- Chimera-users - RBVI Mailing Lists

Color surface by electrostatic potential vs color by value at atom position
by Yu Zhou 22 Feb '20

22 Feb '20

Hi there, I want to color protein surface by electrostatic potential datacalculated using APBS 1.5. I tried two methods in Chimera and got quite differentresults. The resulted images can be found in attachment. In the first attached figure (fig1_ep surface) the surface wascolored by the “Electrostatic Surface Coloring” tool, in the second attachedfigure (fig2_value atom) the surface was colored by the “Values at AtomPositions” tool. Same color palette (red: -35, white: 0, blue: +35) and potential file was used in bothcases. Thanks for your help. Yu Zhou

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Problem during Residue interaction network generation
by Aditya Padhi 20 Feb '20

20 Feb '20

Dear Chimera users, I am using the StructueViz plugin of Cytoscape to launch Chimera and then loading the MD trajectory from Gromacs, where I need to generate the residue interaction network. After this step, when I click "apply" for displaying the interaction network in Cytoscape, it often shows "Importing Residue Network from Chimera", sometimes "getting data for attribute secondarystructure" and sometimes "getting data for attribute ishelix". Even after I wait for half a day, the message continues to show and I am not able to work on Cytoscape. I have even tried to reduce the number of frames of the MD trajectory to see if that helps, but that doesn't work even. Can anyone help me to how to resolve this problem? With best regards Aditya

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Aligning a 2Fo-Fc map with the molecule in Chimera
by Miriam Gochin 20 Feb '20

20 Feb '20

The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom #0" command but got the following error: NameError: global name 'step' is not defined File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box g = volume.grid_data(subregion = 'all', step = step, mask_zone = False) Hoping to figure out how to make it work. Many thanks, --------------------------------- Miriam Gochin Touro University California / LBL miriam.gochin(a)tu.edu mgochin(a)lbl.gov 707-638-5463

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"subtract selected segment from map" from a specific map
by Dominique Gutierrez 20 Feb '20

20 Feb '20

Hello, Can I use the "subtract selected segment from map" in Segger tool to subtract the selected from a specific map and not just the map used for segmentation. In my case the segmented map is from a vop subtracted intermediate used to facilitate segmentation but I would like to quickly subtract several segments from the original map. Or is the only way to do that with vop subtract? Best, Dominique

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Hydrogen labeling scheme
by Jack Fuller 19 Feb '20

19 Feb '20

Hello, I am part of a computational chemistry research group that frequently uses chimera to add hydrogens to pdbs. My coworkers and I have noticed that chimera uses several different labeling schemes for hydrogens. We have been unable to determine how chimera chooses which scheme to use. Is there a way to specify which scheme to use or to know which scheme chimera will choose? Thank you, Jack Fuller

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Mx 230 gpu, chimera and chimerax
by Yehuda Halfon 18 Feb '20

18 Feb '20

Hi all, A friend of mine in my lab wants to buy a new laptop with mx230. Will it work fine with chimera and chimerax? The cpu is i5-10210u and 8 GB of ram. Thanks a lot, Yehuda Halfon PS I know this isn't the chimerax mailing list but I hope to get a double answer in one mail

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BLAST Database error
by Ebrahim Barzegari 18 Feb '20

18 Feb '20

I'm doing Blast protein for a single sequence. After selecting the database (pdb) and setting other params, I receive this error in Reply log: BLAST Database error: Error: Not a valid version 4 database. How can I sort out it? Thanks for help

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SplitCommand python
by Healey, Joseph 17 Feb '20

17 Feb '20

Hi Chimera Team, I’m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I’m only using it for `split`, but I’d like to first test whether a model is already split to avoid unnecessary invocation. I’m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn’t seem to be importable, as when I try: >>> from chimera import SplitMolecule Traceback (most recent call last): File "<pyshell#25>", line 2, in <module> ImportError: cannot import name SplitMolecule I’m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I’ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I’m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ‘layer’ below `chimera` itself. Can you elighten me? I’m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps. If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help. Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

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missing color option in model panel
by abhisek Mondal 15 Feb '20

15 Feb '20

Hi, Newest version of chimera does not have the color option in the model panel. Is this a bug of some sort? Please see the attached image. Regards Abhisek -- *Abhisek Mondal, Ph.D.* *Cardiovascular Research InstituteUniversity of California San Francisco555 Mission Bay Blvd. South. Rm 482Dan Minor's LabSan Francisco, CA 94158USPS address:UCSFAbhisek Mondal, Ph.D.Cardiovascular Research Institute, Box 3122555 Mission Bay Blvd., Floor 4San Francisco, CA 94143*

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Default storage folder, ChimeraX
by Martín González Buitrón 14 Feb '20

14 Feb '20

Dears all, Hope you are well. I have started to use ChimeraX in Ubuntu and I realised that one folder was created with my fetches and other things (i.e. ~/Download/ChimeraX/). How can I change this to other of my own preference? All the best, Martín

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Coloring N-terminal and C-terminal
by Tom Goddard 14 Feb '20

14 Feb '20

You can rainbow color proteins from N (blue) to C (red) terminus to see where the ends are using menu Tools / Depiction / Rainbow, or the command rainbow. Tom > On Feb 14, 2020, at 1:32 AM, Nail Besli wrote: > > how can I detect the N-terminal or C-teminal after docking of two proteins in Chimera > Thanks >

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Map is not visible in COOT
by Dmitry Semchonok 13 Feb '20

13 Feb '20

Dear colleagues, I have cryo-em map saved in chimera. But when we want to open it in with COOT the map is not visible. Could you please give me any suggestions? Thank you Sincerely, Dmitry

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changing density map from surface to mesh view
by Anindito Sen 12 Feb '20

12 Feb '20

Dear All, While making a movie, what will be the command to change view of the density map from surface to mesh. Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu

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problem saving images
by Rapson, Trevor (A&F, Black Mountain) 11 Feb '20

11 Feb '20

Dear Chimera team, I have recently come across a problem saving images in Chimera where it saves the image but it opens as a completely black image (and very small file size). I've tried changing a few different settings and that doesn't help. The error also seems to be there with when I save a video. Your help is much appreciated. Regards, Trevor Dr Trevor Rapson Research Scientist Agriculture and Food CSIRO Phone: +61 2 6246 4104 Trevor.Rapson(a)csiro.au<mailto:Trevor.Rapson@csiro.au>| www.csiro.au<http://www.csiro.au/> Address: P.O. Box 1700, Canberra, ACT, Australia PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.

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Docking
by Greta Hodo 11 Feb '20

11 Feb '20

Hi, I have a problem with the result of autodock Vina. When I load a molecule in “mol2” format and I use AutoDock Vina for docking, the docked molecule is altered. How can be possible? How can I solve my problem? I attach the photo of the real molecule [cid:C2748141-718F-40C4-8964-A212C52FDB1A] And this I how the molecule changes after the docking [cid:C1EDE285-2873-437D-A034-5BB2D031BD67] The 5-term ring becomes aromatic, while it should have only a double bond. ( this happens both if I save autodock vina result in “mol2” format and “pdb” format Hope you can help me!

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S1-8
by 林联云 11 Feb '20

11 Feb '20

Dear management， I am a PHD student from Tianjin University in china. I saw a movie which is done in chimera (see the attachment), i saw they draw a circle around the text (NTD-A). i am very confuse that i do not know how to draw a shape in chimera. i ask for you that tell me how to draw a shape in command line. Thanks very much. Best wishes, Lin l

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Re: [Chimera-users] [chimerax-users] Reproduce exact view
by Tom Goddard 10 Feb '20

10 Feb '20

Hi Elaine, Alexis, You can change a model number by command. So if you replace model #3 with model #8 that you align to #3, then delete #3, then "rename #8 id #3" will change the model id of #8 to be #3. For the step of aligning #8 to #3, if they are aligned already then #8 would open aligned to #3 unless you had moved #3 in which case you could use "view position #8 sameAs #3". Of course if the new model has not been aligned to the old you may need to use the matchmaker command to align them. Tom > On Feb 10, 2020, at 1:44 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Alexis, > We removed the forward-compatibility warning during session saving a while ago, so as long as the version you’re using is not too old, we expect the session files to be forward compatible. Still, I understand a reluctance to rely on them completely when it can take many hours or even days to set up everything the way you want. > > Sometimes I just save the session now. However, sometimes I use a “belt and suspenders” approach by saving not just the session but also a command file that has just about everything I’d used for the setup except for interactive manual positioning. I often include such a script when I add a “feature highlight” to the ChimeraX website. > > I too have often wished for an easy way to replace one model in an existing session with another. Getting the matrices (view matrix), swapping out the model, and then reapplying the matrix may be the most exact way if the models are in the same coordinate system as each other. Otherwise you could open the new model, match or fit it to the one you wish to replace, then close the one you want to get rid of. That leaves you with different model numbers, however, so if it is important to get them the same you’d have to open the new model again, match it to itself, and remove the extra intermediate copy you’d opened first. (Ugh.) > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Feb 10, 2020, at 1:22 PM, Alexis Rohou <a.rohou(a)gmail.com> wrote: >> >> Thanks Elaine, >> >> I should have added some explanation for my workflow: >> 1. I read a while back that ChimeraX sessions may or may not be forward compatible, and I wanted to ensure long-term reproducibility of my figures >> 2. a requirement I have is that I should be able to quickly remake the exact same figure after I change the input files. For example, perhaps I prototype an elaborate figure using a PDB that's a work in progress and later re-make it with an updated PDB. The advantage of a .cxc script is that I just have to change the filename near the beginning of the script and everything else stays the same. I can regenerate all my figures pretty quickly that way. That's the big payoff for investing the time to write a script upfront. >> >> The view functionality does sound very nice though, especially since I don't currently have a way to achieve transitions with my scripts (other than perhaps creating views within the scripts themselves?). Elaine, is there a way to use sessions so that I could replace a model or map with a new version of a file after I've already created a session? >> >> Cheers, >> Alexis >> >> On Mon, Feb 10, 2020 at 9:26 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> Hello, >> Maybe I’m missing something, but the “view” command allows saving and restoring named views. These are included in saved session files. I agree window size is also a factor, so you would make sure to set the same window size too. >> >> E.g. once you have the view you like then use a command like: >> >> view name myview >> >> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> >> >> Then you can save the session file and/or move things around. Later in the same session or after restoring the previously saved session from file, >> >> view myview >> >> …will restore that view. Restoring the session restores window size if you have that Window Preference set: >> <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#window> >> >> or you could have noted the window size when you saved the view: >> >> windowsize >> >> …and then use the reported values later to restore that size, e.g. >> >> windowsize 600 400 >> >> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/windowsize.html> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Feb 10, 2020, at 8:53 AM, Alexis Rohou <a.rohou(a)gmail.com> wrote: >>> >>> Hi Christophe, >>> >>> I prepare my figures using ChimeraX command (.cxc) scripts and I believe I have a workflow that lets me reproduce exact views. I know it's not 100% robust, but it's reliable enough for me. It basically relies on a sequence of close; windowsize; view matrix; zoom; clip; save. >>> >>> Here is a pseudo script. To work out the values you need for the matrices, just move your point of view and your models until you are happy, then do "view matrix". I have not worked out a good way to get the distances for the clip planes. So I just play with them on the command line until I get the look I want, then save the values in my cxc file. >>> >>> Hope this helps & that more experienced users can chime in with improvements. >>> >>> Cheers, >>> Alexis >>> >>> >>> # close anything currently open >>> close >>> # go to relevant directory >>> cd /my/absolute/path >>> # >>> windowsize 1200 1200 >>> camera ortho >>> clip near off far off front off back off >>> # Open files >>> open my_model.pdb name "my model" >>> open my_map.mrc name "my map" >>> # etc. >>> >>> #insert here coloring, styles, for the model/map/background etc >>> >>> # Go to your favorite view point, save a shot >>> view matrix camera 1,0,0,182.59,0,1,0,229.79,0,0,1,352.89 >>> zoom 0.33 >>> clip near off far off front off back off; clip near -100.0 far +100.0 front off back off >>> ~select >>> save my_figure.png supersample 3 transparentBackground false >>> >>> # If you need to move your models >>> view matrix models #1,0.91269,-0.0093359,-0.40855,59.153,-0.40865,-0.018906,-0.91249,368.7,0.00079806,0.99977,-0.02107,-44.893,#2,-0.83654,-0.058918,-0.54474,344.52,-0.54355,-0.035951,0.83861,293.33,-0.068993,0.99762,-0.0019503,-42.032 >>> >>> # then take another shot >>> view matrix camera 0.98289,-0.005269,-0.18408,131.07,-0.17421,-0.3506,-0.92018,70.662,-0.059691,0.93651,-0.34553,163.8 >>> clip near off far off front off back off; clip near -20.0 far +12.0 front off back off >>> save Figures/TRPA1_3551_binding_site_details1.png supersample 3 transparentBackground false >>> >>> >>> >>> >>> On Sun, Feb 9, 2020 at 10:01 AM Christophe Leterrier <christophe.leterrier(a)gmail.com> wrote: >>> Hi, >>> >>> I haven't been able to find how to >>> - log >>> - set >>> - store >>> - recall >>> >>> a precise view (ie get the same exact image if I do a snapshot). >>> >>> First use case would within the same session (fixed computer, window size, no restart of the application in between). Second use case (more tricky?) would be independently of computer / window size / current session. >>> >>> Thanks for your help! >>> >>> Christophe >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users > > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users >

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moving parts of a density map in a Movie
by Sen, Anindito 05 Feb '20

05 Feb '20

Dear All, I have a composite density map with 7 individual reconstructions combined together. For making a movie to show the different components and their organization- What will be the commands to make the individual density maps to move out of their position (in the composite map) and fly back in, (one or multiple density maps at a time). Regards Anindito Sen. Ph.D

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Phosphorylated residues showing up as X
by Daniel Hilger 05 Feb '20

05 Feb '20

Hi, I modeled two phosphorylated residues in my structure. The primary sequence window in Chimera, however, is only showing a “X” at those positions. Is there a possibility to change that to the original amino acid (S or T) or to show them as SEP or TPO in the sequence window? Thanks, Daniel Daniel Hilger, Dr. Group leader Philipps-University Marburg Marbacher Weg 6 35032 Marburg Germany daniel.hilger(a)pharmazie.uni-marburg.de Phone: +49 6421 28 25930

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Chimera Download issue
by Zachary Maldonado 04 Feb '20

04 Feb '20

To whom it may concern, My name is Zachary Maldonado and I am a college student at the University of Missouri-Columbia. I need this program for one of my classes I am taking this semester. I can not seem to open the program and when I try to open it, I get a message from my computer saying that I need to update the application before I can open it. My computer says it is unable to search for "malicious software". If you could assist me that would be greatly appreciated. Thank you! Sincerely, Zachary Maldonado

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Supporting XDG base directory - chimera
by Martín González Buitrón 04 Feb '20

04 Feb '20

Dears all, I realised that you are using a hidden folder (.chimera/) in $HOME directory, linux's distribution. Have you considered supporting freedesktop.org's standard specs? References: - http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html - https://wiki.archlinux.org/index.php/XDG_Base_Directory All the best, Martín

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MD chimera bug
by Fabian Glaser 31 Jan '20

31 Jan '20

Dear Chimera developers, I think I have found abug in the MD movies tool in Chimera, when trying to use the Per-Frame command Script: When selecting residues > :1000 (which have a residue number > 1000) it does not select the the residue, since it adds to the residue number the frame number, for example see the figure attached, with this logic, and trying to apply the script, if the I try to select residue :1000 the script gives a mistake and this is because it tries to select residue frame + residue number (in this case 96000) which of course does not exist. The same sequence works perfectly if the selection is done outside the script Best, Fabian Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701

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conjugate moiety to protein PDB
by Michael Scott Bowers 30 Jan '20

30 Jan '20

Hi power users, I have 2 tasks that I hope you can help with. Both of these require conjugation of a moiety to multiple places on a large, multi chain protein. Command line solutions are fine. Task 1. Conjugate some group like a tosyl to selected cystine residues. There could be about 200 residues needing conjugation across 4 chains of a protein PDB file. Task 2. Conjugate a peptide chain to the N or C terminus of a multi chain protein PDB file. I am already familiar with build structure protein and smiles, but connecting models without severe steric hindrance is problematic. Also, given the number of needed conjugations, it would be great it I could do this via command line (or some other function that I am currently not aware of) so that the tosyl or peptide chains needing connecting do not have to be positioned prior to making the covalent bond. Much thanks to everyone in advance. Best, Scott

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Auto-associate define attribute/render by attribute
by Healey, Joseph 24 Jan '20

24 Jan '20

Hi Chimera team, I’m working on a script to automatically render proteins in a complex by attributes (in this case, a number of scores obtained from different immunogenicity prediction algorithms). I currently have the script outputting attribute files as intended, but ideally I’d like to define the same attributes across all the chains of the model, which are made up of a number of different proteins. Is there any way for me to define the attribute file, or utilise some functionality to auto-associate an attribute file with all of the chains which have the correct sequence (similarly to how the sequence alignment input works at the moment?). Currently the attribute file is only using ‘numbered’ coordinates (:1, :2, :3…etc) , rather than the actual sequence. Since there’s no chain information in the attribute files, I’m not sure how I can go about connecting it to the right structure, other than manually at the moment? Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

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Fourier transform
by Angus McDonald 23 Jan '20

23 Jan '20

I am having trouble using the fourier transform tool in Chimera. I have tried looking for it in the Tools/Volume Data menu and I don't see it. I have also tried the start fourier which returned an error message. I suspect I am doing something wrong . Can you please help with this issue. I am using 1.13.1 build 41965 Platform Windows 64. Thanks for your help -- Angus McDonald amcdonald(a)boisestate.edu

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