- Chimera-users - RBVI Mailing Lists

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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How to set the contour level correctly?
by Selenschik, Philipp 18 Oct '21

18 Oct '21

Hello, my apologies if this is a recurring (and potentially trivial) question that does not directly concern Chimeras functionalities. I am wondering how to properly set the value of the contour level to visualize a Coulomb potential map. When I use the approximation of 1 Da = 1.2 [cid:image003.png@01D7C06B.AA8F9850] ³ to adjust the displayed volume in the Volume viewer dialog almost no secondary structure, but a lot of dust is visible. The same problem occurs when I’d like to visualize, for example, an α-helix of a subunit rigid-body fitted to the density. I use the “zone” command to trim the density at a pre-defined 2 Å around the α-helix. But is there any general guideline on how to properly set the contour level? I often find values between 1 σ to 3 σ. I assume this is the standard deviation of the map. If so, can it be measured via the “Volume Mean, SD, RMS” command? Kind regards Phil

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Select coloured residues with Chimera
by Javier Sanchez Utges (PG Research) 13 Oct '21

13 Oct '21

Hello, my name is Javier and I am a Bioinformatics PhD student in Dundee. I am using UCSF Chimera v1.14 and I am trying to select residues according to the colour they are coloured in, using the following command for blue-coloured residues for example: "sel @/color=blue". This works just fine, however, I struggle when using other colours such as "medium blue" or "dark green". "sel @/color=darkgreen" does not work. It looks like all colours with a single word name work fine, but 2-word name colours do not. Moreover, I can colour residues using RGB codes, such as "col #da70d6 sel" to colour selected residues in orchid. Nevertheless, "sel @/color=#da70d6" does not work. "sel @/color=orchid" works, though. So, is there a way that I can use two-word named colours when selecting by colours, and also, use RGB codes or other colouring codes to select coloured residues? Many thanks, Javier The University of Dundee is a registered Scottish Charity, No: SC015096

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