- Chimera-users - RBVI Mailing Lists

renumbering sequence with gap
by Haghighijoo, Zahra 25 Apr '22

25 Apr '22

Hi, I am editing a retrieved pdb from homology modeling that has two gaps, is there a way to insert the gaps and renumbering pdb? could you please help me ? Thank you, Zahra

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Open Castp file in Chimera X
by Zhang, Bixia 21 Apr '22

21 Apr '22

Good afternoon, I am trying to open .poc file from CASTP server in Chimera X. And I found this chimeraX recipe https://rbvi.github.io/chimerax-recipes/castp/castp.html. However, when I used the command open<help:user/commands/open.html> read_castp.py, it said No such file/path: read_castp.py. I am working on a Linux unbuntu box and I don't know if this is making any difference. Could you please help with this issue? Thank you so much! Best, Bixia Read CASTP pockets file - ChimeraX Recipes<https://rbvi.github.io/chimerax-recipes/castp/castp.html> We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. rbvi.github.io

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Command for measuring distance between centroids and to show dotted lines depicting the measurement
by Shubham Devesh Ramgoolam 21 Apr '22

21 Apr '22

Hi, I hope you are doing well. Is there a command in chimera that allows us to measure the distance between centroids and also to show dotted lines depicting the measurement? I used the command distance but no lines were shown for centroids. I am considering of using the coordinates of the centroids to place dummy atoms and then, use distance. However, I do not know if there is a command for placing dummy atoms in specified positions. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Upcoming deprecation of Chimera webservices
by Zach Pearson 21 Apr '22

21 Apr '22

Hello Chimera users, In the next 12 to 18 months, some Chimera tools that depend on web services may stop working: BLAST protein (which is also used by Multidomain Assembler), Modeller comparative and loop modeling, multiple sequence alignment with Clustal Omega and MUSCLE, Small-Angle X-Ray Profile, and 2D Chemical Diagram (used by Structure Diagram and ViewDock). The reason is that some necessary upgrades to our internal systems may break these web services. However, ChimeraX uses a different type of web service that will continue to work, and we have already integrated the following into ChimeraX: BLAST protein, Modeller comparative and loop modelling. In progress: multiple sequence alignment with Clustal Omega and MUSCLE. We wanted to make sure that our users would be prepared for the need to switch to ChimeraX for these features. If you have comments on how to prioritize integrating the remaining services (Small-Angle X-Ray Profile, 2D Chemical Diagram) with ChimeraX, please let us know. Thank you!

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Loop through hundreds of files and find HBonds
by Samuel Kyobe 19 Apr '22

19 Apr '22

Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe

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Chimera(X) in Centos stream 9
by Antonio Díaz Quintana 19 Apr '22

19 Apr '22

Dear all, I am unable to install Chimerax and Chimera—yes I still use the old one because its great tools—using the rpm package in Centos Stream 9, because lack of LibOSMesa package in this distribution. I tried using dnf, but a mesa-libGL library (21.3.4...) is already installed Similarly, it seems my OS distribution does not contain python Tk, nor I can get suitable python with Tk-devel from repository, so I get the following message. Could I get any help? Meanwhile I got it on my old Win10, 11 years-old laptop. Both programs work well there. Best, Antonio -- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain Phone: +34 954 48 9631

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Command for selecting aromatic ring
by Shubham Devesh Ramgoolam 18 Apr '22

18 Apr '22

Hello, I hope you are doing well. Is there a command on chimera that will allow me to select for the atoms in aromatic rings? I found a workaround by defining the atoms involved in the aromatic rings and then making my selection. However, I would like to use a command (or perhaps combination of commands) from chimera to select the aromatic atoms. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Revised Need Help
by Ali Raza Azeemi 14 Apr '22

14 Apr '22

Hi, hope you are doing well? dear, we have a question about making an animation/movie in chimera. I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you -- *Ali Raza Siddiqui* *Jr. Research Fellow* *Computer-Aided Drug Design (CAAD) unit. P-133, PCMD* H.E.J. Research Institute of Chemistry International Center for Chemical & Biological Sciences University of Karachi, 75270 Karachi- Pakistan.

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Question regarding bond angle
by Prathvi Singh 14 Apr '22

14 Apr '22

Hi again Elaine, Is there a way in chimera or chimeraX to change the angle between three atoms A,B,C where atoms A & B are covalently bonded to each other but neither A nor B is bonded to C ? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Need Help
by Ali Raza Azeemi 14 Apr '22

14 Apr '22

Hi, hope you are doing well? dear, we have a question about making an animation/movie. I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you -- *Ali Raza Siddiqui* *Jr. Research Fellow* *Computer-Aided Drug Design (CAAD) unit. P-133, PCMD* H.E.J. Research Institute of Chemistry International Center for Chemical & Biological Sciences University of Karachi, 75270 Karachi- Pakistan.

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