June 2021 - Chimera-users - RBVI Mailing Lists

multialign viewer
by Jacqueline Vitali 23 Jun '21

23 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

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Regarding problem 'During selection from the graphics window (picking)'
by Dr. Abhay Nanda Srivastava 20 Jun '21

20 Jun '21

Dear Team Chimera, I am using Chimera software in Windows 7, 32 bit computer for viewing Swiss dock prediction results. But, when I try to select the residue or atom in model by using mouse and keyboard button (Ctrl+button 1), no selection is displayed, even hand like cursor seen on the graphics, I am also not able to see the residue or atoms labeling by putting cursor on model. For my confusion removal, I have downloaded and installed the software on another computer of Windows 7, 64 bit. But here also, the same problem persists. Please suggest to me, how to get rid of this problem? Looking forward to hearing from you. Thank You. *Regards,* *Dr. Abhay N. Srivastava* * M. Sc. (Chem.), Ph. D. Head & Asst. Professor,* * Department of Chemistry,* * NC-BRA Bihar University,* * Muzaffarpur-India.* * Contact: +91-9990576112*

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Question regarding the chimera Transform Coordinates feature
by Ritwik Jain 19 Jun '21

19 Jun '21

Respected developers of chimera, I am currently doing a research project related to Cryo-EM map alignment in which I need to use Chimera. Chimera has a feature which transforms the coordinates of a molecule (Img1.jpg) . That feature has an option to move atoms instead of coordinate axes (Img2.jpg). If I uncheck that box and transform, the model just reverts back to its original position after saving and reopening. I was wondering if there was a command line command for the " move atoms instead of coordinate axes " option. I have tried all the move commands ( https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html) and they don't seem to work. I expect your reply soon. Sincerely, Ritwik Jain

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chimera installation problem
by Monojit roy 18 Jun '21

18 Jun '21

sir, please help

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AddH on N atom in N-terminal
by 陈恩博 17 Jun '21

17 Jun '21

Hello. When I use addH to add H atoms on N atom in N-terminal of Peptide chain, I find 3 H were added on this N. Why the addH result is C-NH3 and not C-NH2? Thanks!

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color maps based on real space cross correlation
by manikandank 16 Jun '21

16 Jun '21

Hi Chimera-users, I have aligned two cryoEM maps at certain threshold using 'Fit in Map' option in chimera. Now I would like to color one map based on real space voxel correlation values from 'Fit in Map' operation. Please let me know how this can be done in chimera. thank you with kind regards Mani.

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command line: how to add hydrogens to a phosphate group?
by Sara Luz Gomez Maya 15 Jun '21

15 Jun '21

Hi, I have a system consisting of a molecule intercalated into DNA. For a very specific application, I need to remove all the Sodium atoms from a PDB file and, in turn, add hydrogens to all the DNA phosphate groups (whatever the oxygen). Since for chimera that atom type is identified as O3- (possibly resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, N-oxide), I have tried: labelopt info idatmType label #0 addh spec O3- but it did not work. You can find attached herewith the pdb file. Any help is appreciated. Regards, Sara

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Sending Chimera MD job to remote computer
by Cowie, Connor 14 Jun '21

14 Jun '21

Hello, I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password). However, I want to be able to send a command to a remote computer to improve the computational time especially when running multiple MD simulations; right now, I am running MD simulations on the same computer. I was first thinking of a sequence of commands below: Ctrl+Z bg ssh -y username@detroit05 I know that the Ctrl+Z command temporarily pauses a command, but I believe that the jobs command is first needed to list the current running jobs (that Ctrl+Z can be performed on). However, the running jobs are not listed when I type “jobs”. After using the “top” command to list all of the processes, I have verified that the Kill command works by typing these in succession: Kill -STOP PID# Kill -CONT PID# Can you walk me through how to first have a listing of jobs running in Chimera and then sending it to a remote computer? Best, Connor

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getting surface patches
by Diego Amaya 13 Jun '21

13 Jun '21

Hello all, I'm trying to get surface patches of PDB structures in VTK format. So I want to define a patch as the set of atoms within a given radius of a specific residue, build the surface corresponding to that patch and export the result in VTK format. Additionally, I want to do all this with a python script. Here the code I'm trying but doesn't work : *import pychimerapychimera.patch_environ()pychimera.enable_chimera()import osimport chimerafrom chimera import runCommand as rc* *list_resid = [31, 64]* *radius = 3list_pdbs = ['ensayo.pdb']for resid in list_resid: for line in list_pdbs: list_atoms = [] rc('open '+line) rc('sel :{} za<{}'.format(resid, radius)) for a in chimera.selection.currentAtoms(): list_atoms.append('serialNumber=' + str(a.serialNumber)) sel_atoms = ' or '.join(list_atoms) rc('surfcat patch @*/{}'.format(sel_atoms)) rc('surface patch') rc("export format VTK {}_resid_{}_radius_{}.vtk".format(line[:-4], resid, radius)) rc("close all")* Thanks in advance for your help. -- 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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Minimize hydrogens in water molecules
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 11 Jun '21

11 Jun '21

Hi, I need to minimize two water molecules in the binding site of the protein: I don't want to move the oxygen, so I've selected only hydrogen atoms and then I' ve used the Minimize Structure tool (keeping fixed all atoms that are unselected). I can't do the minimization because there's an error: Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.CYS_394__0_0_1_397__A.N (atom type n) - Atom 0.GLY_393__0_0_1_396__A.peptide.C (atom type C)'' I don't known what this means and what I should do to fix it. I've tried to use the command line, but there's another error. Does anyone have suggestions? Thank you. Francesca

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