August 2010 - Chimera-users - RBVI Mailing Lists

UCSF Chimera Visual Identity
by Jessen Vernon Bredeson 06 Aug '10

06 Aug '10

To whom this may concern, I downloaded the UCSF Chimera 1.4.1 update for Mac OS X and noticed that the Chimera symbol had a grey outline around it, likely due to multiple alpha channels in rendering the image into .ICNS format, so I recomposed the image in higher quality and it is attached below. Also below is an accompanying symbol for MS Windows format (.ICO). These icons are free of charge, keep up the good work. Jessen Bredeson Fourth-Year Genetics, Genomics & Development Molecular and Cellular Biology University of California, Berkeley

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model panel: add/edit note
by Dougherty, Matthew T 03 Aug '10

03 Aug '10

Is there a command to be able to modify notes on the model panel? If not, it would a useful addition when creating a command file to load in & color datasets.

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Small molecules and antechamber
by Jon Rumbley 02 Aug '10

02 Aug '10

I have several small organic molecules constructed in ChemDraw and converted in Chem3D to .mol2 files. I can open them in Chimera but cannot seem to add charges to. I was simply using the add charge menu commands and AM1-BCC and assuming the structures would be read as nonstandard but antechamber reports an error with residue ****. The error log has no real indication of what the trouble might be. Are there additional steps I must take before assigning charges? The structures already have hydrogens added. An example .mol2 file is below: @<TRIPOS>MOLECULE **** 44 45 1 0 0 SMALL USER_CHARGES @<TRIPOS>ATOM 1 C -2.8306 2.5311 -0.9622 C.2 1 **** 0.0000 2 C -2.8728 1.1718 -1.0363 C.2 1 **** 0.0000 3 C -4.0552 0.3840 -0.9622 C.1 1 **** 0.0000 4 C -1.6082 0.4134 -1.1450 C.2 1 **** 0.0000 5 N -5.0052 -0.2769 -0.8917 N.1 1 **** 0.0000 6 O -1.8883 -0.9222 -1.2800 O.3 1 **** 0.0000 7 O -0.4722 0.8459 -1.1451 O.2 1 **** 0.0000 8 C -0.8034 -1.8901 -1.1282 C.3 1 **** 0.0000 9 C -0.3965 -1.8485 0.3585 C.2 1 **** 0.0000 10 C -1.4383 -3.2075 -1.5077 C.3 1 **** 0.0000 11 N 0.6925 -2.6041 0.6991 N.am 1 **** 0.0000 12 O -1.0062 -1.1536 1.1745 O.2 1 **** 0.0000 13 C 1.2426 -2.6055 2.0833 C.3 1 **** 0.0000 14 C 2.4273 -3.5343 2.1380 C.ar 1 **** 0.0000 15 C -3.9592 3.4353 -0.8741 C.ar 1 **** 0.0000 16 C -3.7802 4.6664 -0.1923 C.ar 1 **** 0.0000 17 C -4.8234 5.5702 -0.0757 C.ar 1 **** 0.0000 18 C -6.0611 5.2454 -0.6673 C.ar 1 **** 0.0000 19 C -6.2633 4.0447 -1.3692 C.ar 1 **** 0.0000 20 C -5.2063 3.1490 -1.4690 C.ar 1 **** 0.0000 21 O -7.0408 6.1768 -0.5154 O.3 1 **** 0.0000 22 C 3.5525 -3.2801 1.3388 C.ar 1 **** 0.0000 23 C 4.6333 -4.1642 1.3545 C.ar 1 **** 0.0000 24 C 4.6017 -5.2952 2.1768 C.ar 1 **** 0.0000 25 C 3.4888 -5.5395 2.9865 C.ar 1 **** 0.0000 26 C 2.3994 -4.6635 2.9668 C.ar 1 **** 0.0000 27 H -1.8332 3.0176 -0.9495 H 1 **** 0.0000 28 H 0.0351 -1.5845 -1.7993 H 1 **** 0.0000 29 H -0.6942 -4.0150 -1.5686 H 1 **** 0.0000 30 H -1.9272 -3.1457 -2.4932 H 1 **** 0.0000 31 H -2.2150 -3.5214 -0.7935 H 1 **** 0.0000 32 H 1.1669 -3.2048 0.0167 H 1 **** 0.0000 33 H 1.5395 -1.5662 2.3712 H 1 **** 0.0000 34 H 0.4439 -2.9024 2.8058 H 1 **** 0.0000 35 H -2.8085 4.9012 0.2576 H 1 **** 0.0000 36 H -4.7042 6.5169 0.4530 H 1 **** 0.0000 37 H -7.2285 3.8279 -1.8322 H 1 **** 0.0000 38 H -5.3406 2.2282 -2.0442 H 1 **** 0.0000 39 H -7.9024 5.8992 -0.9622 H 1 **** 0.0000 40 H 3.5844 -2.3950 0.7014 H 1 **** 0.0000 41 H 5.5045 -3.9710 0.7250 H 1 **** 0.0000 42 H 5.4465 -5.9867 2.1870 H 1 **** 0.0000 43 H 3.4659 -6.4183 3.6333 H 1 **** 0.0000 44 H 1.5299 -4.8643 3.5946 H 1 **** 0.0000 @<TRIPOS>BOND 1 1 2 2 2 1 15 1 3 1 27 1 4 2 3 1 5 2 4 1 6 3 5 3 7 4 6 1 8 4 7 2 9 6 8 1 10 8 9 1 11 8 10 1 12 8 28 1 13 9 11 1 14 9 12 2 15 10 29 1 16 10 30 1 17 10 31 1 18 11 13 1 19 11 32 1 20 13 14 1 21 13 33 1 22 13 34 1 23 14 22 2 24 14 26 1 25 15 16 2 26 15 20 1 27 16 17 1 28 16 35 1 29 17 18 2 30 17 36 1 31 18 19 1 32 18 21 1 33 19 20 2 34 19 37 1 35 20 38 1 36 21 39 1 37 22 23 1 38 22 40 1 39 23 24 2 40 23 41 1 41 24 25 1 42 24 42 1 43 25 26 2 44 25 43 1 45 26 44 1 Thanks for any help you can provide. Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 LSci 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

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Chimera-users August 2010