- Chimera-users - RBVI Mailing Lists

Debug
by 안예림 29 Mar '21

29 Mar '21

Hi I have tried to make a movie of MD simulation by Chimera. I could be done one time, then for other MD’s it exits abnormally with the code -1073741819. Even I have decreased the size of .xtc file, it exits abnormally yet. Please check my capture picture. I have reinstalled chimera, but the problem did not resolve.What should I have to do ? I need your assistant. Thanksbe

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Can't open a VTK file in chimera
by Diego Amaya 24 Mar '21

24 Mar '21

Hello, I exported a surface in VTK format with the chimera extension but I can't open this vtk file back with chimera. This behavior is expected ? Best regards -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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how to generate different starting points to do md simulations
by Seera Suryanarayana 22 Mar '21

22 Mar '21

Dear chimera users, I have a small peptide of 20 residue length and I would like to do the simulations of this peptide at different starting points. How could one can generate the different starting points? Can I use the replica exchange MD simulations to generate the different starting points? I request you to please suggest me how to generate different starting points of peptide. Thanks in advance Surya Graduate student India.

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Re: [Chimera-users] select only side chains to calculate contacts
by Elaine Meng 21 Mar '21

21 Mar '21

> On Mar 20, 2021, at 10:03 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Hi Elaine, > > How do I calculate contacts among side chain atoms of a given category (aliphatic, hydrophobic, etc). Even when I select them, I cannot remove the main chain of them in the calculations. > > Thank you. > > Jackie Vitali Hi Jackie, Please send questions to chimera-users(a)cgl.ucsf.edu (CC'd here) rather than my individual address to clarify which program you're using and to ensure it gets answered. I'm assuming you are asking about Chimera. (If you're asking about ChimeraX, there is a different address: chimerax-users(a)cgl.ucsf.edu ...and the answer might be different.) You can use the "select" command and intersect your selection with sidechain only. It's explained in the command-line specification page: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#buil…> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#comb…> Examples: select hydrophobic & without CA/C1' select :phe,tyr & without CA/C1' (or "with" instead of "without" if you wanted to include the alpha-carbon) You can't see the difference if you are showing ribbons. You can only see the difference if displaying backbone atoms, e.g. menu: Presets... Interactive 2 (all atoms) 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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Visualizing Amber Trajectory in MD Movie
by Jatin Kashyap 17 Mar '21

17 Mar '21

Dear UCSF Chimera Community, I am trying to visualize an Amber NetCDF(.nc) trajectory in UCSF Chimera using a tutorial.[1] I have two trajectory files of the same system: first, the solvated system, and second I stripped the water molecules in the CPPTRAJ utility of AMBER. I am using the same .top file for both visualizations; however first one showing me the system, although the water molecules are missing. But the second one is throwing me an error, and nothing appears in GUI window.[2] Please help me find out my mistake in the process as I am a beginner-level user of UCSF Chimera. Thank you very much. [1] http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html [2] Assigning chain ID A to 306 residues, e.g. SER fillCoordSet: coordinates [arg 2] must be same length as atoms TclError Exception in Tk callback Function: <bound method ComboBox._resizeArrow of <_Pmw.Pmw_1_3_3.lib.PmwComboBox.ComboBox instance at 0x7fc164add170>> (type: <type 'instancemethod'>) Module: <module '_Pmw.Pmw_1_3_3.lib.PmwComboBox' from '/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py'> (line: 350) Args: (<Tkinter.Event instance at 0x7fc164ae65a8>,) Event type: ConfigureNotify (type num: 22) Traceback (innermost last): File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py", line 351, in _resizeArrow bw = (string.atoi(self._arrowBtn['borderwidth']) + File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget return self.tk.call(self._w, 'cget', '-' + key) TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848" ================================================ Event contents: char: ?? delta: 0 height: 24 keycode: ?? keysym: ?? keysym_num: ?? num: ?? send_event: False serial: 79507 state: ?? time: ?? type: 22 widget: .140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529344.140468594529488 width: 1194 x: 0 x_root: ?? y: 0 y_root: ?? TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848" File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget return self.tk.call(self._w, 'cget', '-' + key) See reply log for Python traceback. —— Jatin Kashyap Ph.D. Student Dr. Dibakar Datta Group Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435(a)njit.edu

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Orienting mol maps in space?
by Cynthia Lee Page 16 Mar '21

16 Mar '21

HI, I am a newbie with Chimera. I have learned a lot in this process of making reference maps for use in Relion, thanks to the tutorials and rich information available on this list and in the documentation for Chimera. I have followed this tutorial cool tutorial (https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html) for making 14 pf tubes (using EMDB 5194), 1JFF ( alpha/beta tubulin) plus the A chain of 3B6U (KIF3B) to represent the monomer of this motor protein. I made a 15 resolution mol map of the resulting model, then cropped off the ends to make the volume flush at the MT ends using the Subregion selection feature in the Volume Viewer. When I open this map in Chimera it does not open as other mrc files open. Specifically, instead of looking down the microtubule (considered Z axis, I believe) I am looking at the X-Y axis. “Centering" the map in Volume Viewer only centers it horizontally, “orienting” the file does nothing. Where as, if I orient any other reference files (including Relion generated 3D.mrc files) the map volume will orient so that the viewer is looking down the microtubule. Please see the attache image, the yellow volume centers/orients correctly, the pink volume is the one I made via the tutorial and doesn’t orient. I am guessing I am missing a coordinate system to align this volume in space but I haven’t been able to figure out how to add this information to my mrc file. I am also assuming that this orientation information is important to include in the mrc file formats. Any help or insight much appreciated! Thanks, Cynthia PS I did try to "vop resample onGrid” using pink onto the yellow models and learned that’s how you can create the same voxel size (!), but it did not change the orientation capabilities of the pink model. [cid:84AEE0E2-633C-4425-9B01-EA6207A3F276@colorado.edu]

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Occupancy clusters
by Yasser Almeida 16 Mar '21

16 Mar '21

Hello, I want to do an occupancy analysis of a rigid ligand in a MD trajectory. I used the MD Movie > Analysis > Calculate occupancy tool, and obtained the volume maps of each heavy atom of the ligand. To check, I also used the gmx spatial tool from GROMACS and the VolMap from VMD, to obtain the grids for the whole ligand, which have basically the same shape. This grid has a characteristic shape showing that particular orientations are stable through the MD run. I want to extract representative structures of these orientations, something like an "occupancy clustering". Note that I say orientations and not conformations. Since the ligand is rigid, there is no point to calculate the RMSD. So, what I want is to calculate clusters of orientations of the ligand in the binding site. Is this possible with Chimera? Thanks in advance, -Yasser

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Problem with nucleotide objects settings for 1d86
by svle＠tiscali.it 16 Mar '21

16 Mar '21

Hi, I have a visualization that seems not a correct one for 1d86 for DT 20.b when using Actions -> Atoms/Bonds -> nucleotide objects -> settings... . Settings: Show backbone as: Ribbon Show sides( .... ) as ladder Ladder Options: Ignore non-base H-bonds: false Shows stubs: false Rung radius: 0.45 Using existing H-bonds: true In the png file the problem. Where I'm wrong? Thanks Saverio Con Tiscali Mobile Smart 30 4G hai minuti illimitati, 100 SMS e 30 Giga in 4G a soli 8,99€ al mese. http://tisca.li/smart30

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render by attribute displacement of a NMA
by Giorgio Giardina 15 Mar '21

15 Mar '21

Hy, I have a pdb file containing the models (only CA atoms) describing the lowest mode from a NMA. I can easily generate a movie using the morphing tool, but I would like to visualize the mode as an image, using the render by attribute tool and with the displacement of each CA as value of the worm radius. How can I generate this attribute? Thanks in advance for you rhelp! Giorgio -- ------------------------------- Giorgio Giardina, Ph.D. Dep. of Biochemical Sciences (CU027) - Room T2 SAPIENZA - University of Rome Tel. +39.06.49910713 | Lab: http://www.macinmec.it/giorgio-giardina/ | Art: http://www.giorgio-giardina.com/ Art. 33 della Costituzione: *L’arte e la scienza sono libere e libero ne è l’insegnamento* -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.

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Failure Running ANTECHAMBER
by Mailyn Terrado 12 Mar '21

12 Mar '21

To whom it may concern: I am trying to use Chimera for protein Energy Minimization. I encountered a problem in running the program. Please find the attached screenshots of the error details. The problem seemed to be with the ligand BEF (beryllium trifluoride). Any help would be greatly appreciated. Many thanks, Mailyn

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