October 2021 - Chimera-users - RBVI Mailing Lists

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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Questions on moving lables automatically
by 夏前程 12 Oct '21

12 Oct '21

Hi, I've noticed that Chimera can help us to label a lot of things, including atomic partial charge, on chemical systems like a compound. Those atomic labels were set just a distance from atoms' positions. However, I want to set these labels exactly on those atoms. I've known that such operations can be realized through moving them with mouse manually and one by one. Thus, I'm wondering if there is an alternative approach in Chimera that can allow me to set those labels directly on their corresponding atoms automatically. I think this function should exist here. But I've searched for hours and find almost nothing related. With Regards, Qiancheng Xia 2021/10/12

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addh command not working
by Prathvi Singh 12 Oct '21

12 Oct '21

Hi, I have a PDB file which I have trimmed such that it contains only two residues, say residue-10 and residue-25 (I have given the numbers to denote that the residues are far apart from each other in the primary structure of the protein) and saved as a new PDB file. In order to prevent formation of any pseudobonds between the two residues, I manually added a TER row in the PDB file, just after the entry of the last atom of residue-10. Now, when I delete all the atoms of residue-10 except the atoms of its carbonyl group i.e., its backbone C-atom and covalently linked backbone O-atom and run the "addh" command, chimera adds H-atoms to the relevant atoms of residue-25 but doesn't adds H-atoms to the C-atom of residue-10 due to which its valency remains incomplete. Can you please tell me why it is happening? Is there any way to overcome this problem? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Is there any way to export chimera settings
by Prathvi Singh 08 Oct '21

08 Oct '21

Is there any way to export chimera settings to a file & then import those settings to chimera program installed on a different PC? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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superimpose models from inside a python script and access the transformation matrix
by Engeholm, Maik 06 Oct '21

06 Oct '21

Hi there, I'm trying to superimpose two models from inside a python script and get back the transformation matrix. I know I can do something like chimera.runCommand("match #1 #0 showMatrix true") but then the matrix is written to the ReplyLog. (Of course I could save the ReplyLog and then read it in from my script to access the matrix, but that seems quite cumbersome.) Is there a better way to do this? Cheers, Maik

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Blast PDB in Chimera version 1.15
by Feixia Chu 06 Oct '21

06 Oct '21

Hi there, I am teaching a Protein and Function course this semester, and show students how to use Chimera, and integrated Modeller to carry out homology modeling. I use the older version Chimera 1.11.2 and they downloaded current version Chimera 1.15. For some reason, when they use "info" tool and select "blast proteins" in FASTA file window, the Blast query window show blank and never progressed. I don't have any the problem with the older version Chimera installed in my old laptop. Can you advise how to process from here? Thank you! Feixia _________________ Feixia Chu, Ph.D. Associate Professor Molecular, Cellular & Biomedical Sciences University of New Hampshire 46 College Road Durham, NH 03824

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Chimera-users October 2021