March 2021 - Chimera-users - RBVI Mailing Lists

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by Thirumurugan Prakasam 29 Oct '21

29 Oct '21

Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png] -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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ENQUIRY
by ogochukwu ngozi 05 Apr '21

05 Apr '21

Dear Concerned,I am a PHD student from University Putra Malaysia. This is my first time using Chimera, please I need your assistance. I want to use chimera to calculate RMSD values, could you direct me on steps to take please? Thanks as I await your kind reply.Ogochukwu Nwaefulu

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identifying and counting selected residues
by Smit Patel 01 Apr '21

01 Apr '21

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Questions about probabilities in the Dunbrak library
by Moradkhan, Tiglath A 31 Mar '21

31 Mar '21

Hi I'm trying to understand the meaning of probabilities in the Dunbrak library. From what I've found, this parameter is a measure of how probable a particular rotamer is to be found within a given conformation. Is this what this is? Thanks Tiglath

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in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
by Lei Qian 31 Mar '21

31 Mar '21

Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei

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No MMTK name for atom "HD2" in standard residue ASN
by Sina Analoui 31 Mar '21

31 Mar '21

Hi All, I am currently attempting to minimize a large molecule (ACE2 alongside the RBM of a spike protein). I Dock Prep both chains (A chain is ACE2) and then go on to attempt to minimize them. However, I keep returning this error "No MMTK name for atom "HD2" in standard residue ASN" I have attempted to remedy this by rewriting parts of the PDB file and importing it back in and have had no success. Is there any way to either remove NAG that is associated with these residues or change this hydrogen to something feasible? This seems to be an issue for only the ASNs on the A chain and not elsewhere on the molecule Thank you in advance for your help

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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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Chimera-users March 2021