 0 0 0 33 75 1 0 0 0 0 33 76 1 0 0 0 0 33 77 1 0 0 0 0 34 40 1 0 0 0 0 34 78 1 0 0 0 0 34 79 1 0 0 0 0 35 43 2 0 0 0 0 35 80 1 0 0 0 0 36 43 1 0 0 0 0 36 81 1 0 0 0 0 37 44 2 0 0 0 0 37 82 1 0 0 0 0 38 45 2 0 0 0 0 38 83 1 0 0 0 0 39 47 1 0 0 0 0 39 84 1 0 0 0 0 39 85 1 0 0 0 0 40 49 1 0 0 0 0 40 86 1 0 0 0 0 40 87 1 0 0 0 0 41 46 2 0 0 0 0 41 88 1 0 0 0 0 42 48 2 0 0 0 0 42 89 1 0 0 0 0 43 90 1 0 0 0 0 44 46 1 0 0 0 0 45 48 1 0 0 0 0 46 91 1 0 0 0 0 47 50 1 0 0 0 0 47 92 1 0 0 0 0 47 93 1 0 0 0 0 48 94 1 0 0 0 0 49 51 1 0 0 0 0 49 95 1 0 0 0 0 49 96 1 0 0 0 0 50 52 1 0 0 0 0 50 97 1 0 0 0 0 50 98 1 0 0 0 0 51 53 1 0 0 0 0 51 99 1 0 0 0 0 51100 1 0 0 0 0 52 54 1 0 0 0 0 52101 1 0 0 0 0 52102 1 0 0 0 0 53 55 1 0 0 0 0 53103 1 0 0 0 0 53104 1 0 0 0 0 56 60 1 0 0 0 0 57 61 1 0 0 0 0 58 62 1 0 0 0 0 59 63 1 0 0 0 0 60 61 1 0 0 0 0 60106 1 0 0 0 0 60107 1 0 0 0 0 61108 1 0 0 0 0 61109 1 0 0 0 0 62 63 1 0 0 0 0 62110 1 0 0 0 0 62111 1 0 0 0 0 63112 1 0 0 0 0 63113 1 0 0 0 0 M CHG 2 6 -1 17 1 M END
<PUBCHEM_COMPOUND_CID> 16048627
<PUBCHEM_CACTVS_HBOND_ACCEPTOR> 15
<PUBCHEM_CACTVS_HBOND_DONOR> 1
<PUBCHEM_CACTVS_ROTATABLE_BOND> 19
<PUBCHEM_CACTVS_SUBSKEYS> AAADcfB/vABgAAAAAAAAAAAAAAAAAWLFiAAwYAAAAAAAAFgBQAAAHgQECAAADgjB2AQyyYMQAIKoAyXyXHDCAEAhAgAoiBk4ZJgIIDLAkZGEIAhkhCDIyAedyMAPgAQAgAACAAAACAEAAAQAAAAAAAAAAA==
<PUBCHEM_IUPAC_OPENEYE_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate
<PUBCHEM_IUPAC_CAS_NAME> (2E)-1-[5-[(2,5-dioxopyrrolidin-1-yl)oxy-oxo-methyl]pentyl]-2-[(E)-3-[1-[5-[(2,5-dioxopyrrolidin-1-yl)oxy-oxo-methyl]pentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate
<PUBCHEM_IUPAC_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indole-5-sulfonate
<PUBCHEM_IUPAC_SYSTEMATIC_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indole-5-sulfonate
<PUBCHEM_IUPAC_TRADITIONAL_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate
<PUBCHEM_NIST_INCHI> InChI=1/C43H50N4O14S2/c1-42(2)30-26-28(62(54,55)56)16-18-32(30)44(24-9-5-7-14-40(52)60-46-36(48)20-21-37(46)49)34(42)12-11-13-35-43(3,4)31-27-29(63(57,58)59)17-19-33(31)45(35)25-10-6-8-15-41(53)61-47-38(50)22-23-39(47)51/h11-13,16-19,26-27H,5-10,14-15,20-25H2,1-4H3,(H-,54,55,56,57,58,59)/f/h54H
<PUBCHEM_CACTVS_EXACT_MASS> 910.276
<PUBCHEM_OPENEYE_MF> C43H50N4O14S2
<PUBCHEM_OPENEYE_MW> 911.008
<PUBCHEM_OPENEYE_CAN_SMILES> CC1(C2=C(C=CC(=C2)S(=O)(=O)O)[N+](=C1C=CC=C3C(C4=C(N3CCCCCC(=O)ON5C(=O)CCC5=O)C=CC(=C4)S(=O)(=O)[O-])(C)C)CCCCCC(=O)ON6C(=O)CCC6=O)C
<PUBCHEM_OPENEYE_ISO_SMILES> CC1(C2=C(C=CC(=C2)S(=O)(=O)O)[N+](=C1\C=C\C=C\3/C(C4=C(N3CCCCCC(=O)ON5C(=O)CCC5=O)C=CC(=C4)S(=O)(=O)[O-])(C)C)CCCCCC(=O)ON6C(=O)CCC6=O)C
<PUBCHEM_CACTVS_TPSA> 245
<PUBCHEM_OPENEYE_MONOISOTOPICWT> 910.276
<PUBCHEM_TOTAL_CHARGE> 0
<PUBCHEM_HEAVY_ATOM_COUNT> 63
<PUBCHEM_ATOM_DEF_STEREO_COUNT> 0
<PUBCHEM_ATOM_UDEF_STEREO_COUNT> 0
<PUBCHEM_BOND_DEF_STEREO_COUNT> 2
<PUBCHEM_BOND_UDEF_STEREO_COUNT> 0
<PUBCHEM_ISOTOPIC_ATOM_COUNT> 0
<PUBCHEM_COMPONENT_COUNT> 1
<PUBCHEM_CACTVS_TAUTO_COUNT> 9
<PUBCHEM_BONDANNOTATIONS> 25 27 8 25 37 8 26 28 8 26 38 8 27 41 8 28 42 8 37 44 8 38 45 8 41 46 8 42 48 8 44 46 8 45 48 8
$$$$