July 2014 - Chimera-users - RBVI Mailing Lists

surface color by conservation among different sequences
by 李智海 21 Jul '14

21 Jul '14

Hi, I want to show a model in surface style which represents the conservation based on a series of sequences by its color. I have got a result of sequence alignment (.fas file). How can I apply this alignment result to the surface coloring in Chimera? Thanks! best wishes! Zhihai Li

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Re: [Chimera-users] Chimera-users Digest, Vol 135, Issue 20
by Boaz Shaanan 21 Jul '14

21 Jul '14

Hi, On top of what Elaine wrote there is also the interface between Consurf (http://consurf.tau.ac.il/) and Chimera, which is also a very nice option. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Monday, July 21, 2014 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 135, Issue 20 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. surface color by conservation among different sequences (???) 2. Re: surface color by conservation among different sequences (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 21 Jul 2014 23:20:45 +0800 From: ??? <21620101152414(a)stu.xmu.edu.cn> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] surface color by conservation among different sequences Message-ID: <211F19AF-2CA8-4E66-81D4-0F9BC20A868A(a)stu.xmu.edu.cn> Content-Type: text/plain; charset="us-ascii" Hi, I want to show a model in surface style which represents the conservation based on a series of sequences by its color. I have got a result of sequence alignment (.fas file). How can I apply this alignment result to the surface coloring in Chimera? Thanks! best wishes! Zhihai Li

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disulfide bonds ?
by Marek Maly 15 Jul '14

15 Jul '14

Hellow, I just visualized my Amber MD trajectory with protein containing several disulfide bonds. These bonds as well as all the other bonds are written in the given Amber topology (*.prmtop) file, which is read in by Chimera. Moreover the distance of sulfur atoms connected by disulfide bond is in all cases quite reasonable ( 2-2.1 A). In spite these facts Chimera draws some of those bonds in "stick" and some of them in "dashed line" style, even if one sets globally "stick" or "ball & stick" representation. Please see the attached illustrations. Why Chimera is doing such unwanted differences in graphical representations here ? It is possible, to force Chimera to draw all of those bonds unanimously in "stick" representation ? Thank you in advance for your help, Best wishes, Marek Maly -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Calculate RMSD over SSE of NMR ensemble
by Markus Heller 14 Jul '14

14 Jul '14

Hello, The subject says it all. How do I calculate the RMSD of secondary structure elements of an NMR ensemble? I did RTFM, but I'm hoping that I can avoid spelling out the residues comprising the SSEs ... 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:image002.png@01CF9C4B.5C0363C0] 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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Can't open the file generated by NORMAD-REF
by Mahendra B Thapa 14 Jul '14

14 Jul '14

Dear Chimera users, I can't open the pdb file (one of them is attached) generated by NORMAD-REF( http://lorentz.immstr.pasteur.fr/decoys/submission.php) in chimera (version 64-1.9). The format of the pdb file looks like ok while trying to follow the former posts like " http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-June/007704.html". Please help me to find the errors which might have remained unnoticed to me. Thank you, Mahendra Thapa Doctoral Student,Physics University of Cincinnati,OH

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local cross-correlation coefficient
by 李智海 08 Jul '14

08 Jul '14

Hi, I performed tool "Fit in map” to calculate the correlation value, i was wondering whether the value is the same as local cross-correlation coefficient (local CCC). Thanks in advance for your help! Best wishes for you! Zhihai Li

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Chimera Using Problem
by christophe 08 Jul '14

08 Jul '14

Hi,I'm trying to import chimera in python but when i try to make it i've bug, it said to me the following thing just after have execute:>>>from chimera import *Traceback (most recent call last): File "C:\Python27\Lib\site-packages\Chimera 1.9\share\testMM.py", line 1, in <module> from chimera import * File "C:\Python27\Lib\site-packages\Chimera 1.9\share\chimera\__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, XformImportError: No module named _chimeraI'm on windows 8 64 bits and i have chimera 1.9 and python 2.7.7 i've this following structure of directories:C:\Python27\Lib\Site-packages\chimera 1.9And i've run my script under the python.exe of chimera.So can you said to me what is wrong to fix it cause of i need chimera to made a script using superposition ( so with MatchMaker)? Cordially,Christophe Linhard.

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Suggestion - secondary structural element as an additional level in the selection hierarchy?
by Oliver Clarke 07 Jul '14

07 Jul '14

Greetings, Currently, the selection hierarchy in Chimera is as follows - atom<residue<chain<model<all. I don’t know how complicated it would be to implement, but perhaps it might be desirable in a future version of Chimera to include “secondary structural element” (being coil, helix or strand) as an additional level, between residue and chain? This would enable easy/quick selection/coloring of specific loops, helices or strands in a structure. E.g, say I am working on a helical repeat protein like an importin, and I want to color all the helices on the concave, inside surface one color, and all the helices on the outside surface another color - to do that at present is possible, but somewhat laborious, as it is necessary to explicitly specify the boundaries of each helix, and if there are many helices in the desired selection that are not sequence-adjacent then this becomes complicated. If SSE was a level of the selection hierarchy, I could select one residue in each helix on the desired surface, press the up arrow once to broaden the selection and all the helices on the inner surface would then be selected, without needing to know the location in the sequence of each helix. It seems like there would be quite a lot of use cases where this might save time - selecting individual surface exposed loops, or a specific set of helices or strands that form a binding surface for a ligand or partner protein, for example. Best regards, Oliver.

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Change default display settings?
by rswett＠chem.wayne.edu 07 Jul '14

07 Jul '14

Hi, I was wondering if there was a way to change my startup preferences so that the default is to show only ribbons? No atoms?

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How to install chimera as a python module
by Ivan Castro 07 Jul '14

07 Jul '14

Hi everyone, Looks like Chimera can be installed as a python module, but I can't find the first steps to do that. Anyone can suggest me a tutorial or webpage for this purpose. Thanks. -- Iván Castro, B. Sc (Hons). M. Sc Student - Biology at Universidad del Valle, Colombia. Member of Grupo de Estudios en Genética, Ecología Molecular y Fisiología Animal. Member of Fundación Colombiana para la Investigación y Conservación de Tiburones y Rayas.

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Chimera-users July 2014