- Chimera-users - RBVI Mailing Lists

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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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Fwd: video card for chimera?
by Elaine Meng 22 Oct '21

22 Oct '21

> Begin forwarded message: > > From: "Sergei I. Sukharev" <sukharev(a)umd.edu> > Subject: video card for chimera? > Date: October 22, 2021 at 8:37:27 AM PDT > > Colleagues, > I am upgrading my PC and I would take your recommendations about the best video cards that would work with Chimera and Phenix. > Thanks, > sergei sukharev, umd Hi Sergei, We recommend taking a look at using ChimeraX instead of Chimera. We are actively developing ChimeraX (but not Chimera) and in the future it may have features specifically for working with Phenix. I have to leave the video card question for others, but encourage responses about what works well with ChimeraX. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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yum install related question about chimeraX.
by 박시훈 22 Oct '21

22 Oct '21

Dear chimera users, I have question in yum install of chimeraX. I downloaded a CentOS/RHEL7 chimerax package from https://www.cgl.ucsf.edu/chimerax/download.html, and I tried to install by that command; However, I sawed strange messages like this; Can I get some help? *[root@lsb /]# sudo yum install /home/hpclab/Downloads/ucsf-chimerax-1.2.5-1.el7.x86_64.rpm * Loaded plugins: fastestmirror, langpacks Examining /home/hpclab/Downloads/ucsf-chimerax-1.2.5-1.el7.x86_64.rpm: ucsf-chimerax-1.2.5-1.el7.x86_64 Marking /home/hpclab/Downloads/ucsf-chimerax-1.2.5-1.el7.x86_64.rpm to be installed Resolving Dependencies --> Running transaction check ---> Package ucsf-chimerax.x86_64 0:1.2.5-1.el7 will be installed --> Processing Dependency: libgfortran4 for package: ucsf-chimerax-1.2.5-1.el7.x86_64 Loading mirror speeds from cached hostfile epel/x86_64/metalink | 5.1 kB 00:00 * base: mirror.kakao.com * epel: ftp.riken.jp * extras: mirror.kakao.com * nux-dextop: li.nux.ro * updates: mirror.kakao.com base | 3.6 kB 00:00 extras | 2.9 kB 00:00 http://li.nux.ro/download/nux/dextop/el7/x86_64/repodata/repomd.xml: [Errno 14] curl#6 - "Could not resolve host: li.nux.ro; Unknown error" Trying other mirror. nux-dextop | 2.9 kB 00:00 teamviewer/x86_64/signature | 867 B 00:00 Retrieving key from https://linux.teamviewer.com/pubkey/currentkey.asc Importing GPG key 0x0C1289C0: Userid : "TeamViewer GmbH (TeamViewer Linux 2017) < support(a)teamviewer.com>" Fingerprint: 8cae 012e bfac 38b1 7a93 7cd8 c5e2 2450 0c12 89c0 From : https://linux.teamviewer.com/pubkey/currentkey.asc *Is this ok [y/N]: N* teamviewer/x86_64/signature | 2.5 kB 02:00 !!! https://linux.teamviewer.com/yum/stable/main/binary-x86_64/repodata/repomd.…: [Errno -1] Gpg Keys not imported, cannot verify repomd.xml for repo teamviewer Trying other mirror. One of the configured repositories failed (TeamViewer - x86_64), and yum doesn't have enough cached data to continue. At this point the only safe thing yum can do is fail. There are a few ways to work "fix" this: 1. Contact the upstream for the repository and get them to fix the problem. 2. Reconfigure the baseurl/etc. for the repository, to point to a working upstream. This is most often useful if you are using a newer distribution release than is supported by the repository (and the packages for the previous distribution release still work). 3. Run the command with the repository temporarily disabled yum --disablerepo=teamviewer ... 4. Disable the repository permanently, so yum won't use it by default. Yum will then just ignore the repository until you permanently enable it again or use --enablerepo for temporary usage: yum-config-manager --disable teamviewer or subscription-manager repos --disable=teamviewer 5. Configure the failing repository to be skipped, if it is unavailable. Note that yum will try to contact the repo. when it runs most commands, so will have to try and fail each time (and thus. yum will be be much slower). If it is a very temporary problem though, this is often a nice compromise: yum-config-manager --save --setopt=teamviewer.skip_if_unavailable=true failure: repodata/repomd.xml from teamviewer: [Errno 256] No more mirrors to try. https://linux.teamviewer.com/yum/stable/main/binary-x86_64/repodata/repomd.…: [Errno -1] Gpg Keys not imported, cannot verify repomd.xml for repo teamviewer Best regards Si Hoon Park

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Problem with addh command in Python script
by Abhik Mukhopadhyay 21 Oct '21

21 Oct '21

Hi everyone, I am trying to add hydrogen using the command addh. I am using the command in a python script in this form runCommand("addh spec #0 hbond true") or runCommand("addh hbond true") both gives a "KeyError: <_molecule.Atom object at 0x7fa2d115c180>" But deleting hydrogen with this command works runCommand("delete element.H") I have attached the full error report below. Could anyone please help me with this. Thanks in advance, Abhik "Traceback (most recent call last): File "/home/amukhopadhyay/anaconda3/envs/chimera/bin/pychimera", line 4, in <module> __import__('pkg_resources').run_script('pychimera==0.2.1', 'pychimera') File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1469, in run_script exec(script_code, namespace, namespace) File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pychimera-0.2.1-py2.7.egg/EGG-INFO/scripts/pychimera", line 12, in <module> File "build/bdist.linux-x86_64/egg/pychimera/__main__.py", line 6, in run # All rights reserved. This software provided pursuant to a File "build/bdist.linux-x86_64/egg/pychimera/core.py", line 290, in main File "build/bdist.linux-x86_64/egg/pychimera/core.py", line 259, in run_cli_options File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 252, in run_path return _run_module_code(code, init_globals, run_name, path_name) File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 82, in _run_module_code mod_name, mod_fname, mod_loader, pkg_name) File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "chimera_remove_add_hydrogen.py", line 16, in <module> rc("addh spec #0 hbond true") File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/chimera/__init__.py", line 2796, in runCommand makeCommand(*args, **kw) File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/ChimeraExtension.py", line 40, in cmdAddH specInfo=[("spec", "molecules", "molecules")]) File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/Midas/midas_text.py", line 451, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/__init__.py", line 1006, in cmdAddH addHFunc(molecules, inIsolation=inIsolation, **protSchemes) File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/__init__.py", line 554, in hbondAddHydrogens idatmType, hisNs, coordinations, inIsolation) File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/hbond.py", line 386, in addHydrogens if d not in finished and _typeInfo(d).geometry == 4: File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/hbond.py", line 1403, in _typeInfo return typeInfo4Atom[atom] KeyError: <_molecule.Atom object at 0x7fa2d115c180> "

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frames not record for movie making
by Yanhe Zhao 19 Oct '21

19 Oct '21

Good afternoon and greeting there, I use command as below for movie making but no frames were recorded. Could you please help me out on it? movie record directory ./my_movie pattern Movi1-* fformat jpeg; wait; mclip #0 offset -1 slab false; movie stop; Thanks and cheers, Yanhe

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