- Chimera-users - RBVI Mailing Lists

issues with visualization of saxs models in chimera
by Anabel Pacios Michelena 20 Oct '20

20 Oct '20

Dear Chimera team, I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this? Thank you very much in advance for all your help, Kind regards, Anabel

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Writing residues coordinates and COMs
by Yasser Almeida 20 Oct '20

20 Oct '20

Hello, I am writing a python script to iterate through all the residues of my model and write the residue coordinates and its correspondent center of mass. I tried with 'runCommand' with the command 'write' but it only accepts a model to be written, not a specific residue. Any thoughts? Thanks in advance. Yasser

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Query about energy minimisation
by Izzati Mokthar 19 Oct '20

19 Oct '20

Hi, I am Izzati. I have a few queries on UCSF Chimera. I need your guide to use the tools. I have two questions. Below are the questions: 1.I would like to do energy minimisation for protein structure with PDB ID: 2J9F. I click Structure editing > Minimize Structure. To be honest, I don't know how to set the settings. I used the default setting and a warning pops up as the attached picture. Do you have any suggestion of reference that I can refer to, to do the energy minimisation? [image: 5.png] 2. I need to also do molecular dynamics for my research. May I know whether I can use chimera to run molecular dynamics as well. If yes, where can I refer to the tutorials? Thank you in advance for your response. Regards, Izzati.

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atom ID
by Francesco Pietra 18 Oct '20

18 Oct '20

Dear all Which is the quickest way to identify the atom ID? As visualized in the context of a multimer, where three identical subunits, distinct by chain name, bind the same peptide, also distinct by chain name. Atom IDs are needed to build a QM-MM simulation. thanks francesco pietra

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PyChimera addCharge
by Matas Tiskus 16 Oct '20

16 Oct '20

Hello, I was looking for ways to add charges to protein structures in a python script and write a .mol2 file. I believe it is possible to do with importing pychimera into the script, but i can't seem to make it work. How would the code for this purpose look like? Matas

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Re: [Chimera-users] [chimera-dev] Building a dimeric protein model
by Elaine Meng 15 Oct '20

15 Oct '20

On Oct 15, 2020, at 1:41 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > Hi > I've built a monomeric model using Chimera's MODELLER interface. I was wondering whether it's possible to use this model in Chimera to create a dimer. The dimer of the protein that I'm studying is composed of two antiparallel symmetric monomers. > Thank you > Tiglath > Hi Tiglath, Sure, but you would need to know the proper positioning of the two monomers in the dimer. There is nothing in Chimera to figure that out automatically. If there is a known dimer structure of a related protein and you think your modeled protein forms a similar dimer, you can simply (1) save your new monomer model as a PDB file (2) start a new Chimera, open that new PDB file two times so that you have two copies open (3) open the known dimer structure of the related protein, let's say it has chains A and B (4) superimpose one copy of your monomer model onto chain A of the known dimer structure, and superimpose the other copy of your monomer model onto chain B of the known dimer structure. Different methods of superimposing structures are discussed in the link below. Probably the easiest is to use the Matchmaker tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (4) close the known dimer structure, and what you have left is the approximate dimer with two copies of your model, which can be saved as a session, or combined into a single model (see "combine" command) and then saved as a PDB file. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Alternatively if you have a dimeric template structure you can use Modeller to make a dimeric comparative model directly, but to do that you would have to use the Modeller interface in our newer program ChimeraX. The one in Chimera only allows modeling monomers. Modeller interface in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> This chimera-dev e-mail address is mostly for programming questions. For general user questions like this (for future reference) a better address to use is chimera-users(a)cgl.ucsf.edu CC'd here, and there is also a similar address for ChimeraX: chimerax-users(a)cgl.ucsf.edu I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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kill graphics windows after crash
by Dieter Blaas 15 Oct '20

15 Oct '20

Hi, please forgive me when this question is not directly related to Chimera: Sometimes Chimera becomes unresponsive because of a slow network connection. When I then try exiting it or killing it with <ctrl> c from the terminal I used to start it or killing the chimera-related process as shown with ps -ealf|grep UCSF or grep chimera the chimera windows remain and I cannot remove them. Any way of doing so? Thanks for hints, best, Dieter ----------------------------------------------------------------------- Dieter Blaas, Max Perutz Labortories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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how to get specific view
by Shuo 15 Oct '20

15 Oct '20

Dear sir or madam, I wonder how to get specific view parameter in Chimera, just like command get_view in Pymol. So that next time I can easily adjust the view in Chimera. Best Shuo

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Modelling missing residues in a protein
by Edmund Marinelli 14 Oct '20

14 Oct '20

Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD

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MOLE 2.5 plugin
by Reza Khayat 13 Oct '20

13 Oct '20

Hi, I'm receiving the following error when launching the MOLE 2.5 plugin from Chimera. The plugin was installed as suggested by the developers: Favorites -> Preferences -> Add -> Select directory The plugin's icon appears in my tool bar. However, launching it generates the following error in the Reply Log. Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1rc\share\chimera\toolbar.py", line 26, in _guard func() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 954, in <lambda> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 76, in display dialog = find(name, create=1) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 61, in find return d() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' Error in toolbar callback: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: See reply log for Python traceback.? Any help is appreciated. Best wishes, Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Help on using Modeller interface
by Moradkhan, Tiglath A 09 Oct '20

09 Oct '20

Hi I'm currently trying to use the Modeller interface but I'm having difficulties. I am trying to model a monomeric protein but one of the templates is a homotetramer containing chains A, B, C and D. I only need to use chain A to model the protein but I'm not sure how to do it. Whenever I use the Modeller interface, it uses all of the chains which is not what I want. Unfortunately, this is the only template that I can use since the others are either structures that have since been refuted or don't really correspond to the protein I'm studying. I would be very grateful for your help. Thanks Tiglath

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Help for Chimera please
by EMILIE MONTELLIER 09 Oct '20

09 Oct '20

Hello, I have just downloaded your Chimera software. It looks great! I would like to map a list a specific amino acid on p53 protein and I struggle to find a way to do it. I have downloaded the PDB file of 1TUP TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA (at [ https://www.rcsb.org/ | https://www.rcsb.org ] ). For exemple what would be the command to hightlight amino acid 175 + 248 + 273 + 282 on p53 protein? Thanks by advance for your help, Regards, Emilie Emilie Montellier, PhD Postdoctoral Researcher Institute for Advanced Biosciences Team Tumor Molecular Pathology & Biomarkers Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

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Latest nightly broken on Mac (10.15.7)
by Oliver Clarke 09 Oct '20

09 Oct '20

Hi, In the notes for the latest nightly Chimera build, it states "Many user-interface problems on Mac fixed by upgrading the Tk windowing toolkit to version 8.6.10" - this sounds great, but it seems to have broken basic functionality, at least on my system. See screen recording here: https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0 <https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0> Many UI elements are not responsive any more (including the "Report a Bug" dialog, hence why I am reporting here). This is using Mac OS X 10.15.7 on a macbook pro 16", using the trackpad. Cheers Oli

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AutoDOCK plugin for UCSF Chimera
by James Starlight 08 Oct '20

08 Oct '20

Dear Chimera users! Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb

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matchmaker and MSA
by arrafzaher＠campus.technion.ac.il 06 Oct '20

06 Oct '20

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

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Volume eraser accelerator not working properly
by Ahmad Khalifa 01 Oct '20

01 Oct '20

As I keep clicking "es", the shadows / lighting keep changing, but after clicking 10 times or so, it finally erases. Is this something I'm doing? How can I change to a more easier accelerator?

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bound ligand's are exposed to solvent. Current calculations do not protect surface of ligand embedded in protein
by Anne-Frances Miller 01 Oct '20

01 Oct '20

Dear Chimera, I see on-line advice on calculating areaSAS and areaSES, however Chimera is calculating these for my bound flavin as if the protein were not there. I would like to assess the area exposed outside the protein, not total area (on an atom-by-atom basis). Indeed, the show surface command produces two surfaces, one for the FAD and a different one for the protein, even though both are chain A. Can I edit the pdb file to cause Chimera to create a single surface for both chains including both bound FADs, so that SASA calculated will represent the extent to which the FAD protrudes from the protein? (My protein is a heterodimer with two bound FADs, my Chimera version is 1.13.1 running on Mac OS 10.15.6) Thank you, Anne-Frances Novel Meritorious Research (and teaching) —————————————— A.-F. Miller, Ph. D. Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin Chair, Div. of Biological Chemistry, American Chemical Society

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Undo for volume eraser
by Ahmad Khalifa 30 Sep '20

30 Sep '20

Is there a way to undo a recent erasing that I did? Also, are there ways to use custom shapes, or other surfaces to erase density?

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scipy
by Hernando J Sosa 29 Sep '20

29 Sep '20

Is scipy installed with Chimera? If not how can it be installed? Thanks Hernando >From Chimera idle: >>> import chimera >>> import scipy Traceback (most recent call last): File "<pyshell#1>", line 2, in <module> ImportError: No module named scipy ___________________________________

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Re: [Chimera-users] Troubleshooting request for help
by Cain, Cheryl A 29 Sep '20

29 Sep '20

Hi Tanuja, I've added chimera-users(a)cgl.ucsf.edu to this email as they should be able to help you there. Thanks, Cheryl Cheryl Cain cheryl.cain(a)ucsf.edu Operations Coordinator, Department of Pharmaceutical Chemistry Accreditation Project Coordinator, School of Pharmacy UCSF ________________________________ From: Saswat, Tanuja (NIH/NCI) [F] <tanuja.saswat(a)nih.gov> Sent: Friday, September 25, 2020 9:56 AM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Cc: Goins, Jerquan (NIH/NCI) [C] <jerquan.goins(a)nih.gov> Subject: Troubleshooting request for help Hi, I am a researcher at the NIH who uses this software to complete analysis. But as of recently some of the features that I usually use have not been able to access them. Can you guys assist me in finding a resolution. I’ve CC’s my IT support in case there was something above my cresds level. Regards -- Tanuja Saswat, Ph.D. Postdoctoral Research Fellow Laboratory of Dr. Laurie T. Krug HIV and AIDS Malignancy Branch (HAMB) Center for Cancer Research National Cancer Institute tanuja.saswat(a)nih.gov<mailto:tanuja.saswat@nih.gov> Building 10, Room 4A08 Ph:240-858-3201 NCI Website<https://urldefense.proofpoint.com/v2/url?u=https-3A__ccr.cancer.gov_HIV-2Da…>

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vop subtract removing too much of my map
by Ahmad Khalifa 29 Sep '20

29 Sep '20

I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1! how can I get precise subtraction?

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clustering models of a single pdb
by Subhrangshu Das 29 Sep '20

29 Sep '20

Dear sir, I have 100 pdb files. named as output.1.pdb to output.100.pdb what i do manually for clustering is as follows 1. select 100 pdbs -> open in chimera -> golto *File *-> *save PDB.. *-> *Save Multiple Models as PDB File *(renamed as all.pdb) 2. open chimera -> goto *Tools *->* MD/Ensemble Analysis *->* MD Movie* 3. in *Get Ensemble Info *dialogue box set -> *Trajectory format :* *PDB* *PDB frames contained in:* *single file* * Browse *to select File <all.pdb> *Use frames **first **through * *last* 4. on click *OK,* a dialogue box pops out, *MD Movie: PDB trajectory from all.pdb*, in which, goto *Analysis -> Cluster...*5.. on click* Cluster,* a dialogue box pops out,* Get Clustering Parameters,* in which I set *Cluster trajectory *as: *Starting frame: * *1* *step size: **1* *Ending frame:* * 100* *Cluster based on current selection, if any: * *true* *Ignore solvent and non metal ions: true* *Ignore hydrogens: * *true* *Ignore metal ions: * *alkali* 6. on click *OK, *after some RMSD calculation, i get the *Clustering* result, which I save to a text file <cluster> Now, as I need to do this for multiple times, I want to automate these steps by a python script. Can you please help with a scipt or some command help for the aforesaid tasks. Any help will be helpful in these regard. -- Thanks & Regards, Subhrangshu Das Junior Research Fellow, CSIR-IICB Department of Structural Biology & Bioinformatics Contact - IICB TRUE Campus, CN-6, Salt lake, Sector V, Kolkata-700091 *+919804938813*

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tile from command line
by Dieter Blaas 28 Sep '20

28 Sep '20

Hi, I am trying to use the command line command TILE as given here: Usage <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/usageconvent…>: *tile* /models/ [ columns /N/ ] [ spacingFactor /f/ ] [ independentRotation true|false ] [ viewAll true|false ] [ label true|false ] I tried (following the syntax of e.g. "vol all level 0.02": "tile vol all columns 3" or "tile all columns 3" or "tile models all columns 3" or "tile #0, #1, #2, #4, #5, #6 columns 3" but none works can you please give me an example! Thanks, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Is RTX support planned?
by Gokhan Tolun 25 Sep '20

25 Sep '20

Hi Tom, Are there any plans to implement RTX (real-time ray tracing) support to ChimeraX (and even better, allow the use of physically modelled materials and textures)? Thanks, Gökhan Gökhan Tolun<https://scholars.uow.edu.au/display/gokhan_tolun>, M.S., Ph.D. Senior Lecturer School of Chemistry and Molecular Bioscience<https://www.uow.edu.au/science-medicine-health/schools-entities/school-of-c…> | Faculty of Science, Medicine and Health (SMAH)<https://smah.uow.edu.au/index.html> | Room 125 / Building 18 Molecular Horizons Research Institute<https://www.uow.edu.au/molecular-horizons/index.html> Illawarra Health and Medical Research Institute<https://www.ihmri.org.au/researchers/gokhan-tolun/> University of Wollongong NSW 2522 Australia T +61 2 4221 3365 uow.edu.au<http://uow.edu.au/> | Facebook<https://www.facebook.com/UOW> | Twitter<https://twitter.com/uow> | Instagram<https://www.instagram.com/uow/> | LinkedIn<http://www.linkedin.com/edu/school?id=10255> NOTICE: This email is intended for the addressee name and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Please consider the environment before printing this email.

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X-PLOR format, finding a maximum
by Gustaf Olsson 25 Sep '20

25 Sep '20

Hello Chimera users This might be a somewhat “of-topic” question though I thought that this would be a good place to start. When loading density maps (particularly the X-PLOR format density maps) into Chimera the 'volume viewer’ window provides a maximum number of gridpoints for the map. My question has to do with the format of the XPLOR files. The documentation regarding this format is rather sparse and my I have not been keeping my knowledge regarding matrices up to date. Is there a way to identify this maximum value by just inspecting the content of these files? I have a lot of these files and as I en up presenting results only for ligands with grids visible above a specific cut-off, I though it would save me a lot of time and headache if I could just load the density maps with maximum densities above the cutoff. My though was to just parse the files through AWK or similar to find files with a x > a and then only load these. Sadly, I keep looking at the content of these files and I am not able to make much sense of what I am looking at. Any solutions, suggestions or suggested reading to be able to find a way to create a solution would be greatly appreciated. Best regards // Gustaf

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