- Chimera-users - RBVI Mailing Lists

Minimization on complex
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 29 Nov '21

29 Nov '21

Hi, I need an advice regarding minimization of complexes. I've performed a virtual screening and I've selected some molecules of interest. Now, I've looked for the possibile interactions in the binding site and I would like to perform a minimization moving only the hydrogen atoms in the binding site. However, I have to create a new file pdb complex formed by my protein and one molecule from VS results. So, I opened the pdb file of the protein and the mol2 file of the molecule from the VS: now, do I need to save a pdb file of the complex and how to save it? I need the hydrogens to move according to the ligand inside the protein and I don't know if it's possibile with both the type of saving (is it better individual MOLECULE sections or combined MOLECULE section?). Moreover, I don't know if (for this kind of purpose) it's better first to save the complex in pdb file and then to use dockprep and minimization or use dockprep and minimization and only after saving the file of the complex. My main aim is to see if some hydrogens of the residues in the binding site move their places according to the presence of this ligand. Hope someone can help me, thanks.

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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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Solvation question
by Noriega, Heather 09 Nov '21

09 Nov '21

Hello, I have a quick question. I am running the solvate command before the minimization, equilibrium, and production run in Chimera. I click the start solvate tool and put my water box size and apply. This gives me my box and in the command line it says created...with however many water molecules. I then go run parameters, set up everything. Once I hit run, the water box dissappears. I just want to make sure that the solvation did occur even though the water box dissappears from the screen. Everything else ran smoothly to show simulation. I just want to be certain and have confirmation that the solvation does occur as long as I use apply and do not close out of the window. Thanks in advance for your help. Thank you, Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Writing data to a text file
by Prathvi Singh 08 Nov '21

08 Nov '21

Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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the version of Ambertools that are used in the command "Write prmtop"?
by Victor Nazarychev 08 Nov '21

08 Nov '21

Dear Chimera's users, I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release? Best regards, Victor

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Chimera Laucher Error
by Paulo Roberto da Silva Santos 08 Nov '21

08 Nov '21

Hi, I was intalated Chimera 1.5 64bit under Windows 10 64 bit, I was intalated Chimera 1.5 64bit under Windows 10 64 bit, and all was fine until I started executed, Chimera crashed and now it gives me an error at launch and quits, so I cannot run it anymore. After launch, the error window shows: -------------------------------------------------------------------------------- Chimera exited abnormally; the exit code was: -1073741819. Use the --debug command line option for the full error message. -------------------------------------------------------------------------------- Paulo Roberto da Silva Santos Bacharel em Química - UFPB Mestrando em Química - UFPB LCCQS - Laboratório de Compostos de Coordenação e Química de Superfície (83) 99915-5963

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error while running chimera
by Saniya Kate 03 Nov '21

03 Nov '21

Good evening, i am Student and Installed chimera for WINDOWS (chimera-1.15-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…>) from your website but I am unable to run it on my system since it is a 64 bit release and my system is 32 bit. I urgently need chimera for my project work but I'm not able to use it since the 32 bit release of chimera isn't available. please let me know what can be done

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Showbox
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 03 Nov '21

03 Nov '21

Hi, I know that the program showbox is related to Dock, but I can't find a mailing list still active for Dock users... Maybe someone could help me here. I don't understand if ligands that are docked inside the binding site can exit in part from the box the user defines for grid calculation. I think that maybe if sphere centers are very near the boundaries of the box, it could be possible, but I'm not sure. Does anyone know it? Thanks and regards.

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Counting the number of water molecules
by Prathvi Singh 02 Nov '21

02 Nov '21

Hi, Is there a command in UCSF chimera to count the total no. of water molecules in a PDB file? Can we also count, say the total number of alanine residues in a PDB file or any other other residue for that matter? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Bug Report: Chimera exit abnormally: code 1073741819
by Jyoti Singh 31 Oct '21

31 Oct '21

Dear Sir, I have installed Chimera 1.15 successfully.When I try to open it, a window pops-up and gives an exit code: 1073741819 and it never opens for analysis. Below I have shared the start information and please find the attachment. *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* Kindly do needful. Regards. *Jyoti SinghPh.D. Scholar [UGC-SRF]"Molecular Biology and Biotechnology lab"CPMB DIVISION, GARDEN BLOCK.CSIR - National Botanical Research Institute, Lucknow [UP], 226001, 'INDIA'*

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(no subject)
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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Postdoc positions to explore the world of molecules!
by Marc 29 Oct '21

29 Oct '21

Seeking 2 post-doctoral fellows with experience related to Biology/Bioinformatics, Unity3D, Virtual Reality or computer graphics to come to Paris. View this email in your browser (https://mailchi.mp/8702ad4a4ddd/postdoc-positions-to-explore-the-world-of-m…) Dear Colleague , I hope you are well. My apologies for contributing to filling your inbox. I am urgently looking for two new people to join my team and I am depending on your help. The positions I am looking to fill are very good positions in France, described below. They deal with immersive scientific visualization of membrane proteins, their assembly and omic data. Could you please forward this email to anyone you know who might be considered for this position? I would be very grateful for it. Please let me know if you have any questions. With best wishes, Marc ** Come explore the world of molecules! ------------------------------------------------------------ https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id… I am seeking two post-doctoral fellows to start immediately in my lab. My lab is focused on the development of novel approaches for interactive visualization of molecular structures, including using UnityMol to create 3D user interfaces and Virtual Reality applications. The positions will involve the development of novel software components for high throughput molecular visualization, as well as challenging biological applications. We are looking for someone that is passionate about Molecular Biology who also has skills in computer programming and graphics design. See more details at the following links: * immersive scientific visualization of membrane proteins and their assemblies (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) (PDF version) (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) * immersive scientific visualization of omic data (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) (PDF version) (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) More information about the institute and work environment is described through a series of short videos with testimonials and overviews (https://ibpc.us4.list-manage.com/track/click?u=1a86fc891fac34d890ad5fe30&id…) . I hope you will be interested in joining our team! Sincerely, Marc Baaden LBT lab . 13 rue Pierre et Marie Curie . CNRS UPR 9080 / IBPC . Paris 75005 . France You are receiving this email as part of my professional network. Want to change how you receive these emails? You can update your preferences (https://ibpc.us4.list-manage.com/profile?u=1a86fc891fac34d890ad5fe30&id=b29…) or unsubscribe (https://ibpc.us4.list-manage.com/unsubscribe?u=1a86fc891fac34d890ad5fe30&id…) Email Marketing Powered by Mailchimp http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…

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Re: [Chimera-users] [Chimera] Different bond width in the same model
by Elaine Meng 29 Oct '21

29 Oct '21

On Oct 28, 2021, at 4:56 AM, Konstantin Richter <konstantin.richter(a)bbz.uni-leipzig.de> wrote: > > Dear Elaine, > I am currently trying to create molecular figures with the old Chimera (not ChimeraX). I would like to represent different bonds in the same model in different bond widths: in my case, a disulfide bond should be represented thicker than the bonds of a nearby ligand. > > I already learned that the bond width is the product of the stick scale (which is a model attribute) multiplied by the bond radius (which is an atom attribute, if I got it right): https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-November/009289.html > > So changing the bond radius for only the ligand atoms but not the disulfide atoms would do the job for me, right? Unfortunately I have no idea how to change the bond radius in the command line. Is there any command for that? > > Thanks in advance for your help! > > best wishes > Konstantin Richter Dear Konstantin, You can change the bond radius in the Selection Inspector (e.g. select the part you want to change, then click the green magnifying glass in the lower right). In the Selection Inspector, inspect: Bond, and then change the bond radius value for the current selection. If you hold the mouse over the "radius" part of that dialog, a popup balloon says that the name of this bond attribute (for using in commands) is "radius" If you prefer to use commands only, the command to set attribute values is "setattr," e.g. setattr b radius 0.4 .... to change all bonds setattr b radius 0.1 sel ... to change bonds in the current selection (and you can use any other atomspec, not just "sel", e.g. model numbers, residue names or numbers, etc.) The general explanation of this and how to change it is <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#repre…> Selection Inspector <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html#bondprop"> setattr command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> 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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Assistance
by Priyanka Abeyrathne 28 Oct '21

28 Oct '21

Hi, Could you please assist me in how to remove the text after measuring distance (ex: text distance 2.0 A) in the Chimera session. Thank you. Kind regards, Priyanka

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RR Distance Maps: Exporting St. Dev Map
by Woods, Taariq (NIH/NEI) [F] 27 Oct '21

27 Oct '21

Hello, I am doing some analysis on homology models. I generated the RR Distance Map for 5 structures. I wanted to export the standard deviations map only so that I can see the numerical values, but every time I click export in only gives me the option of exporting a map of the distances. I was just wondering if I could have some help with this if I am missing something. Regards, Taariq

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Chimera can't be launched
by salar moniri 25 Oct '21

25 Oct '21

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