- Chimera-users - RBVI Mailing Lists

Solvation question
by Noriega, Heather 10 Nov '21

10 Nov '21

Hello, I have a quick question. I am running the solvate command before the minimization, equilibrium, and production run in Chimera. I click the start solvate tool and put my water box size and apply. This gives me my box and in the command line it says created...with however many water molecules. I then go run parameters, set up everything. Once I hit run, the water box dissappears. I just want to make sure that the solvation did occur even though the water box dissappears from the screen. Everything else ran smoothly to show simulation. I just want to be certain and have confirmation that the solvation does occur as long as I use apply and do not close out of the window. Thanks in advance for your help. Thank you, Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega(a)bison.howard.edu 520-203-1883

3 4

Writing data to a text file
by Prathvi Singh 09 Nov '21

09 Nov '21

Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 4

the version of Ambertools that are used in the command "Write prmtop"?
by Victor Nazarychev 08 Nov '21

08 Nov '21

Dear Chimera's users, I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release? Best regards, Victor

2 6

Chimera Laucher Error
by Paulo Roberto da Silva Santos 08 Nov '21

08 Nov '21

Hi, I was intalated Chimera 1.5 64bit under Windows 10 64 bit, I was intalated Chimera 1.5 64bit under Windows 10 64 bit, and all was fine until I started executed, Chimera crashed and now it gives me an error at launch and quits, so I cannot run it anymore. After launch, the error window shows: -------------------------------------------------------------------------------- Chimera exited abnormally; the exit code was: -1073741819. Use the --debug command line option for the full error message. -------------------------------------------------------------------------------- Paulo Roberto da Silva Santos Bacharel em Química - UFPB Mestrando em Química - UFPB LCCQS - Laboratório de Compostos de Coordenação e Química de Superfície (83) 99915-5963

2 1

error while running chimera
by Saniya Kate 03 Nov '21

03 Nov '21

Good evening, i am Student and Installed chimera for WINDOWS (chimera-1.15-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…>) from your website but I am unable to run it on my system since it is a 64 bit release and my system is 32 bit. I urgently need chimera for my project work but I'm not able to use it since the 32 bit release of chimera isn't available. please let me know what can be done

2 2

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 01 Nov '21

01 Nov '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 30 Oct '21

30 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 13 Oct '21

13 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 01 Oct '21

01 Oct '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 24 Sep '21

24 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 09 Sep '21

09 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 26 Aug '21

26 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

How to recreate point of view
by achatz 06 Aug '21

06 Aug '21

Hello, I have two Chimera sessions which originate from the same pdb. Through rotations and movements the sessions viewpoints diverged over time. Is there a way to synchronize one session with the other so it has the exact same viewing angle? Thanks Stefan

2 1

Question about peptide connection
by Nicole Ostrovsky 27 Jul '21

27 Jul '21

Hello, I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this. Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool? Thank you. Nicole Ostrovsky

3 6

Changing DNA sequence
by Tom Goddard 26 Jul '21

26 Jul '21

Hi Gary, The swapna command lets you change a nucleic acid base, for example, to change residue 18 in chain C from a T to a G use open 1rsb swapna G :18.C Documentation for swapna https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html> Tom > On Jul 26, 2021, at 1:31 AM, <gren(a)lbl.gov> <gren(a)lbl.gov> wrote: > > Dear Tom > Thanks for many answers to our previous questions. > > I have one more question to our loved Chimera program. > > I have a NDA model (PDB), but the sequence is not right. Is there any way to use this DNA model to generate a new model with a right order of sequence? In other word, if is there an automatic/ simple method (by comment lines) to replace the sequence by the correct one in Chimera? > > Thanks a lot!! > Gary > > > Gang (Gary) Ren, PhD > Lawrence Berkeley National Laboratory > Molecular Foundry, Room: 2220 > 1 Cyclotron Road, MS 67R2206 > Berkeley CA 94720-8197 > Phone: (510) 495-2375; Fax: (510) 486-7268 > Email: gren(a)lbl.gov <mailto:gren@lbl.gov>; > https://rengroup.lbl.gov/ <https://rengroup.lbl.gov/>

3 2

Query: Saved pdb doesnt have mutated residue
by ZUNERA JAMAL 26 Jul '21

26 Jul '21

Respected Chimera team! I have a pdb file in which i have done mutation by using swapaa command in IDLE python but once i saved the structure then new saved structure doesn't have mutated residues in it. commands: 1.rc("open filename.pdb") 2.rc("swapaa val #0:2.a") 3.new_file_name="val.pdb" 4.rc("write format pdb #0 C:\\Users\\folder" + new_file_name) 5.rc("save newsession") 6.rc("close session") 7.rc("close all")

2 2

color pdb based on rmsd
by manikandank 21 Jul '21

21 Jul '21

Hi Chimera-users, I have aligned three pdbs using MatchMaker and would like to color one based on rmsd (per residue or per CA atoms). I see that i can use 'rmsd' to calculate CA-CA distance between two models, but i would like to write the distance difference in a file so that the file can be read in 'attribute' coloring scheme. Please let me know how to do this. thanking you with kind regards Mani.

2 1

Doubts about DOCK6.9 and ZINC20
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 20 Jul '21

20 Jul '21

Hi, I’m a student and I’m currently doing a thesis. I’ve never used Dock or Chimera before, so I followed some tutorials but now I’m a bit confused. 1. For five months I’ve saved the prepared receptors and the ligands as mol2, but I didn’t choose “write current selection to @SETS section of file”. I’ve just read on Chimera that it “makes the currently selected atoms as a SET (as used to specify the rigid portion of a ligand in DOCK)”. The docking I’ve performed seemed to go, but is actually everything wrong because I didn't select the option? 2. I’ve generated the receptor without hydrogens after dockprep (so after assigning charges and hydrogens). I’ve deleted only hydrogens but maybe the charges are still there, is that an error? 3. I’ve always saved the receptor without hydrogens in mol2 instead of pdb, because I’ve seen this in some tutorials, but now I’ve read tutorials that save it in pdb. Is this another error? I was able to generate the surface even with mol2 no hydrogens receptor and I’ve always toggle on “use untrasformed coordinates”, but obviously the options to save the file change for mol2 and pdb. 4. I follow a tutorial online to download 3D molecules from ZINC20. Anodyne means there are no PAINS and no reactive groups? Is the most “clean” reactivity pattern? 5. I don’t know how to organize all the directories and subdirectories downloaded with ZINC. I downloaded them in format mol2 and method curl, is that correct or shoul I use fot the virtual screening another format and method? To perform a virtual screening, I need to save them in a single mol2 file? How can I do that without errors? I've seen the option "flat" in downloading method in ZINC, is this a way to download the molecules correctly for virtual screening? 6. I need to use Chimera, but even with ViewDock I’m not able to open so many molecules (190 822), how can I look at the results in the end? 7. I’ve saved the ligands’ mol2 files using sybyl-style hydrogen naming. Is that an error? 8. To perform the virtual screening using 3D molecules from the tranche browser of ZINC20, can I use them as they are or I need to edit them in some way (for example after downloading them, open them in Chimera and using add H and/or add charge)? I need very specific indications about all these questions, because I’ve never done something similar, it’s the very first time with all and I’m afraid of making mistakes. I apologize for the many questions, but I hope that someone can answer all my doubts. Thank you, Francesca.

2 1

Help: Suitable graphic driver
by Nur Nadia Razali 20 Jul '21

20 Jul '21

Hi, I am Nadia, I am a newbie for Chimera UCSF. When I started using Chimera, fetch under uniprot search, the message popped up. [image: image.png] I really need you help regarding this. Is it the issue of graphic card? Could you suggest what is the suitable driver for me to buy. I do have this kind of problem with other software that requires me to have the driver. Thank you, Sincerely, Nadia *ChM. NUR NADIA BINTI RAZALI* Science Officer UKM Medical Molecular Biology Institute (UMBI) *p:* +603-91459187 *f:* +603-91717185 *w:* www.ukm.my/umbi *e:* nadiarazali(a)ukm.edu.my <azrulhisham(a)ukm.edu.my> *a:* Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, MALAYSIA. -- *PENAFIAN*: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat, rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Kebangsaan Malaysia (UKM) adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. _*DISCLAIMER *: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of The National University of Malaysia (UKM) shall be understood as neither given nor endorsed by any of the aforementioned._

2 2

Minimization troubleshooting
by Nicole Ostrovsky 19 Jul '21

19 Jul '21

Hello, I am trying to perform minimizations on some structures I'm examining and each time the minimization is done and I open the reply log, the gradient norm says "-nan" and it tells me that no atoms were updated. I wasn't able to find anything online about how to fix this, so I'm emailing to ask if anyone would know how to troubleshoot this. Thank you. Nicole Ostrovsky

2 1

Blast protein webservice error
by Stefan Dobrev 14 Jul '21

14 Jul '21

Hello! I'm trying to run a homology model on a protein sequence using BLAST, but my Blast: query window shows up empty. At first I got this error in the reply log: File "C:\Program Files\Chimera 1.15\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info import replyobj ImportError: No module named replyobj I solved it by changing the code to "from python import replyobj". Now I can actually see what the error is. A few more functions are called until we get to this: File "C:\Program Files\Chimera 1.15\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) error: [Errno 10054] An existing connection was forcibly closed by the remote host I've allowed chimera through the firewall and I have a modeller license key, I believe I've entered it somewhere in Chimera at some point. Any ideas what might be causing this? Thanks for any advice, Stefan Dobrev

2 1

Flipping the map - resolution question
by Dmitry Semchonok 14 Jul '21

14 Jul '21

Dear colleagues, I heard that flipping the map in Chimera with the command vop zflip # will decrease the resolution of the map https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes> Did I understand that statement correctly? If yes, how to flip the map without losing the quality (resolution)? Thank you Sincerely, Dmitry

2 5

Running/opening issue of chimera on HPC login node
by Rajiv Ranjan Singh 14 Jul '21

14 Jul '21

I am trying to open/run chimer; installed on a cluster login node without root privilege. Installed in Home//.local/UCSF-Chimera64-1.15rc/ Getting the following error. *login1:*~/.local/UCSF-Chimera64-1.15rc/bin $ ./chimera libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 152 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 716 Current serial number in output stream: 717 Kindly advise me to rectify this issue. Best, Rajiv Ranjan Singh

2 2

unable to open more than one map in Chimera
by Merk, Alan (NIH/NCI) [C] 12 Jul '21

12 Jul '21

Hello, I recently updated to Catalina on my Mac and I am now not able to open more than one file at a time in Chimera. Uninstalling the program and then installing the latest version from scratch did not fix the problem. Is there any way to resolve this issue? Alan

3 4

Users group
by Zachary Morton 09 Jul '21

09 Jul '21

Hi, My name is zach morton, I am from UC Santa Cruz and I would like to be added to the user group please. Best, Zach

2 2

WebGL file
by Avnam Ohri 06 Jul '21

06 Jul '21

Hello Chimera Team i have been trying to make a script for looping through a set of pdb files and get WebGL (.html) file as the output import os import chimera import Midas from chimera import exports from chimera import runCommand as rc # use 'rc' as shorthand for runCommand # change to folder with data files os.chdir("E:/files to work/") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: rc("open " + fn) rc("ac wb") rc("ac c2") htmlname = fn[:-3] +'.html' exports.doExportCommand("WebGL",htmlname) rc("close") This is the code I have been using in the script , but the output i get is not working , i have been getting 26kb files instead of 3-5 mb files and it doesn't show anything when I open it. can you please help me with the same as i am new to python code

1 0

Volume subtraction of surface area between homology model and template
by Kovacs, Nicholas (CDC/DDID/NCIRD/ID) 06 Jul '21

06 Jul '21

Hello, I have a homology model that I have made and I would like to create a visual that portrays small surfaces where there is change in the solvent accessible surface area of the homology model compared to the template structure. I am trying to use the "subtract" map from map calculation which requires volume data for the 2 structures. I have tried the following to generate volume data and then subtract the volumes, but I am getting hundreds of small surfaces all throughout the area of the molecule: molmap #1 3 molmap #2 3 volume subtract #3 #4 I know molmap is likely not the command I want to be using since I am interested in the solvent accessible surface area but I have yet to find a command that will generate a volume corresponding to the volume enclosed by the solvent accessible surface area. I would greatly appreciate it if someone could help me find a way to create 2 volumes enclosed by the solvent accessible surface area of the 2 structures in addition to correctly configuring the "volume subtract" command to get my desired output. Thank you, Nick

3 3

Webgl, python script for multiple pdbs
by Avnam Ohri 06 Jul '21

06 Jul '21

Hello Chimera Team i have been trying to make a script for looping through a set of pdb files and get WebGL (.html) file as the output. import os import chimera import Midas from chimera import exports from chimera import runCommand as rc # use 'rc' as shorthand for runCommand # change to folder with data files os.chdir("E:/files to work/") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: rc("open " + fn) rc("ac wb") rc("ac c2") htmlname = fn[:-3] +'.html' exports.doExportCommand("WebGL",htmlname) rc("close") This is the code I have been using in the script , but the output i get is not working , i have been getting 26kb files instead of 3-5 mb files and it doesn't show anything when I open it. can you please help me with the same as i am new to python code

2 1

Error in using chimera with structureviz2 and cytoscape
by SRUTHI NAMBIAR 30 Jun '21

30 Jun '21

Dear all, I have been using chimera for the past 1 year and recently wanted to club it along with the cytoscape software. But whenever I try to launch chimera through the structureviz app, I get the following message: Error message: Cannot run program "/home/students/chimera/": error=13, Permission denied I have changed the settings of structureviz to give the path of chimera which is /home/students/chimera. Still this error is occurring. Could someone help regarding the same? Thank you. Regards, Sruthi

3 2

how to calculate RMSD
by Elaine Meng 30 Jun '21

30 Jun '21

> On Jun 30, 2021, at 7:19 AM, lufeiyu(a)jlu.edu.cn wrote: > > Dear Sir/Madam: > > I have a question about the analysing of the docking. I docked a peptide to the receptor using GALAXYpepDOCK. The results uncontained the scores of RMSD. Some literatures reorted the UCSF could calculate the RMSD. But I didn't get the way after reading the tutorials. Please help me to figure out how to obtain the RMSD of a docking structure .Thanks vwry much. Best wishes for you. > > sincerely yours > Feiyu Lu Dear Feiyu Lu, The chimera-users(a)cgl.ucsf.edu address is recommended for asking questions about how to use Chimera. I CC'd it here, so you do not need to send your question again. (Or if you are using ChimeraX, you should use chimerax-users(a)cgl.ucsf.edu in the future for asking questions.) An RMSD measures the difference between two different locations of a set of atoms. So in Chimera you would need to open not only the docking results, but also the position of that peptide that you want to use as reference to calculate their RMSD. Then, you can use the "rmsd" command to compare them. I cannot give an exact command since I don't know the model numbers you will have, but an example if you had the comparison peptide open as model #3 and the docking result models are #1.1, #1.2, #1.3 ... then your commands could be: rmsd #3 #1.1 rmsd #3 #1.2 [...] See rmsd command help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> The results would be shown in the Reply Log (open from Favorites menu). Also if you don't know what model numbers you have, look in the Model Panel (also can be opened from the Favorites menu). Model Panel help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Join models function on Chimera
by Azad, Roksana 29 Jun '21

29 Jun '21

Hi There, I hope you are doing very well. My name is Roksana Azad, I am a Ph.D. Student at the CUNY ASRC. I have been working on building a full length model of my protein into a cryoEM map, I have models for individual domain but not for the full lenght structure. I am trying to join the domain models using chimera "join models" function, but unfortunately it's not working for me. I tried everything I could find online about the issue, I used the addh command and kssdssp commands and also tried joining them using other bond instead of C-N, however my button for "apply" always grey and I can't click on it (please see the screenshot attached). I also tried this command "#0:127.A@C #1:1.A@N" according to my model # and atom, but its not selecting anything for me. I tried "combine" it also didn't work.? Please let me know if there is something else I am missing or what else I can do to create this bond or connection between two models. Thank you so much for your time and help in advance - very much appreciated. Sincerely, Roksana ________________________________ Roksana Azad<https://asrc.gc.cuny.edu/people/roksana-azad/> Ph.D. Candidate in Biochemistry & Biophysics Advisor: Kevin H. Gardner<https://kglab.ws.gc.cuny.edu/> Structural Biology Initiative; CUNY Advanced Science Research Center 85 St Nicholas Terrace * New York * NY * 10031 Phone: 212-413-3233 Email: razad(a)gc.cuny.edu

2 1

Stuck in adding residue in the C-terminal of a segment
by Prathit Chatterjee 29 Jun '21

29 Jun '21

Dear Experts, This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA. I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO. I followed the tutorial and have given the following command in command line: addaa ala,101 :100.d The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D. Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D. Thank you in advance, Regards, Prathit Chatterjee

2 4

how to know the net charge of my system
by Sara Luz Gomez Maya 29 Jun '21

29 Jun '21

Dear all, I'd like to know if there is a way to know the net charge of a system when opening the pdb file with Chimera. If so, is it possible to do it by means of the command line? Thanks in advance, Sara

2 2

same chain id while saving large coordinate files
by manikandank 28 Jun '21

28 Jun '21

Hi Chimera-users, Chimera 1.15 (build 42258) puts same chain id for all protein chains present in the pdb during 'save pdb/write pdb' . I am using it in linux Ubuntu. Please help. thank you with kind regards Mani.

2 4

Modeller..Waiting for the Opal server
by Hernando J Sosa 26 Jun '21

26 Jun '21

Dear Chimera, Today when trying to use Modeller through the Chimera interface (via web service) the program either stays forever in Waiting for the Opal server or produces a whole bunch of errors. Trying to run Modeller through the local installation also results in errors. Not sure if the problem is with Chimera or Modeller but one day ago Modeller&Chimera were working fine with the same input files that now are causing the errors (???). Thanks Best Hernando

2 2

multi align viewer
by Jacqueline Vitali 25 Jun '21

25 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

2 4

multialign viewer
by Jacqueline Vitali 24 Jun '21

24 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

1 0

Regarding problem 'During selection from the graphics window (picking)'
by Dr. Abhay Nanda Srivastava 20 Jun '21

20 Jun '21

Dear Team Chimera, I am using Chimera software in Windows 7, 32 bit computer for viewing Swiss dock prediction results. But, when I try to select the residue or atom in model by using mouse and keyboard button (Ctrl+button 1), no selection is displayed, even hand like cursor seen on the graphics, I am also not able to see the residue or atoms labeling by putting cursor on model. For my confusion removal, I have downloaded and installed the software on another computer of Windows 7, 64 bit. But here also, the same problem persists. Please suggest to me, how to get rid of this problem? Looking forward to hearing from you. Thank You. *Regards,* *Dr. Abhay N. Srivastava* * M. Sc. (Chem.), Ph. D. Head & Asst. Professor,* * Department of Chemistry,* * NC-BRA Bihar University,* * Muzaffarpur-India.* * Contact: +91-9990576112*

2 1

Question regarding the chimera Transform Coordinates feature
by Ritwik Jain 19 Jun '21

19 Jun '21

Respected developers of chimera, I am currently doing a research project related to Cryo-EM map alignment in which I need to use Chimera. Chimera has a feature which transforms the coordinates of a molecule (Img1.jpg) . That feature has an option to move atoms instead of coordinate axes (Img2.jpg). If I uncheck that box and transform, the model just reverts back to its original position after saving and reopening. I was wondering if there was a command line command for the " move atoms instead of coordinate axes " option. I have tried all the move commands ( https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html) and they don't seem to work. I expect your reply soon. Sincerely, Ritwik Jain

2 3

chimera installation problem
by Monojit roy 18 Jun '21

18 Jun '21

sir, please help

2 1

AddH on N atom in N-terminal
by 陈恩博 17 Jun '21

17 Jun '21

Hello. When I use addH to add H atoms on N atom in N-terminal of Peptide chain, I find 3 H were added on this N. Why the addH result is C-NH3 and not C-NH2? Thanks!

2 2

color maps based on real space cross correlation
by manikandank 16 Jun '21

16 Jun '21

Hi Chimera-users, I have aligned two cryoEM maps at certain threshold using 'Fit in Map' option in chimera. Now I would like to color one map based on real space voxel correlation values from 'Fit in Map' operation. Please let me know how this can be done in chimera. thank you with kind regards Mani.

2 1

command line: how to add hydrogens to a phosphate group?
by Sara Luz Gomez Maya 15 Jun '21

15 Jun '21

Hi, I have a system consisting of a molecule intercalated into DNA. For a very specific application, I need to remove all the Sodium atoms from a PDB file and, in turn, add hydrogens to all the DNA phosphate groups (whatever the oxygen). Since for chimera that atom type is identified as O3- (possibly resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, N-oxide), I have tried: labelopt info idatmType label #0 addh spec O3- but it did not work. You can find attached herewith the pdb file. Any help is appreciated. Regards, Sara

3 2

Sending Chimera MD job to remote computer
by Cowie, Connor 14 Jun '21

14 Jun '21

Hello, I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password). However, I want to be able to send a command to a remote computer to improve the computational time especially when running multiple MD simulations; right now, I am running MD simulations on the same computer. I was first thinking of a sequence of commands below: Ctrl+Z bg ssh -y username@detroit05 I know that the Ctrl+Z command temporarily pauses a command, but I believe that the jobs command is first needed to list the current running jobs (that Ctrl+Z can be performed on). However, the running jobs are not listed when I type “jobs”. After using the “top” command to list all of the processes, I have verified that the Kill command works by typing these in succession: Kill -STOP PID# Kill -CONT PID# Can you walk me through how to first have a listing of jobs running in Chimera and then sending it to a remote computer? Best, Connor

2 1

getting surface patches
by Diego Amaya 13 Jun '21

13 Jun '21

Hello all, I'm trying to get surface patches of PDB structures in VTK format. So I want to define a patch as the set of atoms within a given radius of a specific residue, build the surface corresponding to that patch and export the result in VTK format. Additionally, I want to do all this with a python script. Here the code I'm trying but doesn't work : *import pychimerapychimera.patch_environ()pychimera.enable_chimera()import osimport chimerafrom chimera import runCommand as rc* *list_resid = [31, 64]* *radius = 3list_pdbs = ['ensayo.pdb']for resid in list_resid: for line in list_pdbs: list_atoms = [] rc('open '+line) rc('sel :{} za<{}'.format(resid, radius)) for a in chimera.selection.currentAtoms(): list_atoms.append('serialNumber=' + str(a.serialNumber)) sel_atoms = ' or '.join(list_atoms) rc('surfcat patch @*/{}'.format(sel_atoms)) rc('surface patch') rc("export format VTK {}_resid_{}_radius_{}.vtk".format(line[:-4], resid, radius)) rc("close all")* Thanks in advance for your help. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

3 6

Minimize hydrogens in water molecules
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 11 Jun '21

11 Jun '21

Hi, I need to minimize two water molecules in the binding site of the protein: I don't want to move the oxygen, so I've selected only hydrogen atoms and then I' ve used the Minimize Structure tool (keeping fixed all atoms that are unselected). I can't do the minimization because there's an error: Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.CYS_394__0_0_1_397__A.N (atom type n) - Atom 0.GLY_393__0_0_1_396__A.peptide.C (atom type C)'' I don't known what this means and what I should do to fix it. I've tried to use the command line, but there's another error. Does anyone have suggestions? Thank you. Francesca

2 3

search a sequence in UCSF chimera
by Xiao Lei 11 Jun '21

11 Jun '21

Dear chimera-users, Is there a way to search a short amino acid sequence (for example: DDDDK) in an openned protein structure in UCSF chimera? Thanks ahead, Xiao

2 2

Removing specific water molecules
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 10 Jun '21

10 Jun '21

Hi, I have a problem using Chimera: I need to delete specific water molecules with a specific residue number, but this number is in common with residues that are useful (such as ligands or co-factors). For example, I type "del :546-893" in the command line in order to delete these water molecules, but I delete also the ligand and FAD and I don't want to. I've read the guide about atom specification, but still I don't know how to do it. Hope someone can help me, thank you. Francesca

3 3

Re: [Chimera-users] [ChimeraX] #4232: RFE: make ViewDockX understand SwissDock output
by Elaine Meng 07 Jun '21

07 Jun '21

Hi Michael, I edited out the details of your files below in case you wanted to keep that private, but am CC-ing the chimera users list recommended for asking questions. Since the Swissdock server only keeps the files for a while, I understand you had to save them locally and now you are trying to modify the Chimera web-data files to use the local files. However, I think you can simplify and no longer use a web-data file, but simply a Chimera command file (see below), since the python stuff was just retrieving the files. In that case you would just insert the local file pathnames into the commands that open them. Just name the plain text file containing the commands something.com and open it with Chimera. The command file (plain text) would contain something like this, of course substituting your actual file locations for "[pathname-...]": open [pathname-of-pdb-file] viewdock [pathname-of-docked-ligands-file] color byatom #0 ribbon #0 repr stick :LIG ~disp element.H hbonds intramodel false lineWidth 5 color green Other than the opening of files, you wouldn't necessarily have to use those same commands, you could customize as desired. Further, you could just type in the commands into the command line one by one instead of making a command file, if that's easier. Chimera command files: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 7, 2021, at 9:04 AM, Michael Weber <weberm(a)posteo.de> wrote: > > Dear Elaine, > thank you for your quick response. > > I have a question: when now trying to use Chimera instead of ChimeraX to analyze my SwissDock output files I noted that the files may only be analyzed as long as the entire data set related to that docking experiment is still available online on the SwissDock website. Fortunately, I had downloaded the entire data sets and stored them locally. > SwissDock delivers some sort of script in which Chimera commands and the required input file locations are stored as follows: > > <?xml version="1.0"?> > <ChimeraPuppet type="std_webdata"> > <web_files> > <file name="target.pdb" format="text" loc="http://www.swissdock.ch/files/tmp/[...other stuff...]/target.pdb" /> > </web_files> > <commands> > <py_cmd> > import urllib > import tempfile > from chimera import runCommand > tmpDirectory = tempfile.mkdtemp() > urllib.urlretrieve ("http://www.swissdock.ch/files/tmp/[...other stuff...]/clusters.dock4.pdb", "%s/clusters.dock4.pdb"%tmpDirectory) > runCommand("viewdock %s/clusters.dock4.pdb \"Dock 4, 5 or 6\""%tmpDirectory) > </py_cmd> > <mid_cmd>color byatom #0</mid_cmd> > <mid_cmd>ribbon #0</mid_cmd> > <mid_cmd>repr stick :LIG</mid_cmd> > <mid_cmd>~disp element.H</mid_cmd> > <mid_cmd>hbonds intramodel false lineWidth 5 color green</mid_cmd> > </commands> > </ChimeraPuppet> > > I thought I might cure the situation by replacing the web locations by the local hard drive file locations, so I modified it as follows: > [... edited out...] > Of course it does not work properly because I don't know what exactly the syntax looks like for solving my problem when working with local files. > I hope it is not asked too much, but could you help me how to fix this? > > Best regards, > Michael.

1 0

command line clustering (how to select a subSection?)
by Laura Morris 04 Jun '21

04 Jun '21

Recently I've been clustering in Chimera but running into memory limitations on my system. I'd like to do the clustering on a computer with more RAM, but I need to be able to do this using only the command line. I found an old post (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html) that includes an example script to do the clustering, but I don't know how to change the subSection to the residues and atoms I want. Here's the portion of relevant code: def main(): import chimera modelList = chimera.openModels.list(modelTypes=[chimera.Molecule]) subSelection = None # Change this to CAs or heavy atoms clusterInfo = _cluster(modelList, subSelection) saveReps(clusterInfo, "reps.pdb") # Change file name if needed The "Change this to CAs or heavy atoms" is exactly what I want to do, but I have no idea how to do it. If this were command line in Chimera, I'd use something like "select #0:3-55@CA". I know there's a "runCommand" function that can be included (using "from chimera import runCommand"). Is this used in some way to set subSelection, and if so, how? Any help is appreciated. Regards, Laura ----- Laura C. Morris Scientific Computing Professional Edison & Prestegard Labs Complex Carbohydrate Research Center 706-542-6286 (lab 1075)

2 5

command question
by Yanhe Zhao 01 Jun '21

01 Jun '21

Good afternoon Elaine and users, I have two questions as to Chimera using as below: 1, how can I plane through and rotate volume at same time? For example how to add rotate options to command "volume #2 planes x,0,42,1; wait 43;"? 2, How I can merge volumes (for example 3 volumes) with their own threshold was kept? Thanks and best, Yanhe

2 1

saving segmented copy of a map
by M.S. Islam 01 Jun '21

01 Jun '21

Hi I was just wondering, is there any way that I can save segmented copy of a map so that I don't have to do segmentation, followed by colouring different segments of the segmented map again and again. Thanks a lot in advance. Saif

2 2

Fwd: Cannot see menus on MacBook Mojave
by Elaine Meng 01 Jun '21

01 Jun '21

> Begin forwarded message: > > From: Eric Werner <evwerner(a)gmail.com> > Subject: Cannot see menus on MacBook Mojave > Date: May 24, 2021 at 9:10:48 PM PDT > > Hi, > > Chimera is great. However in the latest download for the Mac, I can no longer see the menus when in Dark Mode on my Macbook Pro using Mojave. > > In the attached file you can see the the transparent background of the menu drop down list makes it even harder. > > Is there a solution to adjust the menu text and background color and making the menu background opaque? > > Thank you for your help. > > Eric >

3 7

Structure to sequence alignment
by Kamil Steczkiewicz 31 May '21

31 May '21

Dear Chimera community, Does Chimera allow to display multiple protein structures as CA trace, colour corresponding residues in 3d, display these proteins' sequences in alignment window and allow to manually alter the alignment to manually align residues coloured as mutually corresponding (preferably by mouse)? Something like was possible in good old and unfortunately not supported any more Insight program... That's what wraps up to so-called structure-based manual multiple sequence alignment. Essential if you're assessing some highly diversified set of structures and want to have a precise alignment for them. Thanks, Kamil *Kamil Steczkiewicz, PhD* Department of Bioinformatics Institute of Biochemistry and Biophysics Polish Academy of Sciences tel. +48 22 592 *5759 *| +48 668 13 02 13

2 2

Getting the median protein structure after comparing.
by Shradheya R.R. Gupta 30 May '21

30 May '21

Hi, I have two PDB's I compared (superimposed) them using the Chimera tool. But some regions are not superimposed. I want to generate the new PDB which have the superimposed regions coordinates and the median coordinates of the region which is not superimposed. Thank you

2 1

Help needed
by Nirban Dey 28 May '21

28 May '21

Hello, I am a Masters student in India currently using chimera for my thesis. I am facing a problem. I have attached a state file of my docked complex. There some residues 251, 245, 243 formed H bonds with the ligand through the O atom. I am not able to display the residue clearly. O atom is looking like a dot. I want to show the residue clearly making bonds with the ligand without hiding the ribbon like the residue 247. Those residues are clearly visible only if I hide ribbons for that residue. Kindly help me to show the residue properly without hiding their ribbon. Regards Nirban

2 2

Quantify the movement between two domains
by Ahmad Khalifa 27 May '21

27 May '21

Hi, I'm looking for a way to quantify the movement between two domains in my structure. I know I can calculate an RMSD between the same domains in different conformations. I can also generate a distance matrix between the two chains in different conformations. I tried to measure the distance between the two centers of mass of my domains, but the change doesn't really capture the magnitude of the movement, also the same domains are not identical in the two conformations in the sense that one domain is missing so many loops, which will affect the com calculation. What other ways to quantify the distance between two different domains? Thank you.

3 2