- Chimera-users - RBVI Mailing Lists

Get Minimization Energy
by Leonard Zhao 26 Nov '21

26 Nov '21

Hello, I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically? Thanks, Leonard Zhao

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question regarding UCSF Chimera FindHBond feature
by Aditi Laddha 25 Nov '21

25 Nov '21

Hello, I have been using the FindHBond feature of Chimera for finding hydrogen bonds between water molecules and the polypeptide chains. I need to use some specific distance and angle criteria to find H-bonds, so I wanted to ask what is the default distance (D....A) and angle criteria (D-H....A) used in the software to find out the H-bonds, -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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how to rectify error No MMTK name for atom
by Smriti Singh 2018RBT01 24 Nov '21

24 Nov '21

hello administrator, I am trying to minimize the Nucleotide sequence (DNA aptamer) through chimera. While performing energy minimisation steps, Chimera error "No MMTK name for atom 'HO5' in standard residue 'DA' showed. Please let me know how to rectify this issue. With warm regards Smriti Singh Research Scholar Department of Biotechnology MNNIT Allahabad

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Color volume series by per voxel variance?
by Oliver Clarke 24 Nov '21

24 Nov '21

Hi all, Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame? When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume. Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible? Cheers Oli

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Chimera compatibility with Window 11
by HK Haris 23 Nov '21

23 Nov '21

Hi, Please confirm can I download the following version of Chimera on my laptop which is operating on Windows 11. Microsoft Windows 64-bit chimera-1.15-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> Size: 152310162 bytes MD5: 6a68ab33f35a298059b9ef89f6372cfc Dec 18, 2020 Instructions <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/win64.html> Documentation <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/docs/> Runs on Windows 7 or later. *Best Regards,Dr. HIRA KHALID* Associate Professor Chemistry Forman Christian College University (A Chartered University) Lahore, Pakistan.54600 Ph: 042-99231581-88 x: 562 www.fccollege.edu.pk ........................ HEC APPROVED Supervisor Advisor ACS Punjab Associate member RSC Member & Ambassador Chemistry ACS Member AOCS Life-time CSP Member IUPAC Young Fellow

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FAD Topology/Parameter Files
by Zehra GÜNEŞ 22 Nov '21

22 Nov '21

Dear all, I am working on a research protein that contains FAD. I have tried to prepare it for simulation but unfortunately I have neither trajectory nor parameter file of FAD. Would it be possible to share with me these files if you have? Thanks in advance, Zehra Güneş

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chimera, H-bonds
by Rio Aquarius 19 Nov '21

19 Nov '21

Dear Developer, I have a specific task for ChimeraX. I want to show H-bonds and hide all amino acid residues. But when I hide amino acid residues, all H-bonds I need disappear. Is there a way to do what I want?

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How to smooth trajectory?
by Saikat Pal 15 Nov '21

15 Nov '21

Dear all, I want to make a movie using chimera. So, what are the steps to smooth the trajectory? Thanks and Regards, Saikat Pal

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Chimera Launch Error
by Cassidy Terrell 12 Nov '21

12 Nov '21

Hello, A student in my course (cced here) is trying to open Chimera 1.15 and this is the error message that appears: "chimera exited abnormally; the exit code was -1073741819. Use the --debug command line option for the full error message." We cannot open the program, which mean we cannot get to the command line. Thoughts about how to proceed? We have already removed/uninstalled previous version and re-downloaded new one. The same messages appears each time. Best Cassidy -- Cassidy R. Terrell, Ph.D. (she/her/hers) Assistant Professor, Biochemistry Center for Learning Innovation | University of Minnesota | Rochester 300 University Square | Rochester, MN 55904 *Always believe something wonderful is about to happen*

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Regarding publication using Chimera.
by Kavya Pandya 11 Nov '21

11 Nov '21

Dear Sir/Ma'am, I am a PhD scholar at the Institute of Advanced Research, India. I have been using the free version of Chimera for the last few days. I wanted to ask if I could publish the images created in Chimera using that free version by citing it appropriately using the citation provided on the website or do I need to buy the license to publish? Would you please guide me for the same. Thank You Kavya PhD Scholar -- Disclaimer : This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) /addressee and may contain confidential and privileged information. If you are not the intended recipient/addressee, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email or any action taken in reliance on this email is strictly prohibited and may be unlawful. The recipient /addressee acknowledges that Institute of Advanced Research (IAR) are unable to exercise control or ensure or guarantee the integrity of/over the contents of the information contained in e-mail transmissions and further acknowledges that any views expressed in this message are those of the individual sender and no binding nature of the message shall be implied or assumed unless the sender does so expressly with due authority of Institute of Advanced Research (IAR). Internet communications cannot be guaranteed to be timely, secure, error or virus-free, thus the sender does not accept liability for any errors or omissions. Before opening any attachments please check them for viruses and defects.

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