August 2013 - Chimera-users - RBVI Mailing Lists

Hide all ribbons not in specific chain
by Thomas Hrabe 16 Aug '13

16 Aug '13

Hi everyone, I want to display one chain from a structure, only. However, I do not understand how to achieve that. After my PDB file opens, I can do select :*.A #select all residues in chain A that I want to have select invert #select everything else not in chain A ~ribbon hides everything. How can I tell ~ribbon to hide everything not in chain A. Or, how can I select everything not in chain A? I am calling chimera through the socket and do not want to parse out every chain. Thanks in advance, Thomas

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File Operations *veery* slow on Win 7
by Markus Heller 12 Aug '13

12 Aug '13

Hi, I'm running the latest release of Chimera (1.8 build 38824), but I've observed this with the 2 previous releases as well. Computer is a core i7 with 32 GB RAM and an Nvidia Quadro FX 1700 with 512 MB DDR2 memory and latest driver. OS is Windoze 7 64 bit. Pretty much every time I click File --> Save mol2 or Save pdb or Save Session As, I get the blue spinning wheel of death and (not responding) in the window title bar. It's not a deal breaker, but it's pretty annoying. Anybody else seeing this? Also, when I start Chimera, the screen goes black for a second and all window title bars change to standard blue. When I exit Chimera, the process reverses. Are these observations related? And how can I provide more information in addition to my vague description? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CE950C.D960A9A0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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Show backbone chain-trace by default
by Thomas Hrabe 09 Aug '13

09 Aug '13

Hi everyone, I was looking for the setting to tell Chimera to open a PDB file in backbone chain-trace mode rather than looking at the ribbon. Is that possible? Thanks in advance, Thomas

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About selection of atom
by Chung Fan LAM 09 Aug '13

09 Aug '13

Hi, I cannot select atoms by using Ctrl+left button/double click left button by using my home PC, but I can do so by using my notebook. I guess the difference between my two computers is the input device. My home PC is using mouse while my notebook is using touch pad. I would like to know if there is any setting I can change, so that I can use the mouse to select atoms. Thanks. Best wishes, Frankie

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Surface calculation failed problem
by Hunter Brown 09 Aug '13

09 Aug '13

Hello, I know this has been a somewhat common problem. When trying to display the molecular surface on a protein (I want to color by hydrophobicity and surface charge) I get the error "Surface calculation failed, mscalc returned code 5." I have tried increasing the VDW radius by 0.5, and lowering probe radius, and turning off 'display disjoint surfaces.' So far I have not been able to display the surface. I have a colleague that has displayed the molecular surface for a viral capsid, so I would think that I should be able to do it for a protein. Is there anything else I can do? It would be really nice to create some hydrophobicity and surface charge images. Thanks in advance! -Hunter Hunter Brown Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major University of New Mexico

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Help with RMSD
by Chee Wezen, Xavier 09 Aug '13

09 Aug '13

Hello, may i know how to i use Chimera to calculate RMSD ? I opened the command line and typed "rmsd #0 #1" but the rmsd that i received from the two molecules above is way too high for something this superimposed. Can someone please suggest what should i do ? Meanwhile, i've also received error warnings for other molecules that i am testing (along the lines of "different number of atoms" found). this should not be the case as the molecules are identical to one another. Any help regarding this is much appreciated ! Thanks !

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ask for help about surface and Label color
by Jian Guan 08 Aug '13

08 Aug '13

Hi, I am Jian, working in Hershey Medical Center, PSU. I am a Chimera User. I have two questions. 1: When I fit protein molecule structure into the density map of Virus particle. Showing the protein molecule in Surface is not allowed by Chimera. An error window popped out said: "surface calculation failed, mscalc returned code 2". I wonder to know how to solve this problem. I want to modify the molecule structure after fitting. 2: When I label the selected residues, they are always with the same color with residues, can I set them separately? Can I edit the label font? Thank you so much. Hope to hear from you soon. Jian

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show middle slice of vol by using command line
by Dieter Blaas 07 Aug '13

07 Aug '13

Hi, I have been trying hard to do the following by using the command line but so far with no avail: select volume #0 and show just the middle slice as solid. Following the way the commands are usually structured I tried something like "vol #0 style solid planes one" but I do get the error "volume invalid planes argument "one" : Value must be x, y ,z, got 'one'''. But when I try ""vol #0 style solid planes x" I get "volume: invalid planes argument 'x'. So what? Thanks a lor for hints, Dieter -- ---------------------------------------------------------------------- Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Constrained movements
by Damien Larivière 07 Aug '13

07 Aug '13

Dear all, The image below shows 2 chains opened separately from 2 PDB files. I would like to move only the cyan chain. For that, I just have to deactivate the white chain. BUT I would also like to keep fixed a specific atom of the cyan chain, for instance the cyan atom in the red circle. This way this atom serves as a pivot point. I know that I can use "Constrained Move". If I understand well, the "origin" is either 0,0,0 or the center of a model bounding box, not a selected atom. Is it possible to manage this? Many thanks for your help Damien

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Shape complementarity
by Hernando J Sosa 07 Aug '13

07 Aug '13

Dear Chimera, Is there a way to evaluate protein-protein interfaces (e.g. using a program like CCP4 Sc) within chimera?. Thanks Hernando

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Chimera-users August 2013