- Chimera-users - RBVI Mailing Lists

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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transform coordinates
by Alex Perálvarez Marín 23 Apr '10

23 Apr '10

Dear all, I would like to change the coordinates (Euler angles) for an EM density map (Tools --> Movements --> Transform molecule coordinates). But in the molecule scroll menu, my map does not appear. Is possible to define the system coordiantes for a EM density map? Thanks in advance, Alex.

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Displacement through vectors
by Elisabeth Ortega 23 Apr '10

23 Apr '10

Dear all, I'm trying to move an atom though a vector but I don't find the correct Python script to do that. The vector starts in the mass center of the molecule and finish in a nitrogen atom. I want to place Helium at 2 angstrom of the nitrogen atom following the mentioned vector. Could you help me with the script? Thanks in advance. Elisabeth Ortega, Ph.D Student @ Universitat Autónoma de Barcelona

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level of detail (vrml)
by Damien Larivière 22 Apr '10

22 Apr '10

Dear all, Chimera is able to display VRML file. Is it able to display VRML file containing level of detail? (My first tentative was not a success but I do not think the file I used respected the format convention). My best reagrds Damien

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Small molecule dimensions
by le monk 21 Apr '10

21 Apr '10

Hello, I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this? Many thanks _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now

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hide dust
by weimin wu 20 Apr '10

20 Apr '10

Sometimes after we remove the dust using the tool of hiding dust, we want to save the map directly instead of using command "mask #0 #0" to generate a maskfile. The reason is that the masked map has minimized map size and different with original one. Even after we recover the map size and origin, it always has half pixel issue, and if we apply this mask to original map, the output will have some masking artifact. The iso-surface of the output will not be as smooth as original map or the map after hiding dust. weimin

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Chimera on Acer Aspire 1410
by Mario J. Borgnia 20 Apr '10

20 Apr '10

Hi, I am running Chimera chimera-1.4.1-linux_x86_64 on my "netbook" style Acer Aspire 1410 with the following specifications: OS: Linux 2.6.31.12-0.2-desktop x86_64 Processor: Intel(R) Celeron(R) CPU 743 @ 1.30GHz Intel Mobile GM45 Express Chipset 1366x768 pixels The program runs well but surfaces disappear upon rotation. This is true for solid surfaces, as soon as I set the opacity to 0.99, the surfaces are no longer affected. Any hints? Thanks Mario Borgnia

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Chimera and Nvidia 3D vision
by Joern Lenz 20 Apr '10

20 Apr '10

Hi there, I am wondering if anyone of you knows if I can use my Nvidia GTX295 together with the 3D vision glasses and a Samsung SyncMaster 120Hz screen to view 3D in Chimera using a Debian Lenny or a Windows 7 OS. About two years ago, Nvidia said they will support Unix systems with their glasses. However, up to now there is no news about that. Do you have any idea or even a way to get 3D on in Chimera using the hardware above ? Many thanks. Cheers, Joern

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