- Chimera-users - RBVI Mailing Lists

fixed: error saving scene with independent rotation
by Elaine Meng 31 Jul '18

31 Jul '18

Hi Yanhe, The bug you reported a few days ago has been fixed! I just confirmed that with the current daily build of Chimera, you can now save scenes with independent rotation and use them in the Animation tool and in scripts. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Is there any tool to write some calculated attribute into a header format?
by Sergio Garay 31 Jul '18

31 Jul '18

Hi All! I would like to know: Is there any way or tool to write some calculated attribute into a header format? I want to see the same color values obtained for some a calculated attribute projected onto a sequence. I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute. Thank you in advance. -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Fwd: Inquiry for new/re-registration license key_Arifuzzaman Sarder
by Elaine Meng 31 Jul '18

31 Jul '18

> From: Sarder Arifuzzaman <arifpharmju(a)gmail.com> > Subject: Inquiry for new/re-registration license key_Arifuzzaman Sarder > Date: July 31, 2018 at 9:08:53 AM PDT > To: chimera-announce-owner(a)cgl.ucsf.edu > > Hi > Greetings. > This is Arifuzzamman Sarder. I am an earlier user of chimera software tool. Recently I installed the updated version (v1.13). However, I could not draw any chemical structure by inputting canonical smiles or any other chemical ID in this tool. Even it can not capture any chemical structure from PDB, unlikely it is giving us only protein structure. Could you please let me know how can I revive this tool, so that I can use it for molecular docking and chemical structure as well. > Thank you very much in advance. I am looking forward for your response please. > Sincerely > Arifuzzaman, Sarder > PhD research fellow > Chung-Ang University > Mobile: 010-2654-2606 > E-mail: arifpharmju(a)gmail.com <mailto:arifpharmju@gmail.com> > Web: https://sarderarifuzzaman.wixsite.com/arif <https://sarderarifuzzaman.wixsite.com/arif> HI Arifuzzamman Sarder, (forwarding to the proper address for asking Chimera questions: chimera-users(a)cgl.ucsf.edu ) There is no reason it should not work as before. Chimera does not use a license key. For example, in Chimera 1.13, command: open pubchem:12123 (- or -) open smiles:C1CCNC1 …shows a small molecule in sticks, and command: open 2gbp … shows PDB entry 2GBP; protein ribbons with ligand (glucose) as sticks and nearby sidechains as sticks. If you mean that your Chimera 1.13 is not showing small molecules, or not showing sticks, I only have two ideas: (A) graphics/rendering problem of your computer or (B) New Molecules preferences was set to show only ribbons. To check (B), show Preferences from the Favorites menu, then change to category: New Molecules and check that the settings are what you want, and then click Save. The behavior I described is for the default, “smart initial display” true. If you had it false, and also had “show atoms” false, it would not show atoms when you open a structure. If you feel it is a bug, you can use menu: Help… Report a Bug and describe in detail what you did and what the problem is. However, if it is a graphics problem of your computer, it is not something we can fix. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Extracting asymmetric unit
by Tom Goddard 31 Jul '18

31 Jul '18

Hi Martin, Fit an atomic model of the asymmetric unit then use volume zone (Volume Viewer menu entry Feature / Zone) then save the map (Volume Viewer / File / Same Map As…). See the maskZone option description in the volume save command for details https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> Tom > On Jul 31, 2018, at 7:00 AM, Martin Moncrieffe <mcm35(a)cam.ac.uk> wrote: > > Hi Tom, > > A quick question. I have a helical reconstruction (EM) and would like to extract the density for the asymmetric unit from the map. How does one do this? > > Best. > > __martin > >

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Surface vertex density
by Tom Goddard 31 Jul '18

31 Jul '18

For a density map you can control the number of surface triangles and vertices by choosing the subsampling “step” size in the Volume Viewer dialog. Step 2 will use every other grid point along x,y,z axes and result in a coarser mesh. For molecular surfaces computed from atoms, change the vertex density as described here http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html> Tom > On Jul 31, 2018, at 5:53 AM, ⁨עמיחי הולצר⁩ wrote: > > And another question - there is "Surface and Mesh options" under the "Features" tab, so one can control the smoothing of the surface, thickness, etc. How can I control the number of nodes of the surface? I mean, I want the mesh not to be so dense. Is it possible? > > Thanks again! > > 2018-07-31 13:38 GMT+03:00 עמיחי הולצר : > When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)? > I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh? > > Thanks, > Amichai > > 2018-07-30 19:37 GMT+03:00 Tom Goddard : > Hi Amichai, > > Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> > > Tom > > >> On Jul 29, 2018, at 3:06 AM, ⁨עמיחי הולצר⁩wrote: >> >> Hi Chimera support, >> >> I have 2 questions: >> >> 1. How does Chimera calculate the mesh from the density map? >> >> 2. How can I save the mesh as a file? >> >> Thanks a lot, >> Amichai Holzer >> Huji >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> > >

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Re: [Chimera-users] [chimera-dev] Save density map as a mesh
by Tom Goddard 31 Jul '18

31 Jul '18

If you want to save atoms, bonds and surfaces and load them into Chimera later, then save a session, menu File / Save Session As…. Tom > On Jul 31, 2018, at 3:38 AM, ⁨עמיחי הולצר⁩ <⁨amiholz(a)gmail.xn--com-yx0a> wrote: > > When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)? > I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh? > > Thanks, > Amichai > > 2018-07-30 19:37 GMT+03:00 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>: > Hi Amichai, > > Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> > > Tom > > >> On Jul 29, 2018, at 3:06 AM, ⁨עמיחי הולצר⁩ <⁨amiholz(a)gmail.com <mailto:amiholz@gmail.com>⁩> wrote: >> >> Hi Chimera support, >> >> I have 2 questions: >> >> 1. How does Chimera calculate the mesh from the density map? >> >> 2. How can I save the mesh as a file? >> >> Thanks a lot, >> Amichai Holzer >> Huji >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> > >

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display floating XYZ axes
by Pranav Shah 26 Jul '18

26 Jul '18

Dear Chimera Users and Devs, Is there a possibility to display the XYZ axes *a la* coot in chimera, so that one can keep a track of the direction of the views in the window? Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Harvard Medical School 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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(no subject)
by Yanhe Zhao 26 Jul '18

26 Jul '18

Hi, This is Yanhe. I want to make movies of side-by side rotaing structures, I set "center of rotation method" to "independent", when I try to save the scenes, chimera give error report as attached file shown. what should I do now? I really appreciate it if you can do me the favor. Best, Yanhe

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Removing structure segment and connecting the edges with dashed line
by Ahmad Khalifa 26 Jul '18

26 Jul '18

Hello, Selecting a segment of a structure and deleting it does remove that segment, but the ends are not connected. How to do the same and make the edges connected with a dashed line? Best regards.

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Problem with minimizing structure
by Renee Arias 26 Jul '18

26 Jul '18

Hello all, I am having a problem with the minimizing structure function in Chimera. I am just trying to change a single residue on a very small protein (88 residues), but I keep getting the error: No MMTK name for atom "H1" in standard residue "GLN". Previous message boards seem to just point to bug fixes in Chimera, but I am running the newest version available for Windows 10. I would appreciate any help! Thanks so much, Renee

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