October 2013 - Chimera-users - RBVI Mailing Lists

Chimera and Mac Mavericks
by Evan Kantrowitz 23 Oct '13

23 Oct '13

I just install Mavericks on my Mac. Chimera starts OK, but if you try to type into a field, like the PDB fetch field, entering key strokes is very hard. Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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hydrophopic interaction
by LU Zen 23 Oct '13

23 Oct '13

Hi All, I have a amphipathic helix/membrane complex assembled with CHARMN-GUI and I'll like to show those residues that come into contact with the lipid bilayer. Using find clash/contact function, I can see many lines joining the atoms of both the residues and lipid bilayer. However, I don't really know how to pick the true hydrophopic interaction from the rest of the clashes/contacts. In addition, is there a way to quatify which these interactions may be tighter than the other. Any suggestion is appreciated. Thanks, ZL -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Create a protein model using Chimera?
by Maja Divjak 18 Oct '13

18 Oct '13

Hello Chimera, I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family. I look forward to your reply! Thank you and best wishes, Dr Maja Divjak, WEHI, Melbourne, Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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Re: [Chimera-users] Cross-section question
by Tom Goddard 18 Oct '13

18 Oct '13

Hi Lawrence, Sure it is easy to see plane 72. Use the Volume Viewer dialog, show the planes panel (menu Features / Planes), press the "One" plane button in that panel and set the plane number entry field to 72. To assure you see the full resolution data make sure "Step" is set to 1 above the volume dialog density map histogram, and that "depth" is set to 1 in the Planes panel. This and other Chimera density map features are described in the Chimera guide to volume data display http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html Tom On Oct 18, 2013, at 10:09 AM, "Tartaglia,Lawrence J" wrote: > Hi Tom, > > Thank you for getting back to me. I should have been a bit more clear. What I want is the exact "central" section. I'm not sure if you are familiar with cryo-electron microscopy? I used a box size of 143 pixels to box my virus particles. What I would like to see if image 72 (central section) of my reconstruction. Is there a way to do that? I've attached an image of an example central section (left hand side) using the program IMOD. I'm sorry for the confusion... > > Best, > > Lawrence > > > On Thu, 17 Oct 2013 09:43:43 -0700, Tom Goddard wrote: >> Hi Lawrence, >> >> I'm not sure what you mean by "exact cross-section". Do you mean >> aligned to the virus map grid axes? If so the Orient button at the >> bottom of the volume viewer dialog will do that. But probably it is >> better to simply specify which planes to show using the Region Bounds >> panel of the volume viewer dialog (Features menu) - specify a z range >> 120 125 1 to show planes 120 to 125 using step 1 (i.e. every plane). >> This will be better than using clip planes. >> >> Tom >> >> >> On Oct 16, 2013, at 11:35 AM, "Tartaglia,Lawrence J" wrote: >> >>> Hello, >>> >>> I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? >>> >>> Thanks! >>> >>> Best, >>> >>> Lawrence >>> -- >>> Lawrence J. Tartaglia, Ph.D. >>> Postdoctoral Scientist >>> Agbandje-McKenna Lab >>> Department of Biochemistry and Molecular Biology >>> College of Medicine, University of Florida >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > > -- > Lawrence J. Tartaglia, Ph.D. > Postdoctoral Scientist > Agbandje-McKenna Lab > Department of Biochemistry and Molecular Biology > College of Medicine, University of Florida<Screenshot-1.png>

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Cross-section question
by Tartaglia,Lawrence J 17 Oct '13

17 Oct '13

Hello, I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? Thanks! Best, Lawrence -- Lawrence J. Tartaglia, Ph.D. Postdoctoral Scientist Agbandje-McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine, University of Florida

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Normal to the plane of the aromatic ring at the centroid
by Pande, Ajay K 16 Oct '13

16 Oct '13

How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande

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(no subject)
by edward el chamy 15 Oct '13

15 Oct '13

Hey i am a student using chimera 1.8 i have a question: how we find on a specific chain the different interaction domains? Thanks a lot

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Fwd: setting or hardware problem?
by Chao Wang 14 Oct '13

14 Oct '13

Hi, chimera users I am starting to use ucsf chimera to analysis protein structure recently. It is an excellent software, and I have no problem using it at school. But when I try to use it on my other pc at home. It doesn't work properly. The ribbon looks flat and dull, not a 3D looking anymore, like the situation showed in pic1 and pic2. My hardwares: School PC: win7 64 bit,cpu E5-1606, Nvidia Quadro 5000, 4G Home PC: win7 64 bit, cpu i5-2500k, AMD Radeon HD6700, 8G I know the video card of school's pc is much better, but I checked the hardware list. HD6700 is also compatible. Can anyone tell me what is wrong? I really appreciate it. [image: Inline image 1] [image: Inline image 1] Jack Wang

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Chimera commands to record MD movies
by psu4＠uic.edu 11 Oct '13

11 Oct '13

Dear Chimera, Since we run a lot of Amber MD simulation in remote clusters, we wonder if there is any Chimera command that can record the Amber MD trajectories remotely and save them as avi (or any other movie file formats)? If this is feasible, then we don't have to download all the trajectories to local and make the trajectory movies manually. We have searched the Chimera user manual but didn't see any command. If there are related commands which we didn't see, please forgive us : ) Thanks. * There is a way to activate X11 forwarding and use remote Chimera GUI to do this, but it's extremely slow and prone to freeze the computer. Cheers, Henry

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font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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