- Chimera-users - RBVI Mailing Lists

Save Image problem
by James Boyd 20 Mar '18

20 Mar '18

Hi, I am a new Chimera user although I have used other molecular graphics programs from time to time. I like the CHimera feel and the menus are pretty easy to navigate. I am trying to save on screen images as .jpg files. I keep getting an error message that says that the file doesn't exist ( e.g. C:\Users\james\desktop\protein\protein.jpg does not exist.) When I look in the folder an image file by that name has been created but it has no image in it. (see NADPH2 for an example). I was able to get an image saved correctly one time (NADPH.jpg) but not again so things appear to be working, it's just that I am doing something wrong. Any suggestions? Thanks, Jim James G Boyd, PhD HealthTell, Inc. 145 S 79th St Chandler, AZ 85226 james.boyd(a)healthtell.com (cell) 860-941-9566 (off) 925-215-5615 (x1001)

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Metal Geometry
by Pascal Auffinger 16 Mar '18

16 Mar '18

Dear All, Metal Geometry is a great tool. However, it can be tedious to use it when the list of metals is long like in some ribosomes where sometimes over 200 of them are found. Is there a quick way to move from a given metal to the next one without using the pulldown menu ? Thanks a lot, Pascal ----- Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffinger(a)ibmc-cnrs.unistra.fr <mailto:p.auffinger@ibmc-cnrs.unistra.fr> -----

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Topology file creation
by Sankaran SV . 16 Mar '18

16 Mar '18

Hi users, Currently Iam working on protein glycosylation. Can anyone could give me a reference for topology file creation for running the simulation of glycosylated protein. -- Sankaran.s.v bbin

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Permission to use Chimera for non-academic purposes
by Helander, Jon 16 Mar '18

16 Mar '18

Hello, I'm a computational biologist at Wash U. in Saint Louis and have been using Chimera for some years now. I also do some stock market research in biotech and write informative articles about some companies that do small-molecule research. To aid in this, I would like to include some Chimera-generated images. Would this be alright and can I obtain some written confirmation if so? Thanks Jon Helander

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Surface picking
by Priit Eek 15 Mar '18

15 Mar '18

Hi, I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn’t work. I checked the surface attributes and ‘selectable with mouse’ was true. I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn’t find anything referring to this in the docs. Best regards, Priit

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Animation
by David Bhella 14 Mar '18

14 Mar '18

Dear All, I have noticed that the animation tool appears to begin encoding movies before the final frame settings are set, consequently all my movies are missing the last frame. I can see a way to fix this but, it would be better if it didn’t happen. Has anyone else noticed this? D. Dr David Bhella Director - Scottish Centre for Macromolecular Imaging MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch [University of Glasgow: The Times Scottish University of the Year 2018]

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Re: [Chimera-users] ellipsoids
by Tom Goddard 12 Mar '18

12 Mar '18

Hi Carlos, The fix is in tonight’s daily build, the one that will be compiled in about 14 hours (2 AM Pacific time). It is not available yet. Chimera does not handle small molecule crystals. It is for protein and nucleic acid structures. So it does not handle the small molecule cif format which has extra symmetries that occur only in small-molecule crystals — you will need other software for that. Tom > On Mar 12, 2018, at 12:04 PM, Carlos Romero wrote: > > Hello Tom, > > thank you for your quick answer. I just installed the daily build however the problem persist. Any suggestion? > Moreover i have a new problem, a cif file that contain totally symmetric molcule, Chimera only represent half! while other softwares confirm that the cif file is correct. An expert in crystallography said that it might because a special inversion center and that " the program should apply the symmetry to complete the molecule" could you help me with this too? i thank you very much for your valuable help > > Carlos > > On Mon, Mar 12, 2018 at 7:06 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Carlos, > > The Chimera unit cell tool was not copying the anisotropic b-factor information. I fixed that in tonight’s daily build. > > Tom > > > > On Mar 12, 2018, at 6:16 AM, Carlos Romero wrote: > > > > First of all congratulations for the your software Chimera, it renders really beautiful images and helps attracting the interest of students for science! > > > > I have a question. I am representing an X-ray structure from cif file. I am able to build up the unit cell, but i would like all the atoms to be represented with the thermal ellipsoids. However, i can only apply the ellipsoids to one molecule of the unit cell. Would it be possible to display all molecules with the ellipsoids and not only one? i was unable to find a solution. > > > > Thanks a lot in advance for any help > > > > kind regards > > > > Carlos > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > >

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ellipsoids
by Carlos Romero 12 Mar '18

12 Mar '18

First of all congratulations for the your software Chimera, it renders really beautiful images and helps attracting the interest of students for science! I have a question. I am representing an X-ray structure from cif file. I am able to build up the unit cell, but i would like all the atoms to be represented with the thermal ellipsoids. However, i can only apply the ellipsoids to one molecule of the unit cell. Would it be possible to display all molecules with the ellipsoids and not only one? i was unable to find a solution. Thanks a lot in advance for any help kind regards Carlos

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Looking for help on starting of Chimera 1.11 on win32
by 杨超 10 Mar '18

10 Mar '18

Hi Chimera users, I am Ph.D. student who foucing on genetic study of skin disease from Anhui Medical University, Hefei, China. Recently, I want to used Chimera to draw a protein structure. But after I installed Chimera 1.11 on my win 7(win32 system), I can't open it. It showed such error when I started the --debug command. Could anyone give me a hand? Thank you so much. Chao Yang Anhui Medical University Hefei, China

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Cannot save PDB as multiple chains of a single model.
by Matthews-Palmer, Teige Rowan Seal 09 Mar '18

09 Mar '18

Dear Chimera-users, I have a PDB file containing a single chain, that I have copied and applied turns about a symmetry axis. So now I have several models with transformed positions. When I save PDB>save multiple models in a single file, my output PDB does not seem to handle CHAINID properly. If my input PDB has CHAINID A and ends with TER, then my output PDB has everything as CHAINID A, no TER, and instead separates the models by MODEL 1 […] ENDMDL MODEL 2 [...etcetera] I would like to save a PDB with these symmetrical copies as different chains A,B,C… (and not different models). Can anyone suggest a way to do this? Help greatly appreciated. Teige

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