- Chimera-users - RBVI Mailing Lists

benchmark
by Dougherty, Matthew T. 14 May '07

14 May '07

nvidia quadro fx 4500 macpro Dual-Core Intel Xeon clock 2.66 GHz macos 10.4.9 pci express date 5/11/7 chimera 2382 graphics memory 512 MB main memory 2GB unknown apple graphics driver Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 4439.0 4263.0 827.0 828.0 4344.0 1201.0 11755.0 1YTI (798): 4285.0 4034.0 307.0 307.0 4119.0 475.0 3562.0 2GBP (2575): 3384.0 3217.0 103.0 102.0 3139.0 166.0 1063.0 1GOT (6449): 1833.0 1602.0 41.0 41.0 1702.0 67.0 395.0 2HMG (12189): 461.0 478.0 22.0 21.0 489.0 35.0 143.0 2PDA (18894): 271.0 293.0 14.0 14.0 297.0 22.0 76.0 1YNJ (24369): 211.0 230.0 11.0 11.0 232.0 18.0 56.0 1F4H (33805): 154.0 166.0 8.0 8.0 169.0 13.0 38.0 Matthew Dougherty *** 713-433-3849 *** National Center for Macromolecular Imaging***

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Normal Modes, arrows and more...
by Jean-Didier Marechal 14 May '07

14 May '07

Dear All, I am trying to use chimera to draw arrows of the Normal Modes vectors I previously calculated with charmm. I see different possibilities to provide chimera with the vectors, but how can I draw the arrows? I found a request on the list from Mingfeng Yang that Petter answered in october 2004 regarding a similar problem. Unfortunately the link indicated for VRML does not work anymore. What are the actual features of chimera that would allow me to do something like this ? All the best, JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

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Re: [Chimera-users] imod model viewing
by Tom Goddard 11 May '07

11 May '07

Hi David, The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure. Tom David G. Morgan wrote: > Tom, > > I was trying to use the new IMOD file reader and must be doing something > foolish. I downloaded the newest chimera snapshot release (1.2392) and > the imod.zip file and made a new installation. I can load my IMOD > volume into chimera without any trouble. I then "opened" the IMOD model > file (it opened as an "IMOD segmentation" type). That works without > trouble, but I don't ever see the model. Even trying to use "focus" to > bring it into the field of view gives me a blank field. > > It's possible that my model is the wrong type - I'm playing with chimera > in preparation for needing to do something fancy, so I simply created a > set of spheres of different colors and different radii in IMOD, saved > that model and tried to read it into chimera. I thought I'd simply be > able to read this into chimera and see a couple of spheres, but I don't. > I'm sure I'm doing something silly, but figured I'd bother you while I > play around with it. > > David Gene Morgan > University of California at Davis >

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Question about background transparency
by Vanacore, Roberto M 09 May '07

09 May '07

What are the system requirements to run -bgopacity option in a windows machine? I've tried adding to option (--bgopacity) to the startup command but I can not get a transparent background I'm using Chimera 2.2199 Thanks! Roberto Roberto Vanacore, PhD B-3101 Medical Center North Vanderbilt University Medical Center 1161 Twenty-first Ave South Nashville, TN 37232-2372 Phone: 615-322-7306 Fax: 615-322-7381

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contour levels in Morph Map
by Gabor Papai 09 May '07

09 May '07

Dear all, Is it possible with the Morph Map tool to set the contour levels of the two maps differently? For e.g. if I would like to morph between a map, which is obtained from single particle analysis and has the right contour level of 0.2 - and a second map, which is obtained from tomography and has the right contour level of 2.2, it gives weird result. Other question: does somebody consider to make chimera able to read Imagic files? Thanks for the help! Regards, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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chain selection in a multi-conformatin pdb file.
by Hong Liang 09 May '07

09 May '07

Hi Chimera fans, 1. If a pdb file contains more then one struture, how can I select and keep just one and get rid of the rest. Such as 1X95. It is a big mess after Chimera load the the DNA pdb structure. How can I leave just one double helix? 2. Can Chimera do the extension of DNA. Such as 1X95 has the hexamer with the sequence of ATGCAT, can Chimera double it to a dodecamer with a sequence ATGCATATGCAT? It Chimera can not do that, do you know which software has such a function. I tried PyMol but did not get what I wanted. Thanks a lot. Hong

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Defining a zone around a point defined by x, y, z coordinates
by Jean-Didier Marechal 08 May '07

08 May '07

Dear all, We are having difficulties in defining a certain type of selection zones in chimera. Our problem is that we don't want to centre the zone on an atom selection but on one point of the space defined by its 3D coordinates. Typically we want to give chimera the x,y,z coordinates and select all the atoms included in a sphere of 25 angstroms around this point. How can we do so? Thanks a lot JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

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Find Hbonds in batch
by Stefan Bienert 08 May '07

08 May '07

Hello Chimera fans! Is there a way to use chimera for finding hydrogen bonds for tons of molecules? I'm thinking of something like a command line script, which loads a pdb file, fetches the hbonds and writes them to a file. I got around 1000 pdb files and therefore doing everything manually is not an option ;-) greetings, Stefan -- Stefan Bienert Zentrum fuer Bioinformatik Universitaet Hamburg Bundesstrasse 43 20146 Hamburg Germany Email: bienert(a)zbh.uni-hamburg.de Phone: +49 (40) 42838 7345 Fax: +49 (40) 42838 7332

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importing sdf files from PubChem
by Mark Andrake 07 May '07

07 May '07

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(a)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 $$$$

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Suggestion for Metal Geometry Feature
by Walter Fast 07 May '07

07 May '07

Hi Elaine (I think!), I know there is a measure angle feature in Chimera. I have been using this to define metal ligand geometries in our protein structures (for example, distinguishing between square pyramidal and trigonal bypramidal geometries). Maybe if there is enough interest, this could be an automated feature in the future where a metal ion is selected and then all of the ligands and angles are automatically displayed along with an assigned geometry. We've been using the following reference for assigning them. Just a suggestion! Many thanks, Walt -- Walter Fast, Ph.D. Assistant Professor The University of Texas at Austin College of Pharmacy The Division of Medicinal Chemistry Phone: (512) 232-4000 Fax: (512) 232-2606 Lab: (512) 471-5839 Email: WaltFast(a)mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html

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