October 2020 - Chimera-users - RBVI Mailing Lists

(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

3 7

How to setup Nvidia 3D Vision on Ubuntu
by Tom Goddard 03 Nov '20

03 Nov '20

Hi Wei, I'd suggest using Ubuntu 20.04, the latest Ubuntu, the current Chimera 1.14 or daily build will work fine on that. I am not certain that Quadro FX 4800 graphics drivers will be available for Ubuntu 20, probably they will be, but you might want to look for that online before proceeding. That graphics cards is very old, from 2008. The other thing to know is that Nvidia discontinued support for Nvidia 3D Vision stereo glasses in 2019 https://nvidia.custhelp.com/app/answers/detail/a_id/4845 meaning those glasses and emitter will no longer work using just the current Nvidia graphics driver. But they claim that there is a separate driver for the USB emitter that allows it to work. https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-dri… <https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-dri…> I have not tried it. If you get it to work I'd be interested in hearing about it since we have an old Nvidia 3D Vision system. Tom > On Oct 29, 2020, at 6:41 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: > > Hi Tom, > > Hope everything is well. > > One university's computer lab recently retired some workstations that were used for 3D visualization before. I managed to get a couple workstations with the 3D glasses and emitters. But I need to reinstall the operating system on those machines. > > The graphic card of the workstation is Nvidia Quadro FX4800. > The emitter is NVIDIA P854. > The glasses are NVIDIA-P854 and ViewSonic-PGD250. > > I plan to install Ubuntu. I am wondering which version of Ubuntu is suitable for using UCSF Chimera. Do we need to install cuda to make it work? Do we need to install an older version of Chimera? > > Sorry I just sent the message to you to follow the previous chain of conversation. Shall I email the chimera-user in the future with such questions? > > Thank you, > > Wei >

4 5

Capping in VRML
by Greg Williams 02 Nov '20

02 Nov '20

When I export a vrml file to process in my Cinema 4D application, the ends of the helices, coils and sheets are capped at the ends with a material that is different then the material I use to color the secondary structure features. In Cinema 4D, I have to change every capped end individually. Where do I change the vrml export settings so that the individual objects are capped with the right material? Thanks!

4 4

Select multiple files and open in the same instance
by Ahmad Khalifa 30 Oct '20

30 Oct '20

I used to have Chimera configured to select multiple files, click open, and have them all open in the same instance. After I reinstalled it, now it opens an instance for every file, how can I change it back? Regards.

3 3

Chimera: Per-model clipping and contour level
by Selenschik, Philipp 30 Oct '20

30 Oct '20

Hello, I really enjoy working with Chimera (version 1.14), however I encounter two problems: I fitted the X-ray based crystal structure of apoferritin to my cryo-EM density map, determined the symmetry and based on that the algorithm fits 24 subunits to the map. Really nice. Now I would like to show a "sliced" image of both map and structure. I tried doing so by "Side view", enabling "clip". That works, but I would like to rotate the clipped object. Then I tried per-model-clipping. Here I can clip the map and structures separately. However, I have to choose all fitted (e.g. 12 out of 24) substructures and the clipping works only partially. What am I doing wrong? Also, I tried to figure out the best contour level setting. It seems there is no guide as to which is ideal? Based on a tutorial, I assumed 1 A³/Da for a globular protein, which turns out to be around 620*10³ A³ for my protein. The problem here is: If I slide beyond approx.. 550*10³ A³ all that remains is a square. What's wrong? I hope you can help me out :) Kind regards Philipp

2 4

Help with something really simple
by M. Elizabeth Stroupe 29 Oct '20

29 Oct '20

Hi ChimeraX team, I need to measure a simple angle between three atoms, two within one model and the third in another model to describe a domain motion. In Chimera I could do this from the Structure Analysis tab but now it seems you can only measure distances. I tried the following command(s) and they both gave me an error. I also tried including commas between the angles. What am I doing wrong? angle #1/A:602@C7m,:222@CB,#17/A:602@C7M measure angle #1/A:602@C7m #1/A:222@CB #17/A:602@C7M Thank you! Beth

2 1

MD Simulation on Chimera
by Samiha I Amer 27 Oct '20

27 Oct '20

Please may I know the ideal system specification to run a successful molecular Dynamics simulation on Chimera? Thank you Sent from Yahoo Mail on Android

2 1

REGARDING CHIMERA SESSION FILE
by ASIF JAHAN SHUVRO 26 Oct '20

26 Oct '20

Dear concern, this is Asif from BRAC University, Biotechnology program. I hope you're in good health. I need a little help from you. Recently, I have joined two peptide fragments by forming a peptide bond between them using your standalone UCSF Chimera software. The file has been saved as a Chimera session fle. However, I'm not finding any clue on how to convert it into an entire pdb file. I'm not being able to do any other modification to it since a pdb file is required for this purpose. Could you please help me out on this regard? kindly let me know how can I generate a pdb file from that session file format. I wish to hear your reply. Thanks in advance! Regards, Asif Jahan Shuvro Biotechnology Program Department of Mathematics & Natural Sciences BRAC University

2 2

Morphing PDB
by Reza Khayat 26 Oct '20

26 Oct '20

Hi, Is it possible to morph multiple chains serially? I have a trimer in two different conformations, I would like to morph Chain A in conformation 1 to Chain A in conformation 2. Then, I'd like to do this with chain B and finally chain C. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

Running Chimera on X server
by Ahmad Khalifa 26 Oct '20

26 Oct '20

The refresh rate of Chimera running on a linux server is very slow. I'm connected to the server with an ssh client with X server. I wonder if it's because Chimera is not configured properly or possibly the X server. I also tried to make some movies but they are always blank (black screen). Any suggestions?

2 1

Chimera-users October 2020