- Chimera-users - RBVI Mailing Lists

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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Error reading multiple models
by Francesco Pietra 25 Sep '20

25 Sep '20

In my hands CHIMERA can't read multiple models as in .trj.xyz provided by ORCA software in QM calculations Error reading 5-sulf-min_trj.xyz: Coordinate line of XYZ file '/home/francesco/work_AGAs/VITTORIO/5-sulf-min_PBE0_OPT_FREQ_SMD/ 5-sulf-min_trj.xyz' is not element,x,y,z: '36' That is no problem for Jmol, however I would be interested in opening the models with also CHIMERA (which can open these models as a single-model-file. thanks for advice francesco pietra

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Open .mrcs stack in chimera
by Ahmad Khalifa 24 Sep '20

24 Sep '20

Can I open a .mrcs stack in chimera? What file type should I pass to Chimera in order to do that?

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Re: [Chimera-users] Stereo Red Cyan
by Greg Couch 24 Sep '20

24 Sep '20

Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book. -- Greg On 9/21/2020 11:43 PM, Michael Elbaum wrote: > Red-cyan, sorry. No, I didn't look for stereo at all, just to > reproduce the condition posted that one channel appears in red and the > other in gray. Is that normal? > Michael > ------------------------------------------------------------------------ > *From:* Greg Couch <gregc(a)cgl.ucsf.edu> > *Sent:* Tuesday, September 22, 2020 4:57:50 AM > *To:* Michael Elbaum <michael.elbaum(a)weizmann.ac.il> > *Subject:* Re: [Chimera-users] Stereo Red Cyan > > Are you wearing red-cyan glasses to see the stereo? It doesn't work > without them. > > > -- Greg > > > On 9/21/2020 1:08 PM, Michael Elbaum wrote: >> >> I'm confirming the problem with a different dataset (optical >> deconvolution in tif format). Red-green shows red and gray, >> green-magenta shows green and gray. This is with version 1.14 on linux. >> >> regards, >> Michael >> >> >> >> ------------------------------------------------------------------------ >> *From:* Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf >> of Angus McDonald <amcdonald(a)boisestate.edu> >> *Sent:* Monday, September 21, 2020 9:46:24 PM >> *To:* chimera-users(a)cgl.ucsf.edu BB >> *Subject:* [Chimera-users] Stereo Red Cyan >> I am looking at some cryo em data. When I try to view a a 3D stack of >> em dat with the Red-Cyan stereo setting I seem to only get Red and >> grayscale. The data is in 32-bit floating point and is in MRC2014 >> header format. I cannot figure out what I am doing wrong. Is anything >> obvious? >> >> Thanks for your time. >> >> >> >> -- >> Angus McDonald >> amcdonald(a)boisestate.edu <mailto:amcdonald@boisestate.edu> >> >> _______________________________________________ >> Chimera-users mailing list:Chimera-users@cgl.ucsf.edu >> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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electrostatic interactions
by Ruchika 23 Sep '20

23 Sep '20

Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika

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Fitting structure in rescaled map
by Ahmad Khalifa 23 Sep '20

23 Sep '20

Hello, How to fit an atomic model after downscaling my map (map shrinks)? Are atomic models built to scale?! Regards.

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Writing a SINGLE pose (with ligand and protein) to a PDB file
by Edmund Marinelli 22 Sep '20

22 Sep '20

Hello: I used ViewDock to open a pdbqt file generated by use of AutoDock Vina. The ligand was shown in the graphics window. Then I opened the protein pdb file that was used in the docking experiment. The ViewDock dialog lists the poses obtained and I can select each and view the resulting pose in the graphics window fine. I opened the Model Pane. I selected from the list of models the first pose (#0.1) and the protein (#1) in the list. I assumed that saving these two into a file would give a file that contained only the protein and the ligand bound as in the best pose . I want to save the best pose as a pdb file wherein the protein and ligand are present. I gave a filename Test.pdb . Chimera returned the following error message: "You must provide a filename that contains either $name or $number , which will be changed to the model name or model number (respectively) in the final saved file name." I do not understand what this means. I tried using the pose number and also the protein name but it gave the same error. I don't understand what is meant by $name and $number - what do they refer to ? What do I need to do to save a single pose containing protein and the ligand to a unique file not containing other poses? The screenshot below is what I see: Note that in the models list I selected the best pose #0.1 and also the protein, which is at the bottom of the list, hence it is not visible in the picture. What is the filename syntax that I need to use to save a pose with protein to a single PDB file? Stated more plainly: Can you give a viable example of what I need to enter as a filename that will allow saving of the file? Or am I going about this all wrong? Sorry for the verbose email. [image: image.png]

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Stereo Red Cyan
by Angus McDonald 21 Sep '20

21 Sep '20

I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious? Thanks for your time. -- Angus McDonald amcdonald(a)boisestate.edu

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Using iBabel to convert Chimera's pdb to pdbqt
by Jatin Kashyap 19 Sep '20

19 Sep '20

Dear UCSF Chimera Community, I am trying to minimize a complex[1] and saving it in a pdbqt format. I minimize it in Chimera and saved in pdb[2], followed by using iBabel (GUI of open babel for Mac) to convert pdb into pdbqt. Here are two things: first, if I convert without using any flag then output gives me pdbqt file with BRANCH information which is not supported by Vina. To solve it I am using -XR flag in iBabel to trim the BRANCH information so that resulting pdbqt file can be read by Vina. But in that case iBabel is giving me weird looking structure and upon inspection of pdbqt file[3] I realized the complex was split into different models. I had successfully followed the same workflow for other minimization code i.e. YASARA. Can anybody please help me to fix it. I am attaching files below with corresponding citations. Thank you. [1] [2] [3] —— Jatin Kashyap Ph.D. Student Dr. Dibakar Datta Group Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435(a)njit.edu

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Setting a pathway/trajectory for a molecule
by Rani Wiswedel 19 Sep '20

19 Sep '20

Good day, I am an honours student attempting to set up my first molecular dynamics simulation, and am having some trouble trying to understand how to set a pathway for a substrate through a pore in Chimera. I am very unsure of how to do this, and was wondering if you could provide some help. I tried following the Trajectory and Ensemble Analysis tutorial, but essentially cannot get past the first step of downloading leap.top etc. I am also not sure if this is the correct tutorial to follow for what I am looking to do? Any advice would be greatly appreciated, I am in way over my depth. Thank you Kind regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

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Re: [Chimera-users] alpha carbon atom as sphere
by Elaine Meng 18 Sep '20

18 Sep '20

On Sep 18, 2020, at 1:58 PM, Ruchika <Ruchika(a)ucsf.edu> wrote: > Hi Elaine > I am trying to select just alpha carbon on the atom and show it as a sphere, but I am having hard time doing that. When I select the atom, and go to actions and sphere, I must show the side chain and then going to sphere, shows the whole side chain as a sphere instead of just alpha carbon as sphere. Could you please help me with this issue ? > Thanks a lot !! > Regards > Ruchika Hi Ruchika, Assuming you are using Chimera, we recommend sending such questions to chimera-users(a)cgl.ucsf.edu (CC'd here) or else they may fall through the cracks. It doesn't make sense to me that you would need to show the sidechain. I can only guess that maybe you're showing ribbon and that is causing the confusion. If you are showing ribbon, you cannot see or select the alpha-carbon with the mouse, because ribbon normally hides the backbone atoms. If you select the ribbon it selects the whole residue. If you want to show backbone atoms at the same time as ribbon, use command "ribbackbone" or alternatively, just hide the ribbon, and then show whatever atoms you want. Select only the CA and then change it to sphere. Explanation of "ribbackbone" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> Example commands: open 1gcn ribbackbone show :5@CA repr sphere :5@CA 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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Backbone RMSD
by Zhang, Bixia 18 Sep '20

18 Sep '20

Hi, I am trying to get the backbone RMSD between two structures. However I tried selecting backbone and use matchmaker, it gives me same value with the whole protein. So there must be something wrong. Could you please teach me a command that can do this? Thank you so much for helping! Best, Bixia

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