- Chimera-users - RBVI Mailing Lists

internal coordinates (z-matrix) in chimera
by Chinh Su Tran To 21 Mar '13

21 Mar '13

Hi, I have some results after running docking from DOCK. I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix). Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out. I have bunch of conformations, so I may not use the gui. Thank you. Chinh

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importing maps into chimera
by Arnaout, M. Amin,M.D. 21 Mar '13

21 Mar '13

What format does Chimera accept for ED maps? I tried .mtz files but did not work. Thank you. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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re
by Larry Simpson 21 Mar '13

21 Mar '13

Hi I have a strange problem with Chimera 1.7. My computer (Windows 7 64 bit) just had Microsoft updates last night and now Chimera does not see any drives but C and D. I usually use files on virtual drives E, etc. I tried rebooting, reinstalling Chimera but it is still the same problem. Any suggestions? Larry

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how to make super8.msf.
by han xiaodon 21 Mar '13

21 Mar '13

dear professor. would you share me how to make super8.msf.

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MSI Installer
by Yanni 20 Mar '13

20 Mar '13

Hello Do you have a chimera MSI installer available to download? Many thanks Yanni

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Re: [Chimera-users] show alpha-carbon as sphere in chimera
by Elaine Meng 19 Mar '13

19 Mar '13

On Mar 18, 2013, at 8:07 PM, Feixia wrote: > Hi Elaine, > Is there a way to show alpha-carbon only in Chimera as sphere? I can show beta-carbon, but always together with alpha-carbon. Alpha-carbon for some reason doesn't show by itself. Thanks a lot. > Best, > Feixia Hi Feixia, Maybe you are also displaying ribbon. By default when the ribbon is shown, the alpha-carbon will not show. You can allow showing both ribbon and alpha-carbon with command: ribbackbone <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> However, you can see the "real" position of the alpha-carbon is not exactly on the ribbon. Sometimes it will seem to float away, and the image might not look good. That is because the default ribbon is a smooth interpolation. Possible ways to handle this issue: (a) don't show ribbon (b) make the alpha-carbon sphere(s) big enough and/or change the viewing angle so it is not obviously floating away from the ribbon. Whether this is possible depends on which positions you are displaying and the specific backbone conformation in those areas. (c) change the ribbon from the default B-spline to cardinal spline, with or without some compromise smoothing, for example with commands: ribspline cardinal ribspline cardinal smooth strand <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html> More discussion/explanation of this issue: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon…> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Fwd: Re: Version 1.7 on linux
by Greg Couch 19 Mar '13

19 Mar '13

(Forgot to reply to list as well.) Hi Austin, What's your alias? chimera should *not* be on your PATH, it expects to find its version of various system libraries. Instead put a symbolic link to CHIMERA/bin/chimera in one of the directories on your PATH. Not sure what you mean about two threads, a screenshot would help. HTH, Greg On 03/19/2013 12:31 PM, Austin B. Yongye wrote: > Hello Chimera users, > I just installed version 1.7 on my centos v5.4 machine. When I launch > it using an alias, there is a splash across my entire screen and two > threads are shown on the bottom panel. This splash persists for long, > and I get the usual GUI only after switching between the two threads a > couple of times. When I proceed to open a structure, nothing shows up > on the GUI though it says a structure has been opened. > All these problems go away when I launch chimera directly from the > installation directory. > Any suggestions? Thanks. > Austin- > >

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How to change water molecule from triangle stick to folded line stick?
by 강현아 19 Mar '13

19 Mar '13

Hello, Chimera Users! I am just a beginner and haven’t learned much about Chimera. When I load water molecules in Chimera main window, (TIP3P water) they have triangle shape. Then, I have changed option to stick or ball&stick. (action>atoms/bonds>stick or ball&stick) But, they are still triangle. It looks like there is H-H covalent bond in H2O. How can I remove this unwanted bond? Is there any other option for molecule shape? Like licorice… Please let me know how can I draw water with folded line stick shape, not triangle. Thanks in advance. Best regards, Hyeona Kang

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simple question
by Francesco Malatesta 19 Mar '13

19 Mar '13

Hello I would like to ask a simple question on selection. In the GroEL-GroES complex (pdb 1aon) how do you select, for example, hydrophobic or acidic residues or both in the say J chain? thank you very much Francesco Malatesta

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Colors of van der Waals speheres
by Rosa Miralles 19 Mar '13

19 Mar '13

Hi, I would like to create an image with van der Waals radii colored in only one color instead of being colored as the corresponding atoms. Is it possible to choose the color of the van der Waals spheres? Thanks for your help, Rosa.

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