- Chimera-users - RBVI Mailing Lists

Showbox
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 03 Nov '21

03 Nov '21

Hi, I know that the program showbox is related to Dock, but I can't find a mailing list still active for Dock users... Maybe someone could help me here. I don't understand if ligands that are docked inside the binding site can exit in part from the box the user defines for grid calculation. I think that maybe if sphere centers are very near the boundaries of the box, it could be possible, but I'm not sure. Does anyone know it? Thanks and regards.

2 1

Counting the number of water molecules
by Prathvi Singh 02 Nov '21

02 Nov '21

Hi, Is there a command in UCSF chimera to count the total no. of water molecules in a PDB file? Can we also count, say the total number of alanine residues in a PDB file or any other other residue for that matter? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

Bug Report: Chimera exit abnormally: code 1073741819
by Jyoti Singh 31 Oct '21

31 Oct '21

Dear Sir, I have installed Chimera 1.15 successfully.When I try to open it, a window pops-up and gives an exit code: 1073741819 and it never opens for analysis. Below I have shared the start information and please find the attachment. *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* Kindly do needful. Regards. *Jyoti SinghPh.D. Scholar [UGC-SRF]"Molecular Biology and Biotechnology lab"CPMB DIVISION, GARDEN BLOCK.CSIR - National Botanical Research Institute, Lucknow [UP], 226001, 'INDIA'*

2 1

(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

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…

1 0

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

2 1

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

2 1

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

2 1

Chimera can't be launched
by salar moniri 25 Oct '21

25 Oct '21

2 1

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

3 2

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

2 2

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> "

2 1

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

2 2

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

4 8

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

2 1

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

2 2

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

2 1

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

2 2

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

3 2

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

2 2

Atomistic Simulation Center - Invitation to virtual inauguration symposium
by Harald Lanig 04 Oct '21

04 Oct '21

1 0

Error to run chimera remotely on a GPU computer from Mac computer
by Zongli Li 30 Sep '21

30 Sep '21

Dear listers, I ssh with "-Y" from my Mac desktop to a GPU computer and process my data there. Quite often I need to look at the 3D volumes with chimera. This had been working nicely for long time. But all suddenly it stopped working and game the error 3: X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1400 Current serial number in output stream: 1400 Did anyone encounter the same error? Any suggestions or tips to overcome this problem would be appreciated. Thanks, Zongli

4 3

Surface exposed residue in a protein assembly
by Alessandro Strofaldi 30 Sep '21

30 Sep '21

Dear Chimera developers, I’m working on a protein complex and I’d like to analyse the SASA and hydrophobicity on the surface. I have worked with Chimera before so I know how to do those basic tasks for a monomeric protein; however, since I have five monomers interacting together I was wondering how to calculate the SASA (and later showing the hydrophobic residues of the surface) excluding the monomer-monomer interfacial regions. I would also need those values tabulated to show hydrophobicity vs primary sequence but still excluding the monomer-monomer interfaces! It seems like there is no basic tool to do that (or am I missing something?); is there any procedure I could apply? Unfortunately I can’t code in Python so I’m looking for a solution that involves using the GUI. Thank you, Best regards, Alessandro Strofaldi, PhD University of Bristol

2 1

Select model based on its position and orientation
by Yu Zhou 29 Sep '21

29 Sep '21

Dear all, I tried global docking of two proteins and ended up with hundreds of possible poses. Is it possible to automatically select the poses based on the position and orientation of one partner, for example, the ones in which the ligand protein is close to the transmembrane region of the receptor protein and oriented with its N-terminus on the extracellular side? Thanks Yu Zhou

2 2

questions
by ARLEY REY PAEZ 29 Sep '21

29 Sep '21

Best regard, My name is Arley, I am a postgraduate student at the federal university of Lavras, Brazil. I write this message because I have doubts about how to calculate the RMSD between two ligands after docking and redocking. My question is if Chimera works well to perform that calculation, since when for example I have two structures (ligands) that are, visually well superimposed and I calculate the value of RMSD with the use of the rmsd # 0 # 1 command, their value is high when compared With a structure that is not visually superimposed, why does that happen? Is it that chimera is not useful to carry out this task? I appreciate you can help me with that concern. Att; Arley -- Este e-mail foi enviado por um estudante da Universidade Federal de Lavras (UFLA). Caso esta mensagem possua algum conteúdo não apropriado, favor desconsiderá-la.

2 2

Crashes during Dock Prep
by Justin Trickett 27 Sep '21

27 Sep '21

Hello, I am prepping 43 structures for docking using the "Dock Prep" feature in Chimera 1.15, and it crashes every time it gets to "Retrieving rotamers from Dunbrack library." Am I doing something wrong? Many thanks, Justin -- Justin Trickett Graduate Student College of Pharmacy, University of Rhode Island (603) 505-1061

2 1

question on protein structure change after matchmaker (position-change) operation
by Lei Qian 27 Sep '21

27 Sep '21

Dear users, After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001). Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation? Thanks! Lei

2 2

Running 3D-FSC script causes freeze
by Oliver Clarke 23 Sep '21

23 Sep '21

Hi, Running the chimera command file included with the example data for 3D-FSC (https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/C… <https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/C…>) causes the latest daily build of Chimera to freeze - it executes lineplot.py, but then just locks up and does not respond. This happens whether I run it as `chimera 3DFSCPlot_Chimera.cmd` or load the command file after opening the GUI. Am I doing something wrong, or has something changed in Chimera that has broken this script? Cheers Oli

2 1

Connecting ends of a peptide
by Nicole Ostrovsky 22 Sep '21

22 Sep '21

Hello, I am trying to connect two sides of a peptide together to make it cyclic. Is there a way to do this that doesn't involve adding in another amino acid? I have been adding a glycine by individual atom using the modify structure tool but I'm wondering if I can do it a different way. Best, Nicole Ostrovsky

2 2

Visualize chain break in Chimera
by Yu Zhou 22 Sep '21

22 Sep '21

Dear all, I am going through a Rosetta protein-protein docking tutorial using Chimera as the structure viewer. There is a chain break in the structure used for this tutorial (3gbn), which is caused by a severed connection between residue 127 and 128. Such chain break needs to be identified and fixed in a structural model before it could be used for Rosetta simulation. This chain break can be easily identified in Pymol as it is displayed as a dotted line. However, I cannot see this chain break in Chimera (and ChimeraX) as the segment is rendered as a beta-sheet. Is there a way to visualize such chain break in Chimera? Thanks, Yu Zhou

2 2

question about label chain?
by 朱玉威 22 Sep '21

22 Sep '21

Dear developer， Could you kindly tell me how to label each chains. I need it to make a movie. Thank you very much. Best wishes!

2 1

How to sequentially open PDB files using a "for loop" in the UCSF chimera's command line?
by Prathvi Singh 18 Sep '21

18 Sep '21

Greetings, Is it possible to use a "for loop" in the UCSF chimera's command line to open a PDB file, perform an action (say delete an atom), save the PDB file & close it, open the next PDB file, perform the same operation, save it & close it and so on. Thanks, Prathvi

2 2

Setting Default Colors
by joshloecker＠icloud.com 16 Sep '21

16 Sep '21

Hello, I have recently started using Chimera and I am having a problem setting a default color when starting a session (if this is possible). When I open a model, it opens in a tan color, which I like because it is easy to pick out other molecules, such as SO4, etc. However, when closing the session and opening the same model, it opens in a variety of other colors, such as bright red, pink, purple, orange, etc. that are distracting to what I am trying to do. I have found the section in Preferences > New Molecules to not use a new color for each model, but then if I load multiple models I cannot distinguish between them. I was wondering if it was possible to set a default color to open models in, or if I have to quit Chimera each time I open a single model in order to get the easy-to-see tan color? -- Thank you, Josh Loecker

2 2

Question about using Chimera
by Zhuangwei Zhang 16 Sep '21

16 Sep '21

Hello, Dear Chimera developers， I encountered some problems when dealing with complexes of peptide-protein docking，Chimera could not correctly recognize the peptide as a single ligand, but recognized the peptide as model 2 and the receptor protein as model 1. Like this: I would appreciate it if you could help me answer this question. Thank you. Zhuangwei zhang Zhejiang Oeacn University

2 3

local docking
by Yanhe Zhao 08 Sep '21

08 Sep '21

Greeting, I tried sequential fitting to fit 3 models to my maps. I was wondering that if I want to fix one model and do local fitting of another models with limited shift and rotation, what command with options should I use? Thanks and regards, Yanhe

3 3

Fwd: Split, Crash out
by Tom Goddard 07 Sep '21

07 Sep '21

MJ reports that rebooting the computer fixed the Chimera crashes. > Begin forwarded message: > > From: Jeremy Jin > Subject: Re: [Chimera-users] Split, Crash out > Date: September 5, 2021 at 10:28:02 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu>, Tom Goddard <goddard(a)sonic.net> > > Hi Elaine adb Tom, > Sorry to bother, I tried again today, it worked, seems something wrong with my system or reboot several times works. I am also will try ChimeraX! Thanks! > > Best Regards! > MJ > > MJ, Mingliang Jin > Postdoc of Yifan Cheng’s Lab > Genentech Hall, UCSF Missionbay > Main Email: m.jin(a)msg.ucsf.edu > Tel: 415-2835-171 > > > >> On Sep 3, 2021, at 12:53, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi MJ, >> >> Most Chimera crashes are caused by graphics driver bugs. Updating your graphics driver is the usual fix. You might try our newer program ChimeraX. We have only done basic maintenance on Chimera for the past 5 years. ChimeraX does a better job reporting diagnostics if a crash happens. >> >> Tom >> >>> On Sep 3, 2021, at 12:26 PM, Jeremy Jin via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi, >>> >>> When I use chimera, I want to split a mode, as long as I split, the software just crashes out. >>> >>> It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command. >>> >>> Best Regards! >>> MJ >>> >>> MJ, Mingliang Jin >>> Postdoc of Yifan Cheng’s Lab >>> Genentech Hall, UCSF Missionbay >>> Main Email: m.jin(a)msg.ucsf.edu >>> Tel: 415-2835-171 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

1 0

Copy protein orientation
by SANDOVAL, KENNETH 06 Sep '21

06 Sep '21

Hello, I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following: 1) Identify orientation of protein A in session 1 2) Copy that orientation 3) Apply that orientation to protein A in session 2 4) Have protein B in session 2 remain aligned to protein A despite the new orientation Thank you, Kenneth Sandoval

3 8

Split, Crash out
by Jeremy Jin 03 Sep '21

03 Sep '21

Hi, When I use chimera, I want to split a mode, as long as I split, the software just crashes out. It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command. Best Regards! MJ MJ, Mingliang Jin Postdoc of Yifan Cheng’s Lab Genentech Hall, UCSF Missionbay Main Email: m.jin(a)msg.ucsf.edu Tel: 415-2835-171

3 2

matchmaker for more than one chain
by manikandank 02 Sep '21

02 Sep '21

Hi ChimeraX-users, I have used recently the mmaker cmd to align two pdb each have multiple chains as below. mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true But the sequence view shows only the alignment of chain L and S. 1. I would like to have aligned sequences of all chains used in mmaker alignement. 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb? 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb? 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name. [similar to 'Edit sequence name' in the sequence viewer in chimera] Please let me know how this can be done. thank you very much with kind regards Mani.

2 1

Ribbon scaling in a script
by Esser, Lothar (NIH/NCI) [E] 01 Sep '21

01 Sep '21

Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks, Lothar Dr. Lothar Esser National Institutes of Health 37 Convent Dr. Rm2122B Bethesda, MD 20892

3 6

Re: [Chimera-users] Making oligomers from Alphafold predictions
by Tom Goddard 01 Sep '21

01 Sep '21

Hi Tiru, If the center of symmetry is at 0,0,0 for your model and it just needs 6 rotated copies placed use Chimera command sym #0 group c6 where #0 is the model number of your monomer. If you do not know the center of symmetry or how the monomers interface with each other (ie their orientation in the hexamer), then that is a protein-protein docking problem and the sym command does not solve that. For that case you would need to fit in a cryoEM or X-ray map of the hexamer, or align the monomer to a known homologous hexamer, or find some amazing oligomeric structure prediction tool. Tom > On Sep 1, 2021, at 11:24 AM, Tiru Hcu <tiru.hcu09(a)gmail.com <mailto:tiru.hcu09@gmail.com>> wrote: > > Hi Tom, > > Thank you for your response. My protein symmetry is a hexamer. Please would you mind sharing a little elaborate how to to do in chimera. Thank you. > > Best regards, > Tiru > > On Wed, 1 Sep 2021, 21:10 Tom Goddard via Chimera-users, <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: > Hi Smith, > > Do you know the symmetry of the oligomer you are trying to make? Is it just a matter of applying positions that you already know? Or do you need some computational protein-protein docking to figure it out (a vastly harder problem)? If you know the symmetry you want the Chimera and ChimeraX sym command can place copies of a structure using standard symmetries or a list of position matrices (rotation + translation). > > tom > > >> On Sep 1, 2021, at 1:29 AM, tim smith via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >> >> Thank you, Elaine and Kevin, for your response. >> The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry. >> >> Thank you. >> >> Best >> Smith >> >> On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude(a)stanford.edu <mailto:kjude@stanford.edu>> wrote: >> Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server >> >> https://rosie.rosettacommons.org/symmetric_docking <https://rosie.rosettacommons.org/symmetric_docking> >> -- >> Kevin Jude, PhD (he/him/his) >> Structural Biology Research Specialist, Garcia Lab >> Howard Hughes Medical Institute >> Stanford University School of Medicine >> Beckman B177, 279 Campus Drive, Stanford CA 94305 >> Phone: (650) 723-6431 <tel:%28650%29%20723-6431> >> On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >> Hi All, >> Apologies for the nonrelated question!! >> >> Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you >> >> Best >> Smith >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

1 0

Making oligomers from Alphafold predictions
by tim smith 01 Sep '21

01 Sep '21

Hi All, Apologies for the nonrelated question!! Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you Best Smith

4 4

Capture click event
by jeni_zen2004＠yahoo.co.in 30 Aug '21

30 Aug '21

Hi, Is there a way to capture the Chimera click event or a way to work around?I'm trying to do something from python code like., when a user clicks on a residue, it pops up a tooltip or shows the centroid. Thanks,Catherine

2 1

ITasser model looks different once PDB opened in UCSF Chimera
by Athena Andreosso 25 Aug '21

25 Aug '21

Hi, I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page - it had less beta strands. When I clicked on model 2 it was better but there's still a visible discrepancy. Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ? Any help is appreciated. Cheers Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso(a)qimrberghofer.edu.au<mailto:AthenaAndreosso@qimrberghofer.edu.au> | www.qimr.edu.au<http://www.qimr.edu.au/> 300 Herston Road, Herston QLD 4006

2 4

3D Visualization
by Song, David 25 Aug '21

25 Aug '21

Hi, My name is Dave Song, and I am a graduate student interested in visualizing protein structures in 3D. I was wondering if you had any recommendations in regards to computer hardware requirements for maximum performance while using Chimera/ChimeraX. Additionally, do you have any suggestions on monitors and 3D glasses that work well with Chimera? Thank you for your time, and I look forward to hearing from you. Best, Dave

2 1

Chimera not responding
by Pritam Dey 23 Aug '21

23 Aug '21

Cannot execute 'gzip': no automatic decompression of .Z files Return code: -1073741819 Press return or enter to to exit

2 1

Hollow Sticks When Exporting as STLs?
by Josh Moon 17 Aug '21

17 Aug '21

Hello, I hope to make this question as direct and simple as I can! When I export a scene of a molecule displayed as a ball-and-stick as a STL, I find that many of my "stick" portions are hollow. This creates thin, weak walls for 3D printing. I've included a screenshot of an intended plane cut from Meshmixer so that you can see the internal structure. What am I doing incorrectly? Is there something I can do in Chimera to export a solid object with no "hollow tubes." Fixing this with 3d programs can be time consuming. Sincere thanks, Josh ----------------------------------------- Josh Moon, Ph.D. (he/him/his) Educational Technology Specialist Kalamazoo College (269) 337-7415

2 1

Fc dimer fall apart after fusion with a GS linker
by tiger wang 16 Aug '21

16 Aug '21

Dear Ms/Mr helper: I encounted an issue when I try to fuse one (G4S)x linker to one of the Fc "C" terminal using "join bond". Once selected the "C" atom on Fc C terminal and "N" atom on (G4S)x N terminal and hit "apply" button, the Fc dimer fall apart but the (G4S)x linker was connected to the C terminal of Fc. How to avoid the Fc dimer from falling apart? Thanks very much for your help Sincerely TW

2 1

How to get random velocities?
by Seera Suryanarayana 11 Aug '21

11 Aug '21

Dear chimera users, Dear VMD users, I was asked to do simulations five times with the same starting structure and number of processors. But the velocities should be different. Here my query is "How do you generate velocities in the gromacs?". I request you to guide me how to do it. Thanks in advance Surya Graduate student India.

2 2

Problems with installing on a Windows 10 expedition Dell laptop
by Alice Chen 10 Aug '21

10 Aug '21

Hello, I'm on a Dell XPS 9500 laptop running Windows v. 10.0.2.1000. When my IT specialist tried to install it, it would run the install program but at the very end the install would fail. We were able to install the old non-X version of Chimera. Is there something we should/can do to check, settings-wise? Cheers-Alice Kitterman Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com

3 9