May 2021 - Chimera-users - RBVI Mailing Lists

Transfer of docked substrate co-ordinates
by Jayashree Chittari 08 May '21

08 May '21

Respected sir/ma'am Greetings for the day!!! I have docked ligand into an enzyme which contains two active sites. My docked ligand is in one active site. I want to transfer the ligand conformation from one active site pocket to another using superimpose option in chimera. Find herewith the attached file of PDB in which i want to transfer propionaldehyde coordinates from one active site to another is there any way that we can transfer the docked confirmation coordinates into another chain. Kindly, help me to solve this issue. It will be helpful if you suggest the process. Thank you Regards Chittari Jaya Shree

2 1

Measuring rmsd without having exact number of atoms
by Ahmad Khalifa 07 May '21

07 May '21

Hi, Is there a work around measuring rmsd between two structures of the same protein, with one of them missing some segments, without having to rebuild / model the missing parts?! I'm thinking of writing a quick script to check for the matching segments, calculate rmsd for those and take an average of these measurements, unless there's a quicker way to do it! Regards.

2 1

Chimera - remote start up issue
by Filip Kadlec 07 May '21

07 May '21

Good afternoon! I haven't found a solution to this problem in one of your user threads, internet and I haven't succeeded resolving the issue. I have installed chimera 1.15 today and it runs well when working on the desktop. However, it would be very convenient if I could run chimera remotely. Chimera is installed on Centos 7, I am trying to remotely operate this PC with Windows 10 PC using MobaXterm. When I run chimera as chimera --debug: initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 146 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 2711 Current serial number in output stream: 2711 With OpenGL on Centos-7 PC glxinfo | grep "OpenGL": OpenGL vendor string: Mesa Project OpenGL renderer string: Software Rasterizer OpenGL version string: 1.4 (2.1 Mesa 10.5.4) OpenGL extensions: Have you encountered such problem? Could the problem be with coliding OpenGLs, or graphical transfer through mobaxterm? It would be a major help if you could point me in the right direction. Thank you in advance and have a great day! Kind regards Filip Kadlec

2 1

The app is not working
by Fatma Elzahra Alhuassein Elfourtia 07 May '21

07 May '21

HI I am trying to use the app for my gene but When I try to open the gene in the Chimera because it shows me an error. Please reply me as soon as possible Thank you IMPORTANT NOTICE OF DISCLAIMER The information in this e-mail and any attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you are not an intended recipient, please delete the message and any attachments and notify the sender of misdelivery. Any views expressed by an individual within this e-mail do not necessarily reflect the view(s) of UCSI University wholly owned by UCSI Education Sdn. Bhd. and shall include but not limited to UCSI Group Holdings Sdn. Bhd. and all of its subsidiaries and associated companies.

2 1

Adjust torsion angles
by Moradkhan, Tiglath A 07 May '21

07 May '21

Hi I'm using the adjust torsions tool in Chimera. I was wondering whether there is an easier way of selecting several amino acids at once and adjusting their torsion angles rather than selecting them individually. I'm working with dimers and trying to select individual amino acids would take a very long time. Thank you Tiglath

2 1

job opening for ChimeraX developer
by Elaine Meng 06 May '21

06 May '21

Hello everybody, We're looking for somebody to join the ChimeraX development team! Please see this posting for details: <https://sjobs.brassring.com/TGnewUI/Search/Home/Home?partnerid=6495&siteid=…> On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Contact in angstrom
by Arthur Pereira da Fonseca 06 May '21

06 May '21

Hello, I’m trying to measure contacts between a protein and a peptide using Chimera. I have to do this with different angstroms distances, 2, 3 and 4 Å. I'm using the command line: findclash :.A test :. B overlap -0.4 hbond 0.0 namingStyle simple save However I don’t know exactly how to modify the overlap to the desired distances. Which values can I use to measure contacts within 2, 3 and 4 Å. Thanks in advance, Arthur Pereira

2 2

python code to loop over molecules
by Julian Tirado-Rives 04 May '21

04 May '21

Dear Chimera (and ChimeraX) team: I need to find some python example or code snippet capable of looping over all the molecules in a particular model and do some actions separately in each one. In our research we use several different docking programs and other ways of generating poses of protein-ligand complexes, and using several different programs to analyze them gets quite complicated. Instead, we've found that the easiest way is to generate from each code, or using conversion utilities such as babel, a pdb file of the host and a sdf or mol2 file containing all the ligand poses and read them into chimera. An excellent program, by the way. We use it all the time. I would love to automate the process even further by doing all the coloring, rendering, Hydrogen Bond and contact analysis, etc. in Python rather than manually. I have been trying to do this, but have not found a way to do the following: If we have, for instance, the host in model #0, and the ligand poses in model #1 (#1.1, #1.2, ..., #1.N): - Get from chimera the number of molecules in model #1 (e.g what is N) - loop from the first #1.1 to the last #1.N molecule - do some cations there (e.g select, color, find HB's, etc) I think this should be a problem other people have encountered and solved before, but I have not been able to find an example in your depository, the mailing lists, or even the book ... I would appreciate your input. Thanks for your help, and for an excellent program! - Julian - -- ----------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives(a)yale.edu | | New Haven, CT 06520-8107 | | -----------------------------------------------------------------

4 5

Rotate model
by C.J. 03 May '21

03 May '21

Hi all, I tried "turn y 180 #1" ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html) but it doesn't work. It said "turn frame arguement must be an integer". While I tried "turn y 180 0 #1" or "turn y 180 1 #1", it said "wait_frames arguement not implemented". Even "turn y 180 0 0 #1" doesn't work. Did I miss something? Thank you! Jianhao

2 2

Combine focuse refined maps in Chimera
by Zheng, Fengwei 03 May '21

03 May '21

Dear Chimera developers: Thank you so much for developing this powerful and elegant software for our community! I am a newbie in cryoEM, and recently I got a consensus map, and split it into two parts to do the further focused refinement, after that I want to combine them together, and then to build my model. I learned that the command "vop maximum #0 #1" can achieve this, what I did is that, firstly, I used this command to merge my consensus map with one focused map, and then merged the resulted map with my second focused map, but it seems that the order of those two maps in my executable command (e.g. #0 #1 or #1 #0) will lead to slightly different resulting map~ I just wondering if this is the correct way to combine my focused maps, or there are other commands can achieve this better? Appreciate! Best, Fengwei

2 2

Chimera-users May 2021