- Chimera-users - RBVI Mailing Lists

Assistance required for Chimera software download
by Parnian Soleimani 18 Oct '24

18 Oct '24

I hope this email finds you well. I am having trouble accessing the Chimera software download site. I would greatly appreciate your guidance on how to resolve this matter. Thank you in advance for your help.

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Oct 14-20 Chimera(X) website downtime
by Elaine Meng 10 Oct '24

10 Oct '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, October 14, 10 AM PDT and continuing for several days, potentially through the following weekend (October 14-20). Apologies for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Center and Orient
by Hernando J Sosa 09 Oct '24

09 Oct '24

Dear Chimera, What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer menu tab? Thanks H.

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How will hydrogen bonds be highlighted in the final rendering
by 姜恩誉 09 Oct '24

09 Oct '24

Hello, when chimera software was used to analyze the interaction between small molecular ligands and proteins, the hydrogen bond width was set to 24, but the hydrogen bond in the rendered picture was very thin and difficult to distinguish. How can I solve this problem？ Looking forward to your reply 姜恩誉 2023111025(a)stu.njau.edu.cn

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Request for authorization to use Chimera software
by Stany Tsom 03 Oct '24

03 Oct '24

Dear UCSF Chimera software Coordinator, I am Tsomene Stany Lionel, I have a master's degree in Organic Chemistry obtained at the University of Yaoundé 1, a well known University around central Africa, my studies was focused in isolation, synthesis, characterizations, in vitro and in silico studies, I have worked under the direction of Dr. Messi Angelique Nicolas. Since 2020, during the pandemic there is an increase demand in computerized aided research of bioactive compounds. At the same time, it helps us focus on specific bioactive compounds showing better results. At Yaoundé 1 University, there is a large need in learning and usage of your software for in silico purposes, that is for molecular docking studies, with your permission we will like to organize a series workshops at the University to help masters students, Ph D students and also Professors for the better understanding of molecular docking and help then have better results for their research purposes. We will like at the end of each workshop deliver a certificate for this software learning. Software coordinator, we will really be glad if you accept directing, giving us permission for this use of your software for these workshop Organization and while not coordinating this future. At the end we will with your permission co sign the certificates we will deliver to the participants. References Dr. Messi Angelique Nicolas, Senior Lecturer at University of Yaoundé 1 messiangeliquenicolas(a)gmail.com Dr. Ngomo Orleane , Senior Lecturer at University of Yaoundé 1 orleansn(a)yahoo.fr All the details of my informations are in the attachment -CV/resume - Masters degree (masters 2 and 1 transcripts) -Bachelors degree While waiting for an answer from you UCSF Chimera Software coordinator, receive my distinct greetings. Sincerely Tsomene stany

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Software copyright consulting
by 姜恩誉 27 Sep '24

27 Sep '24

Hello, is the application of your Chimera X software for paper publication a non-commercial use？ Looking forward to your reply。 Thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

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Gaff type for Mn2+ to run antechamber
by Medhanjali Dasgupta 25 Sep '24

25 Sep '24

Dear all, I am trying to generate the electrostatic surface for a protein that contains Mn in the 2+ state in its active site. I've tried to go about it in two ways but keep getting stuck. 1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+ so it cannot run anyechamber to allocate the atomic charge to Mn2+. Am i missing an update? Is there any way to get around this? Can I run antechamber myself to recognise my ion of interest, and then determine the charge, input it into the .pqr file and run APBS? 2. I have used the online server hosted at poissonboltzmann.org to run pdb2pqr and apps but run into the problem of not knowing what the atomic charge is for Mn2+. Any help would be appreciated. Thanks!!! Medhanjali

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question about non-standard amino acids
by Jessie Jaynes 23 Sep '24

23 Sep '24

Hi Folks, I have a short peptide (O=ornithine) FEFOGGOFEF Is it possible to construct this peptide in Chimera? Thank you, Jesse

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Generating a single electrostatic potential surface for a protein + ligand complex
by jadeshi88＠gmail.com 22 Sep '24

22 Sep '24

Hi, New user to ChimeraX here, would really appreciate some help! I'm trying to generate an electrostatic potential surface for a protein-ligand complex. Currently, I am using the surface/coulombic, and surface ligand/coulombic ligand commands to generate surfaces separately for the protein and ligand, and then exporting to an .obj file. However, by doing so I'm left with two separate surface meshes, and what I really want is a single surface that encapsulates both entities. Is it possible to do this? Thanks in advance!

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MD on Chimera
by Manon Bulliard 20 Sep '24

20 Sep '24

Good afternoon, I was using chimera to do molecular dynamic simulation. I had to download Chimera on my new computer and now have the 1.18 version. It seems this feature is not anymore present under Tools>MD/Ensemble Analysis>molecular dynamic simulation. Do you know where I can find it to still be able to perform my modeling as previously? Thank you in advance, Manon Manon Bulliard, PhD EPFL | ISREC | Prof. Constam group SV2837 | Station 19 | CH-1015 Lausanne manon.bulliard(a)epfl.ch

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