- Chimera-users - RBVI Mailing Lists

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

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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

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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

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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.

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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)

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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

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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

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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 >

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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

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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

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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

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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.

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Chimera wont start
by Gmail 26 May '21

26 May '21

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Web services down
by Eric Pettersen 25 May '21

25 May '21

Hi all, Due to computing cluster maintenance starting this evening (5/25) through tomorrow evening (5/26), the web services in Chimera and ChimeraX that use our cluster will be down. The frequently used web services are BLAST and Modeller for both programs, and for Chimera only: sequence realignment via Clustal Omega or MUSCLE; SAXS2; and 2D ligand depiction. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Fwd: Chimera - remote start up issue
by Greg Couch 24 May '21

24 May '21

tl;dr -- VirtualGL worked. -------- Forwarded Message -------- Subject: Re: [Chimera-users] Chimera - remote start up issue Date: Mon, 24 May 2021 13:16:18 +0000 From: Filip Kadlec <Filip.Kadlec(a)vutbr.cz> To: Greg Couch <gregc(a)cgl.ucsf.edu> Good evening, I'm writing to you with feedback since I remembered you wanted to let know if any of the methods worked. I got to it a bit later than expected (sorry for the delay) and let me tell you it was painful indeed. However the final solution was with VirtualGL with Cygwin combination - Installed Cygwin with all tools needef for X11 forwarding, server... including the VirtualGL client. On server installed VirtualGL server. Then using XLaunch (cygwin provides) and setting the right $DISPLAY variable it is possible to run and quite smoothly operate with visualisation programs (vglconnect, vglrun). Chimera, ChimeraX and also PyMOL works just fine. Thank you for the previous help and advice, it pointed me in this direction! Have a great day. Kind regards Filip ------------------------------------------------------------------------ *Od:* Greg Couch <gregc(a)cgl.ucsf.edu> *Odesláno:* pátek 7. května 2021 20:35 *Komu:* Kadlec Filip (191426) <Filip.Kadlec(a)vutbr.cz>; chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> *Předmět:* Re: [Chimera-users] Chimera - remote start up issue Yes, as you discovered, remotely displaying 3D graphics is problematic. Sometimes it works, usually if the graphics driver on the remote computer and the local computer are the same (same manufacturer, same operating system, i.e., same variant of Linux and version). In your case, I'd recommend installing the VirtualGL package on the CentOS 7 computer, along with a graphics card and its driver. That way the 3D graphics are done on the CentOS 7 computer and an image is sent to your computer. VirtualGL is available from the epel repository and virtualgl.org. This is also the solution for nomachine and x2go. An alternative would be to try the free cygwin.org X11 server, or a commercial X11 server, like Exceed 3D. If either of those work, please let us know. Good luck, Greg On 5/7/2021 4:28 AM, Filip Kadlec wrote: > Good afternoon! > > I haven't found a solution to this problem in one of your user > threads, internet and I haven't succeeded resolving the issue. > I have installed chimera 1.15 today and it runs well when working on > the desktop. However, it would be very convenient if I could run > chimera remotely. Chimera is installed on Centos 7, I am trying to > remotely operate this PC with Windows 10 PC using MobaXterm. When I > run chimera as /chimera --debug/: > > initializing general preferences > loading Tix > initializing graphics > create application > loading Pmw > creating main window > creating menus > creating toolbar > creating viewer > initializing OpenGL > X Error of failed request: GLXBadCurrentWindow > Major opcode of failed request: 146 (GLX) > Minor opcode of failed request: 5 (X_GLXMakeCurrent) > Serial number of failed request: 2711 > Current serial number in output stream: 2711 > > With OpenGL on Centos-7 PC /glxinfo | grep "OpenGL":/ > OpenGL vendor string: Mesa Project > OpenGL renderer string: Software Rasterizer > OpenGL version string: 1.4 (2.1 Mesa 10.5.4) > OpenGL extensions: > > Have you encountered such problem? Could the problem be with coliding > OpenGLs, or graphical transfer through mobaxterm? It would be a major > help if you could point me in the right direction. > > Thank you in advance and have a great day! > > Kind regards > Filip Kadlec > > > > _______________________________________________ > Chimera-users mailing list:Chimera-users@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>

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What do you do for comparative modeling if the pdb is so new it's not in UniProt?
by Ralph Loring 24 May '21

24 May '21

Hi, I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial. Thanks for your help, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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excluded bilayer in chimera
by Yanhe Zhao 22 May '21

22 May '21

To whom may concern, This is Yanhe Zhao, from UT Southwestern Medical Center. I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information. Thanks a lot in advance for any input. Best regards, Yanhe

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Measuring rotation
by JAVAD KARIMBAYLI 19 May '21

19 May '21

Greetings dear sir/madam I was trying to measure the rotation of my protein before vs after activation using the "measure rotation #0 #1" command, which worked smoothly. Then I wanted to check the rotation of specific residues. However, when I tried to specify residues, for example, residue 45 of model0 vs model1, the code didn't work. I have gone through Chimera documentation but didn't really find how to solve the issue. So, I kindly ask for your suggestions about how I may get residue-specific rotations. Thank you in advance Javad Karimbayli

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Covalent bond making and docking
by Zhang, Bixia 14 May '21

14 May '21

Good evening, I was trying to make a man made side chain, which is serine plus uracil. I used the command "bond sel" to connect the oxygen and nitrogen. Then I was trying to do docking to see if this mutation changed the binding affinity. However, after I ran dock prep, the uracil was got rid of because of "poor connection". I am wondering if this arbitrary bond is feasible in chimera and can I do docking with this artificial model? Thank you, Bixia

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Question about error: "the exit code was: -1073731819"
by Sergio Garay 13 May '21

13 May '21

Dear Chimera Users My name is Sergio Garay, I have installed chimera-1.15-win64.exe on Windows 10pro 64bit. But when the program starts to run, the system gives me the following error message and the program closes: chimera exited abnormally; the exit code was: -1073731819. use the -- debug command line option for the full error message I tried installing the two previous versions of the program, with the same result. My PC has a Radeon RX 580 series videocard, and the system uses a WDDM 2.7 video controller. Could you give me any advice on how to fix this problem? Sincerely -- *Prof. Dr. Sergio Garay* *Càtedra de Práctica Profesional de Bioquímica* *Cátedra de Bioinformática* *Facultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Enquiry regarding application
by Prem Rajak 13 May '21

13 May '21

Dear Sir/madam, I have a query regarding the use of UCSF Chimera for molecular docking studies. I am a faculty at an University and would like to analyse my molecular docking research studies using UCSF Chimera. Moreover, I would like to publish the images thus analysed in national/international standard journals. Publications may be multiauthored. Therefore, please let me know whether I can use the software free of cost or I have to purchase the licence. Looking forward to your reply. Thanks and regards, Dr. Prem Rajak Kazi Nazrul University West Bengal, India

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Help for Chimera launch fail
by 黄华 13 May '21

13 May '21

Dear Eric Pettersen, This is a Chimera User in South China Normal University(Guang zhou, China).  Now, I found I can not start the Chimera even after I reinstalled. Would you tell me how could I fix this problem? This is the message after I launch Chimera-debug: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics Return code: -1073741819 Press return or enter to to exit thanks for your help! hua ------------------ Hua Huang Principal Investigator School of Life Science South China Normal University Guangzhou, China 黄华华南师范大学M邮箱/未归类/生命科学学院/教职工/办公华南师范大学始建于1933年，是一所学科门类齐全的国家“211 工程”重点建设大学。 “艰苦奋斗、严谨治学、求实创新、为人师表 ”是华南师范大学校训。  

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BLAST fix
by Eric Pettersen 12 May '21

12 May '21

Hi all, The RCSB switching off http access and only allowing https (which had been announced) unfortunately broke the fetching of PDB info associated with BLAST results, basically breaking the BLAST tools in both Chimera and ChimeraX. Fixes have been applied and will be available in tomorrow's daily builds. For ChimeraX, also available in the 1.2.3 release candidate -- hopefully also out tomorrow. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] S33C .mrc file
by Elaine Meng 11 May '21

11 May '21

Dear Neha, Now you tell me that you opened 1qwa as the pdb (atomic structure) file, so this mrc file is completely irrelevant. I believe you just used the wrong steps to save the pdb. You need to use menu: File... Save PDB, and in that dialog "Save models" area, choose the atomic structure model. (Hiding the map does not matter, centering the view does not matter, it is only what you choose in the dialog). Then as Tom already said, you also have to turn on the "Save relative to model" option and chose the map model as the one you want to save the PDB relative to. Here is the help for the Save PDB dialog: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> I hope this helps, Elaine ---- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2021, at 9:15 PM, Neha Goel <nehagoel24march(a)gmail.com> wrote: > Dear Elaine, > Thank You. Here I .mrc is attached. I was using a reference pdb like 1qwa from pdb database. > Regards > Neha Goel

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Unable to save file in pdb
by Neha Goel 10 May '21

10 May '21

Dear Chimera, I have a .mrc file. I reopened the file in chimera and would like to save it in pdb. I am unable to save it. It needed the molecular model pdb. Kindly guide me the way to save it. Regards Neha Goel

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Rotate chains independently
by Roy Batty 10 May '21

10 May '21

I have a pdb with a homodimeric conformation for two alpha helix transmembrane domains. This structure features a cross-like conformation, interacting at given residues. I want to rotate each of the domains 15º along the z-axis. So for example, something like this would be fine: select :.A (select chain A) turn z -15 *@*ca,cb (rotate chain A 15º, from the residues given as an anchor point) Is there anything like this? Thx

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Transfer of docked substrate co-ordinates
by Jayashree Chittari 08 May '21

08 May '21

Respected sir/ma'am Greetings for the day!!! I have docked ligand into an enzyme which contains two active sites. My docked ligand is in one active site. I want to transfer the ligand conformation from one active site pocket to another using superimpose option in chimera. Find herewith the attached file of PDB in which i want to transfer propionaldehyde coordinates from one active site to another is there any way that we can transfer the docked confirmation coordinates into another chain. Kindly, help me to solve this issue. It will be helpful if you suggest the process. Thank you Regards Chittari Jaya Shree

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Measuring rmsd without having exact number of atoms
by Ahmad Khalifa 07 May '21

07 May '21

Hi, Is there a work around measuring rmsd between two structures of the same protein, with one of them missing some segments, without having to rebuild / model the missing parts?! I'm thinking of writing a quick script to check for the matching segments, calculate rmsd for those and take an average of these measurements, unless there's a quicker way to do it! Regards.

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Chimera - remote start up issue
by Filip Kadlec 07 May '21

07 May '21

Good afternoon! I haven't found a solution to this problem in one of your user threads, internet and I haven't succeeded resolving the issue. I have installed chimera 1.15 today and it runs well when working on the desktop. However, it would be very convenient if I could run chimera remotely. Chimera is installed on Centos 7, I am trying to remotely operate this PC with Windows 10 PC using MobaXterm. When I run chimera as chimera --debug: initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 146 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 2711 Current serial number in output stream: 2711 With OpenGL on Centos-7 PC glxinfo | grep "OpenGL": OpenGL vendor string: Mesa Project OpenGL renderer string: Software Rasterizer OpenGL version string: 1.4 (2.1 Mesa 10.5.4) OpenGL extensions: Have you encountered such problem? Could the problem be with coliding OpenGLs, or graphical transfer through mobaxterm? It would be a major help if you could point me in the right direction. Thank you in advance and have a great day! Kind regards Filip Kadlec

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The app is not working
by Fatma Elzahra Alhuassein Elfourtia 07 May '21

07 May '21

HI I am trying to use the app for my gene but When I try to open the gene in the Chimera because it shows me an error. Please reply me as soon as possible Thank you IMPORTANT NOTICE OF DISCLAIMER The information in this e-mail and any attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you are not an intended recipient, please delete the message and any attachments and notify the sender of misdelivery. Any views expressed by an individual within this e-mail do not necessarily reflect the view(s) of UCSI University wholly owned by UCSI Education Sdn. Bhd. and shall include but not limited to UCSI Group Holdings Sdn. Bhd. and all of its subsidiaries and associated companies.

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Adjust torsion angles
by Moradkhan, Tiglath A 07 May '21

07 May '21

Hi I'm using the adjust torsions tool in Chimera. I was wondering whether there is an easier way of selecting several amino acids at once and adjusting their torsion angles rather than selecting them individually. I'm working with dimers and trying to select individual amino acids would take a very long time. Thank you Tiglath

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job opening for ChimeraX developer
by Elaine Meng 06 May '21

06 May '21

Hello everybody, We're looking for somebody to join the ChimeraX development team! Please see this posting for details: <https://sjobs.brassring.com/TGnewUI/Search/Home/Home?partnerid=6495&siteid=…> On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Contact in angstrom
by Arthur Pereira da Fonseca 06 May '21

06 May '21

Hello, I’m trying to measure contacts between a protein and a peptide using Chimera. I have to do this with different angstroms distances, 2, 3 and 4 Å. I'm using the command line: findclash :.A test :. B overlap -0.4 hbond 0.0 namingStyle simple save However I don’t know exactly how to modify the overlap to the desired distances. Which values can I use to measure contacts within 2, 3 and 4 Å. Thanks in advance, Arthur Pereira

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python code to loop over molecules
by Julian Tirado-Rives 04 May '21

04 May '21

Dear Chimera (and ChimeraX) team: I need to find some python example or code snippet capable of looping over all the molecules in a particular model and do some actions separately in each one. In our research we use several different docking programs and other ways of generating poses of protein-ligand complexes, and using several different programs to analyze them gets quite complicated. Instead, we've found that the easiest way is to generate from each code, or using conversion utilities such as babel, a pdb file of the host and a sdf or mol2 file containing all the ligand poses and read them into chimera. An excellent program, by the way. We use it all the time. I would love to automate the process even further by doing all the coloring, rendering, Hydrogen Bond and contact analysis, etc. in Python rather than manually. I have been trying to do this, but have not found a way to do the following: If we have, for instance, the host in model #0, and the ligand poses in model #1 (#1.1, #1.2, ..., #1.N): - Get from chimera the number of molecules in model #1 (e.g what is N) - loop from the first #1.1 to the last #1.N molecule - do some cations there (e.g select, color, find HB's, etc) I think this should be a problem other people have encountered and solved before, but I have not been able to find an example in your depository, the mailing lists, or even the book ... I would appreciate your input. Thanks for your help, and for an excellent program! - Julian - -- ----------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives(a)yale.edu | | New Haven, CT 06520-8107 | | -----------------------------------------------------------------

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Rotate model
by C.J. 04 May '21

04 May '21

Hi all, I tried "turn y 180 #1" ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html) but it doesn't work. It said "turn frame arguement must be an integer". While I tried "turn y 180 0 #1" or "turn y 180 1 #1", it said "wait_frames arguement not implemented". Even "turn y 180 0 0 #1" doesn't work. Did I miss something? Thank you! Jianhao

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Combine focuse refined maps in Chimera
by Zheng, Fengwei 03 May '21

03 May '21

Dear Chimera developers: Thank you so much for developing this powerful and elegant software for our community! I am a newbie in cryoEM, and recently I got a consensus map, and split it into two parts to do the further focused refinement, after that I want to combine them together, and then to build my model. I learned that the command "vop maximum #0 #1" can achieve this, what I did is that, firstly, I used this command to merge my consensus map with one focused map, and then merged the resulted map with my second focused map, but it seems that the order of those two maps in my executable command (e.g. #0 #1 or #1 #0) will lead to slightly different resulting map~ I just wondering if this is the correct way to combine my focused maps, or there are other commands can achieve this better? Appreciate! Best, Fengwei

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Fwd: Hydrogen bond
by Eric Pettersen 03 May '21

03 May '21

> Begin forwarded message: > > From: shakira shukoor <shakirashukoor1993(a)gmail.com> > Subject: Hydrogen bond > Date: May 2, 2021 at 3:09:46 PM PDT > To: chimera-bugs(a)cgl.ucsf.edu > > Dear sir > Does chimera software have any option to set the distance and angle criteria to view the hydrogen bond. I was not able to see any hydrogen bond in my system although hydrogen bonds do exist which I have confirmed from vmd. Why is it not visible in chimera then? > > -- > Best Regards > > Shakkira E > PhD student INSPIRE Scholar > Department of Chemistry > sdmdlab <http://sdmdlab.xyz/>-iitp.com <http://iitp.com/> > IIT Patna > Bihta > Patna 801106 >

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Problem downloading Chimera
by Mahmoud Soliman 02 May '21

02 May '21

Hello there, We are trying to download Chimera, however, the link below never works, not sure if the server is down, but we have been trying for a few days with no luck. Can you please guide us on how to download chimera perhaps you send us a working link. <%0b%0dhttps:/www.cgl.ucsf.edu%20›%20chimera%0d> https://www.cgl.ucsf.edu › chimera<%0b%0dhttps:/www.cgl.ucsf.edu%20›%20chimera%0d> Thanks & Best Regards -------------------------------------------------------- Prof. M Soliman Professor of Pharmaceutical Chemistry M.Pharm, B.Pharm, MPhil/PhD (Bath, UK) Discipline of Pharmaceutical Sciences School of Health Sciences University of Kwazulu-Natal Westville Campus, Durban 4000 Email: soliman(a)ukzn.ac.za<mailto:soliman@ukzn.ac.za> Webpage: http://soliman.ukzn.ac.za/ ---------------------------------------------------------

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2D panorama view of a 3D model
by Kandolf,Susanne 30 Apr '21

30 Apr '21

Hello, I was wondering if it is possible to display a 3D model as a 2D panorama view? I would like to show all sides of a holoenzyme and instead of taking several pictures of each view, I thought it would be more convenient to have one picture displayed as panorama showing all sides at the same time. Thank you for your help, Susanne …………………………………………………………………….. Susanne Kandolf Research Technician at Haselbach Lab Mobile: +43 699 17250493 susanne.kandolf(a)imp.ac.at<mailto:susanne.kandolf@imp.ac.at> www.imp.ac.at<http://www.imp.ac.at> IMP Research Institute of Molecular Pathology Campus-Vienna-BioCenter 1 1030 Vienna, Austria Part of Vienna BioCenter www.viennabiocenter.org<http://www.viennabiocenter.org>

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Problem Saava9ng merged PDB Files
by Stephen P. Molnar 30 Apr '21

30 Apr '21

I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux computer and have run into a problem saving a pdb file containing two pdb files. The files are attached to this email.This is a portion of the combined flies: The structure of the D21.pdb file isthe ball image. I followed the instructions in the Building Structures, Modifying and Saving Data in the Help pages. However, when I open DD21Mod1 in LigPlot to identify the docked ligand I get: Clearly, this is not the ligand docked int the active site. I have used LigPlot on a number of pdb files with good results and am forced to conclude that there is a problem with D21Mod1.pdb. I would appreciate help in solving this problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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problem (exit code -1073741819)
by Ichrak Benamri 23 Apr '21

23 Apr '21

Hello, I hope you are doing well. I have problem launching the chimera tool (error code: -1073741819), I don't know exactly where the problem is. Please, can you help me? Thank you [image: image.png] -- *Ichrak BENAMRI* PhD Student in Bioinfomatics *+212648548583* ichrakbenamri(a)gmail.com Systems and Data Engineering Team, National School of Applied Sciences, Abdelmalek Essaâdi University, BP1818 Route Ziaten, 90 000, Tangier, Morocco Chlamydiae and Mycoplasma Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco

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Four letter residue names
by Francesco Pietra 21 Apr '21

21 Apr '21

Hi all A pdb file deriving from a mmCIF file (with chimerax) and comprising both nucleotides and proteins, shows the protein residue names with four characters (i.e., using also column 21), such as ALAM in one subunit, or GLNm in another subunit. I read on passing somewhere (and I am unable to trace that back) that chimera accepts such four character names but was unable to find a description from chimera help. I also got lost in deciphering the intricacies of mmCIF files. What is the scope of the column 21 character? Could that simply be ignored, or deleted, for use with the CHARMM FF? Thanks for advice francesco pietra

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Chimera Errors
by Henry Shook 18 Apr '21

18 Apr '21

Chimera Team, I have been using Chimera to test several Sialic Acid isomers on the Sars-CoV-2 spike protein over the past couple of months and a couple of days ago, I have been getting this error telling me that there was an "application stderr" and "application stdout". Previously to a couple of days ago, anytime I tried to run it during the day, this message would show up, however, I was able to run the docks from 9-12 pm at night without any problem, so I just worked on the docking during that time. Now, no matter what time I run the docks at, this message shows up. I have not changed any procedures from when I started until now. Is there a way I can fix this problem? I attached a screen recording of my procedures and how I arrived at the problem. Here is a link <https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=…> if the video does not load. Thanks! Henry Shook Screen Recording 2021-04-18 at 11.19.06 AM.mov <https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=…>

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ADP EM Chimera plugin
by Eric Pettersen 15 Apr '21

15 Apr '21

Hi Vilde, Since ADP EM is a third-party plugin, I don't know that I know that much more than you about how it works. Hopefully the plugin developers will get back to you. Nonetheless, I can offer some generic advice about seeing/finding the fitted structure. First, check the Model Panel (Favorites→Model Panel) to ensure that the structure model is shown (the "Shown" column for the structure model is checked). Second, type the 'window' command (Favorites→Command Line) to ensure the view is large enough to show the position of the structure. Third, click on the color well in the Volume Viewer panel (the square next to "Color") and adjust the 'A' component of the color (A = alpha, or opacity) so the the contour surface is semi-transparent, in case the structure is completely within a contour. --Eric Eric Pettersen UCSF Computer Graphics Lab > Hello, > > I’m trying to use the ADP EM molecular fitting tool (Chimera Plugin) to fit my PDB-models into a low resolution map. The plugin works as it should, but I’m having trouble visualizing the solutions. Once the fitting is finished (the table with all the coordinates is produced) and I chose for example solution 1, the PDB structure disappears in the Chimera Window. The EM map is still showing. If I click on the “Back to initial”-button, the PDB structure comes back, but in the initial position, of course. I have tried to save the solutions, but they are still not showing (the solutions are selected as “show” as a cartoon in the model panel). According to the description of the plugin developers, the solutions/fits should be visualized just by selecting one, no extra steps needed. > I’m doing something wrong in Chimera or is there a bug? > I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result. > > Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far. > > Best regards, > Vilde Leipart > PhD-student, > > Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences > Høgskoleveien 12, 1430 Ås, Norway > > Honey Bee Research Lab, Arizona Sate University > 427 East Tyler Mall, Tempe, AZ 85287

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Pixel size/box size and map display
by Cynthia Lee Page 14 Apr '21

14 Apr '21

Hi, I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. Can someone set me straight on this? Many thanks, Cynthia

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Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 14 Apr '21

14 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made. 1. Connection to 13.107.4.52 on tcp/80 (www.msftconnecttest.com) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 13 Apr '21

13 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made. 1. Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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combine models
by Francesco Pietra 11 Apr '21

11 Apr '21

Hi (1) I am faced by the coordinates for a nucleics/protein assembly being given in several bundle.pdb, while I need a sequential, continuous pdb file that comprises all nucleotides and proteins, not made of models (2) If I load all the bundles to chimera, I see all expected ligands around the small molecule. (3) With all models selected, copy/combine (adopting default first model as reference and allowing renaming chains) generates a new model. The new model laks some proteins that should lie near the ligand, as described at (2). I feel that I am missing something. Thanks for advice francesco pietra

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greeting and acknowledgement
by kajihara 09 Apr '21

09 Apr '21

Dear Prof. Ferrin, Dear stuff of Chimera, I am prof Yasuhiro Kajihara, Department of chemistry, Osaka University. Last April, Corona pandemic suddenly attack us, and our university closed in-person style classes. I needed to do online class of biochemistry. I recommended students to download UCSF Chimera for understanding protein structure and behavior. The Chimera soft wear was great help for us under the terrible Corona Pandemic and all students enjoy to deal with Chimera. They got unbelievable knowledge through the Chimera. I could not find a suitable word to express my thank. I thank you again for your great support and kindness to deliver it as free. Within a week 80 students will start download chimera. So, I need to send greeting e-mail to give my thanks. Sincerely Yasuhiro Kajihara, Ph. D. Department of Chemistry Osaka University Machikaneyama, 1-1, Toyonaka, 560-0043 Japan kajihara(a)chem.sci.osaka-u.ac.jp

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Where does Chimera copy command save images?
by Martti Tolvanen 09 Apr '21

09 Apr '21

I have tried to use the command copy on command line to save images, with a goal to do that in a script. The messages of rendering a high-res image and image saved come up, but the file is nowhere to be found. My guess is that the default save location is in the Chimera program folder, which would not be permitted, but Chimera just doesn't see it as a failed attempt. I do have a workaround of including the full path in a filename, but I'm just curious where the file would be going by default, and whether there is some command to change the working folder by a command. FYI it's Chimera 1.15 in Windows 10. Martti Tolvanen University Lecturer in Bioinformatics U of Turku, Finland

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