April 2010 - Chimera-users - RBVI Mailing Lists

something flakey with measure buriedArea?
by Scott Classen 27 Apr '10

27 Apr '10

I'm seeing some very odd results coming from the measure buriedArea command if I use different values for probeRaduis and then grep for WARNINGs I get the following results: probeRadius # of WARNINGs 1.50 = 12 1.40 = 4 1.39 = 14 1.35 = 59 1.30 = 3 1.20 = 0 Here are some examples of the types of warnings I'm seeing: WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 1735 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 2557 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 1836 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 2090 WARNING: class_arete2: warning hole in a reentrant face 1925 WARNING: compute_SES_area: ERROR: Solide angle (-1.972093) for contact face 3142 too large or too small Should I be concerned? Another unusual thing is that for certain calculations I get some crazy answers. For example the following command measure buriedArea '#0:.A,.B & #0:10.Dz<8' #0:10.D probeRadius 1.4 vertexDensity 2 outputs: B1SES = -583.491, B2SES = 51.4762, BaveSES = -266.007 but the same command with the probeRadius changed to 1.37 measure buriedArea '#0:.A,.B & #0:10.Dz<8' #0:10.D probeRadius 1.37 vertexDensity 2 outputs: B1SES = 53.9334, B2SES = 51.7969, BaveSES = 52.8652 Why would B1SES be so radically different for these two measurements? Thanks, Scott ps When doing these calculations Chimera randomly crashes with the following mscalc crash report: Process: mscalc [25532] Path: /Applications/Chimera-1.5b.app/Contents/Resources/bin/mscalc Identifier: mscalc Version: ??? (???) Code Type: X86-64 (Native) Parent Process: python2.6 [25482] Date/Time: 2010-04-27 17:23:08.864 -0700 OS Version: Mac OS X 10.6.3 (10D573) Report Version: 6 Interval Since Last Report: 402 sec Crashes Since Last Report: 1 Per-App Crashes Since Last Report: 1 Anonymous UUID: D0B1026B-AD5E-454C-8E35-49CCF7598339 Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Crashed Thread: 0 Dispatch queue: com.apple.main-thread Application Specific Information: abort() called Thread 0 Crashed: Dispatch queue: com.apple.main-thread 0 libSystem.B.dylib 0x00007fff83cc7886 __kill + 10 1 libSystem.B.dylib 0x00007fff83d67eae abort + 83 2 libSystem.B.dylib 0x00007fff83c7fa75 free + 128 3 mscalc 0x00000001000218e5 MS_delete_SES_face + 920 4 mscalc 0x00000001000361f4 MS_update_ses + 919 5 mscalc 0x0000000100034f68 MS_restart_from_ses + 613 6 mscalc 0x0000000100036963 MS_update_ses + 2822 7 mscalc 0x0000000100037d94 MS_restart_from_triangulation + 591 8 mscalc 0x0000000100046c66 MS_triangulate_SES_component + 925 9 mscalc 0x00000001000066f6 MS_compute_surface + 443 10 mscalc 0x0000000100000ea2 main + 382 11 mscalc 0x0000000100000d1c start + 52 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000000000001 rcx: 0x00007fff5fbfd998 rdx: 0x0000000000000000 rdi: 0x00000000000063bc rsi: 0x0000000000000006 rbp: 0x00007fff5fbfd9b0 rsp: 0x00007fff5fbfd998 r8: 0x0000000000000e03 r9: 0x0000000000000000 r10: 0x00007fff83cc38ca r11: 0x0000000000000206 r12: 0x00000001001e4000 r13: 0x0000000100200000 r14: 0x0000000000000000 r15: 0x00000001004f7c70 rip: 0x00007fff83cc7886 rfl: 0x0000000000000206 cr2: 0x000000010022a000 Binary Images: 0x100000000 - 0x10004eff7 +mscalc ??? (???) <AF86E566-5546-A8C8-DE97-4A16408CB1BC> /Applications/Chimera-1.5b.app/Contents/Resources/bin/mscalc 0x7fff5fc00000 - 0x7fff5fc3bdef dyld 132.1 (???) <B633F790-4DDB-53CD-7ACF-2A3682BCEA9F> /usr/lib/dyld 0x7fff83c78000 - 0x7fff83e37ff7 libSystem.B.dylib 125.0.1 (compatibility 1.0.0) <CB9A4929-61AF-DE71-5635-133E9EC95783> /usr/lib/libSystem.B.dylib 0x7fff885a7000 - 0x7fff885abff7 libmathCommon.A.dylib 315.0.0 (compatibility 1.0.0) <95718673-FEEE-B6ED-B127-BCDBDB60D4E5> /usr/lib/system/libmathCommon.A.dylib 0x7fffffe00000 - 0x7fffffe01fff libSystem.B.dylib ??? (???) <CB9A4929-61AF-DE71-5635-133E9EC95783> /usr/lib/libSystem.B.dylib Model: MacPro1,1, BootROM MP11.005C.B08, 4 processors, Dual-Core Intel Xeon, 2.66 GHz, 14 GB, SMC 1.7f10 Graphics: ATI Radeon X1900 XT, ATY,RadeonX1900, PCIe, 512 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x87), Broadcom BCM43xx 1.0 (5.10.91.27) Bluetooth: Version 2.3.1f4, 2 service, 19 devices, 1 incoming serial ports Network Service: Built-in Ethernet 2, Ethernet, en1 PCI Card: ATY,RadeonX1900, Display, Slot-1 Serial ATA Device: ST3250824AS P, 232.89 GB Serial ATA Device: WDC WD2500JD-00HBC0, 232.89 GB Serial ATA Device: WDC WD1002FBYS-01A6B0, 931.51 GB Serial ATA Device: WDC WD1002FBYS-01A6B0, 931.51 GB Parallel ATA Device: SONY DVD RW DW-D150A USB Device: Hub, 0x05ac (Apple Inc.), 0x9131, 0xfd400000 USB Device: iPhone, 0x05ac (Apple Inc.), 0x1292, 0xfd430000 USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1005, 0xfd410000 USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x021d, 0xfd412000 USB Device: Apple Cinema HD Display, 0x05ac (Apple Inc.), 0x9223, 0xfd420000 USB Device: Hub, 0x05ac (Apple Inc.), 0x9122, 0xfd300000 USB Device: Apple Cinema HD Display, 0x05ac (Apple Inc.), 0x921e, 0xfd320000 USB Device: USB Receiver, 0x046d (Logitech Inc.), 0xc525, 0x1d200000 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8206, 0x5d200000 USB Device: Back-UPS CS 500 FW:806.q5.D USB FW:q5, 0x051d (American Power Conversion), 0x0002, 0x5d100000 FireWire Device: built-in_hub, Up to 800 Mb/sec FireWire Device: unknown_device, Unknown

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help with simple python script
by Scott Classen 27 Apr '10

27 Apr '10

Hi all, I have a number of PDB files that I would like to open, run a buriedArea calculation, save the results to a file, and exit I can put a bunch of commands in a file and launch it from a terminal shell chimera --nogui --nostatus --script calculate_buriedArea.com > results.txt the calculate_buriedArea.com file looks like this: open my.pdb measure buriedArea #0:.A #0:B This works, but is a bit cumbersome. I would like to make a python script so I can call my calculation with the name of the PDB file on the command line like this: chimera --nogui --nostatus --script calculate_buriedArea.py -- my.pdb .... so can someone please get me started here? import chimera myfile = chemera.somefunctiontoopenaPDBfile($1) Thanks, Scott

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ChemGroups
by Mauro Truglio 27 Apr '10

27 Apr '10

Hi, I got to understand the syntax to edit and even create "new" chemical groups for chimera to select (I successfully edited the file __init__.py in ChemGroups). Now I'm facing this problem with aromatic amines: when selecting, for example, primary aromatic amine, *I'd like to include also che C atom in the selection* - not only N,H,H. With other chemical groups this was easy, thanks to the [1,1,1,0,1]-like notation. But these aromatic amines are described in a different way, through the function findAroAmines in miscFind.py, and I'm finding it difficult to edit it. Can you help me? Thanks Mauro Truglio

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Daily Builds
by Jon N. Rumbley 27 Apr '10

27 Apr '10

Why is it that the Windows Daily Builds continue to say March 20, 2010 while the other operating system show the current date? Is the Windows version being built daily? Thank you, Jon Rumbley Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 Life Sciences 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

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saving attribute to file
by Scott Classen 26 Apr '10

26 Apr '10

Hello, When I save attributes to a text file from the "Render/Select by Attribute" dialogue box the values are written to the file apparently in a random order. Is there a way to get the residues or atoms to be written in a sensible way? i.e. by residue/atom number. Thanks, Scott Classen

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POV-Ray setting for movie making
by Paul Brandt 26 Apr '10

26 Apr '10

Hello, I am using chimera alpha version 1.3 (build 2577) running in linux (sled11) to make a movie using POV-Ray. The quality of the first few frames is stunning but thereafter becomes fuzzy around the edges of the molecule. Is there a way to fix this so that the entire movie is as clear and nice as the first few frames? Is there something wrong with my settings? Is what I'm seeing an artifact of mpeg compression? I am using the following POV-Ray settings to make an Mpeg1 movie Quality 11 Antialias: true Antialias method: recursive Antialias depth: 3 Antialias threshold: 0.3 Jitter: True Jitter amount: 1.0 Transparent background: false Wait for POV-Ray to finish false Keep input files: false Thanks for the help!! Paul

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please stop these emails
by Dr. Ahmed Sofy 26 Apr '10

26 Apr '10

Dear chimera organizing Thanks alot for your efforts but i want stop these emails of users Thanks alot again for your efforts

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HELP: I'm wondering about how to access the surface data
by "郑捷凯" 26 Apr '10

26 Apr '10

Hi chimera users, I'm wondering about several question: I installed chimera in my home dir, what's path to import in python? how can I access the data generated by mscalc in python?

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placeFragment
by Elisabeth Ortega 26 Apr '10

26 Apr '10

Dear all, I'm trying to place a fragment in certain position. I did this (on Python IDLE): from BuildStructure import placeFragment placeFragment( fragment, resName, model = 'scratch', position=None) Where fragment = benzene and resName = RING6 but I am not sure about that . Could you give me an example of placeFragment code? Thanks in advance. Elisabeth Ortega , Ph.D Student @ Universitat Autónoma de Barcelona

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"cutoff" parameter in Find clashes/contacts option
by Anna Feldman-Salit 24 Apr '10

24 Apr '10

Dear All, I was unsuccessfully looking for the explanation to what exactly "cutoff" parameter means. I'm using the Find clashes/contacts option to identify the contacts and not clashes, by assigning the default values of -0.4A and 0.0 to "cutoff" and "allowance" parameters. However, I do not understand how it is used. I would very much grateful for the information, since I also want to include it in my dissertation. Best regards, Anna Feldman-Salit

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Chimera-users April 2010