October 2019 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

2 6

Trouble initializing ChimeraX on CentOS
by Brown, Alex 18 Oct '19

18 Oct '19

Hello and good morning, I have always had a great experience using Chimera and so I was hoping to try out ChimeraX for some of our larger cryo-em data sets. However, following download and an install that did not seem to produce an error message, I can not seem to initialize the program. I have copied the output from the command prompt below. Beyond that, I should probably also mention that we are running the centos-release-7-6.1810.2.el7.centos.x86_64 operating system with intel chips and nvidia graphics cards. [root@gaolab ~]# chimerax-daily NOTE: available bundle cache has not been initialized yet WARNING: could not retrieve bundle list from toolshed NOTE: Traceback (most recent call last): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py", line 871, in <module> exit_code = init(sys.argv) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py", line 580, in init check_available=opts.get_available_bundles) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 1681, in init _toolshed = Toolshed(*args, **kw) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 359, in __init__ if not available.has_cache_file(self._cache_dir): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/available.py", line 109, in has_cache_file return os.path.exists(os.path.join(cache_dir, _CACHE_FILE)) File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType BUG: TypeError: expected str, bytes or os.PathLike object, not NoneType File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80, in join a = os.fspath(a) _See log for complete Python traceback._ Thanks in advance for any support you may be able to provide on this! -Alex Alexander Brown IV, PhD Postdoctoral Researcher Horae Gene Therapy Center Li Weibo Institute for Rare Diseases Research University of Massachusetts Medical School 368 Plantation Street, AS6-2011 Worcester, MA 01605 Phone: (508) 856-3316 Email: alex.brown(a)umassmed.edu<mailto:alex.brown@umassmed.edu> Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.

2 1

problem of chimerax
by 陈柳青 18 Oct '19

18 Oct '19

Hello! I tried install either daily builds or release 0.9 of chimeraX on my win10 64 system, but both encounter the same problem showed in the attachment. After startup, i can't see any menu! but when i move mouse on the menu , it will appear sub menu. How can solve this bug? sincerely Liuqing chen

2 1

macOS Catalina gives PermissionError opening files
by Tom Goddard 15 Oct '19

15 Oct '19

If you are thinking of upgrading to the new macOS Catalina (10.15) and want to use ChimeraX on it you might hold off. We have found that opening files using the ChimeraX open command or the recent files thumbnails often causes PermissionError and fails to open the files. This is caused by a new macOS Catalina security feature when any app that tries to open a file under Desktop, Downloads, or Documents must first raise a permission dialog asking if the app is allowed to open files from that directory. When using the ChimeraX File / Open dialog (from the File menu) the permission dialog is shown and works. But if you use the ChimeraX open command of recent files thumbnails on directories that you have not granted permission for with the Open dialog, then those fail with PermissionError -- apparently those methods of opening are not able to show the permission dialog. Other applications (e.g. photo editing program Gimp) have the same problem. We do not yet know how to solve this. Tom

2 2

Re: [chimerax-users] [Chimera-users] surface color
by Elaine Meng 14 Oct '19

14 Oct '19

Hi Mike, So close! You’re only missing the “palette” keyword before “rainbow” … try: color height #1 center 0,0,0 axis z palette rainbow <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#distance> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> (By the way, there is a chimerax-users(a)cgl.ucsf.edu list CC’d here if you have questions specifically about ChimeraX.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 14, 2019, at 2:43 PM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu> wrote: > > I’m trying to do the same thing as Chimera’s “Surface Color”, but in ChimeraX, on the command line. After reading the docs, I tried “color height #1 (the map designation) center 0,0,0 axis z rainbow”. It gave “expected a keyword”. What did I miss? > Thanks, > Mike

1 0

show stands' arrows a little werid
by Meinan Lyu 14 Oct '19

14 Oct '19

Dear Dr., The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much！ Best regards, Meinan CWRU

3 5

Soft lighting changes when additional model is displayed
by Gabor PAPAI 14 Oct '19

14 Oct '19

Dear ChimeraX team, If I open a second model in ChimeraX (0.91) the ambient occlusion in soft lighting mode on the first model disappears or becomes diminished. How can I revert this effect? I attach an image to illustrate this phenomenon. The only change between the two displays that I opened a model of DNA and placed close to the first model. Best regards, Gabor [cid:6AAD58A0-1B6C-4362-8C29-57D033327EBF@igbmc.u-strasbg.fr] --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

2 4

issues with rotamers tool
by Llorente, Alejandro 09 Oct '19

09 Oct '19

Hi, I am new PhD student using ChimeraX and I am very interested in learning how to work with this program. I am trying to introduce some mutations in my protein in some specific amino acids that I have selected. When I introduce an Alanine in my position of interest (using dunbrack) I have no issues, but when I try any other amino acids (as Phe or Thy) the program has no problem giving me the prediction for the rotamers, but I have some issues. After select some of the most probable rotamers, all the amino acids of my protein change to that kind of amino acid (not just the specific one that I have selected). Another problem is that I have is that when I select a specific atom of an amino acid, the program also select similar atoms but in all the others amino acids of my protein. I really hope that someone can help me with these issues. Thank You very much Alejandro Llorente. Lab of Dr. Nancy Carrasco. Department of Molecular Physiology & Biophysics, Vanderbilt University. 2215 Garland Ave Nashville, TN 37232-0615, room 711. Mobile phone: +34 626586236

2 1

Unable to use Viewdockx
by Abhijeet Kumar 07 Oct '19

07 Oct '19

hi, I am a college student and I am working on a project on protein docking visualization and came across ChimeraX. I am not able to use Viewdockx and the user guide for viewdockx gives a 404 page not found error. So, can you help me with this? Thank you.

2 2

Cuved helix tubes
by Ernesto Arias Palomo 02 Oct '19

02 Oct '19

Good morning, We are using the modeHelix tube to represent the secondary structure. However, our structure contains some long and curved helices, and the representation does not follow their shape with enough precision. Is there any option to increase the fit of the tube to the overall shape of long helices? Thank you very much for your help. Kind regards, Ernesto. -- Ernesto Arias Palomo, PhD Group Leader Biological Research Center (CIB-CSIC) Ramiro de Maeztu, 9. 28040. Madrid. Spain earias(a)cib.csic.es +34 91 837 31 12 ext 4446

2 3

ChimeraX-users October 2019