- ChimeraX-users - RBVI Mailing Lists

ChimeraX image saving automation
by Attana, Fedaa 19 Jan '23

19 Jan '23

Hi all, I have started to use Chimera recently and found it very cool. I liked the way I can edit all of my structure with one command when no model is selected. However, to save images, I have to manually show each structure (model) and run the same saving command with a new name. I wonder if there is an easier way to do this or if somebody did automate this process so one can save images of individual models with a script? Thanks in advance, Fedaa

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scalemol extension not working
by André Graça 19 Jan '23

19 Jan '23

Hi everyone, I hope to at least get a reply from Tom, but this may need a bit of troubleshooting (?). I looked into a very old post of yours, Tom, about rescaling an atomic model (see it at the end of my email). I put everything in place but I get an error and I wonder if anything has changed with the PDB format since 2005, or some incompatibility with new chimera versions... If there is actually a way of doing the same with ChimeraX, that would be incredible =) Cheers! André Error and forwarded message comes now: __________________________________________________ AttributeError Exception in Tk callback Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x00000000079092C8>> (type: <type 'instancemethod'>) Module: <module 'Midas.midas_ui' from 'C:\Program Files\Chimera 1.16\share\Midas\midas_ui.pyc'> (line: 618) Args: (<Tkinter.Event instance at 0x00000000198D8AC8>,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\Midas\midas_ui.py", line 628, in processCommand midas_text.makeCommand(cmdText) File "C:\Program Files\Chimera 1.16\share\Midas\midas_text.py", line 69, in makeCommand f(c, args) File "C:\Program Files\Chimera 1.16\share\scalemol\ChimeraExtension.py", line 23, in scale_molecule x, y, z = a.coord().xyz.data() AttributeError: '_chimera.Point' object has no attribute 'xyz' ================================================ Event contents: char: delta: 0 height: ?? keycode: 13 keysym: Return keysym_num: 65293 num: ?? serial: 14638 state: 8 time: 154527203 type: 2 widget: .121252488L.126915336L.428746824L.428747592L.428747720L width: ?? x: 228 x_root: 288 y: -22 y_root: 941 ______________________________________________________________________ ------- Start of forwarded message ------- Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT) From: Thomas Goddard <goddard at cgl.ucsf.edu<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> Hi Jinghua, By "virus cage pdb file" I guess you mean you placed atoms at icosahedral positions, and want to show them connected up to show some icosahedral pattern. I think the easiest approach is to open your old session, run a command to change the diameter of the cage, then save a new session. Below is some Python code that provides a "scalemol" Chimera command. Make a directory chimera/share/scalemol in your Chimera distribution and put the code below in file chimera/share/scalemol/ChimeraExtension.py. Then start Chimera, open the cage PDB model, use menu entry Favorites/Command line, and type a command: scalemol 0 1.5 to make model number 0 bigger by a factor of 1.5. If you have more than one model open you can see the model numbers using Favorites / Model Panel, the model number is shown in the left hand column. Tom - ---- scalemol/ChimeraExtension.py code follows: # ----------------------------------------------------------------------------- # def scale_molecule(cmdname, args): from Midas.midas_text import error fields = args.split() try: model_num = int(fields[0]) factor = float(fields[1]) except: error('Syntax error: scalemol <model-number> <factor>') return import chimera mlist = chimera.openModels.list(id = model_num) if len(mlist) == 0: error('scalemol: No model number %d' % model_num) return for model in mlist: for a in model.atoms: x, y, z = a.coord().xyz.data() c = chimera.Coord() c.x, c.y, c.z = (factor*x, factor*y, factor*z) a.setCoord(c) # ----------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('scalemol', scale_molecule) ------- End of forwarded message -------

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missing or invalid sequences
by Liang, Junyi 19 Jan '23

19 Jan '23

I would like to predicate interaction between two proteins, and tried chimerax version 1.5 after noticing a youtube video https://www.youtube.com/watch?v=6lXeCPuTePs. [https://www.bing.com/th?id=OVP.95Ygyv4AXQTgCS0WB9iXtgHgFo&pid=Api]<https://www.youtube.com/watch?v=6lXeCPuTePs> Running AlphaFold to Predict Protein Complexes from ChimeraX<https://www.youtube.com/watch?v=6lXeCPuTePs> How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html www.youtube.com I input the two protein sequences in same way as shown in the video and hit predict. But your software says "missing or invalid sequences". How come? Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Is RR Distance Maps implemented in ChimeraX?
by Michael Bruist 19 Jan '23

19 Jan '23

I use RR Distance Maps in Chimera for my teaching. I want to switch to ChimeraX, but I have not bee able to find this tool. Is it available in ChimeraX? Mike Bruist Michael F. Bruist Professor of Biochemistry Department of Chemistry and Biochemistry St. Joseph’s University 215-596-8530 mbruist(a)sju.edu

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Reasign secondary structure for back-bone trace
by Enrico Martinez 19 Jan '23

19 Jan '23

Dear Chimera-X users! I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command? Many thanks in advance Cheers Enrico

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incomplete output from matchmaker embedded in python script
by Borchert, Milan 19 Jan '23

19 Jan '23

Hello ChimeraX community, I have been trying to use the Chimerax tool to sequentially check one query pdb against multiple (later up to 10000) pdb files. For this I have been working with the python scripting functionality. With the following code I was able to get the resulting data (number of matched atoms and resulting RMSD) saved as a html log file: import os from chimerax.core.commands import run as rc # change to folder with data files os.chdir("/home/ubuntu/Desktop/Chimerax_search/N_crassa_pdb") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # give path to query file to be searched against pdb library query = "/home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb" # open the query file as #1 in ChimeraX rc(session, "open /home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb") # loop through the files for fn in file_names: # open first target pdb as #2 rc(session, "open " + fn) # match both structures rc(session, "match #1 to #2") # save log with ID matching input filename, close #2 and clear log rc(session, "log save " + fn.split(".")[0] + ".log") rc(session, "close #2") rc(session, "log clear") Instead of trying to gather the relevant data from thousands of rather large html output files I instead would prefer to only get then resulting values from matchmaker. I learned that the command actually has all the values I wanted as return values, so I tried to write a modified script, that saves these values in a variable and collects the values for every target pdb file in a dict: import os from chimerax.core.commands import run as rc # change to folder with data files os.chdir("/home/ubuntu/Desktop/Chimerax_search/N_crassa_pdb") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # give path to query file to be searched against pdb library query = "/home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb" # open the query file as #1 in ChimeraX rc(session, "open /home/ubuntu/Desktop/Chimerax_search/query/BDFB_007497.pdb") # create empty dict to collect matchmaker output output = {} # loop through the files, opening, processing, and closing each in turn for fn in file_names: id = fn.split("/")[-1].split(".")[0] rc(session, "open " + fn) match = rc(session, "match #1 to #2") output.update({id : match}) rc(session, "log save " + fn.split(".")[0] + ".log") rc(session, "close #2") rc(session, "log clear") # display dict print(output) For now I just used 4 target pdbs with my query and only tried printing the result to quickly check if it fits. However the result is a bit baffling to me. I do get the RMSD values, but not the other data: {'NCU01382': [{'full match atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1944492130>, 'full ref atoms': <chimerax.atomic.molarray.Atoms object at 0x7f194448f610>, 'final match atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1946694430>, 'final ref atoms': <chimerax.atomic.molarray.Atoms object at 0x7f1946694550>, 'full RMSD': 63.065617285514556, 'final RMSD': 1.365365439813019, 'transformation matrix': <chimerax.geometry.place.Place object at 0x7f194669c130>, 'aligned ref seq': <chimerax.atomic.molobject.Sequence object at 0x7f19f7b8f8b0>, 'aligned match seq': <chimerax.atomic.molobject.StructureSeq object at 0x7f19f7b8f610>} here is one of the resulting hits, for my first target pdb (NCU01382). As you can see, the RMSD scores are correctly given, but for other values the internal object names and no resulting value are displayed. Any help with figuring this out would be greatly appreciated. Best Wishes Milan Borchert

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select displayed atoms via command line / transfer saved views
by Helge Paternoga 18 Jan '23

18 Jan '23

Dear ChimeraX users, I have to unrelated questions: 1) Is there a way to select displayed atoms via the command line? 2) Is it possible to transfer saved views from one session to another one? Many regards and thank you for reading, Helge

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Clipper's strange behaviour
by André Graça 16 Jan '23

16 Jan '23

Hi everyone! Is there any known issue with Clipper plugin for ChimeraX? After installing clipper and restarting ChimeraX, the software is not responding after I execute the Open command. I expect that it takes some time to open an .mtz file as the map needs to be calculated, however I have waited more than 45 minutes and ChimeraX keeps unresponsive... I am using Chimera 1.5 and I installed the (hopefully compatible) version of Clipper 0.19.0 Did anyone faced the same problem? Let me know if you have a fix or trick ;) Thanks for any feedback in advance, André ____________________ [cid:image001.png@01D9272E.120B2740]

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Movie clipping planes in chimera x
by Greg Martin 13 Jan '23

13 Jan '23

Hi, I’m trying to make a movie where I highlight different parts of a large complex. For one scene, I’m trying to interpolate between a zoomed out view of the whole complex (view p1), and then a zoomed in view of an interface (view p2), which shows a series of interactions. What I want is a smooth transition of both the view and clipping plane from p1 to p2. However, when I give the command: view p1 p2 100 it interpolates the two positions/zooms fine, in 100 frames, but then after the movement adjusts the clipping plane all at once. Is there a way to have the plane adjusted smoothly during transition between p1 and p2? I’ve also tried fly, but this disregards clipping planes altogether. Views are saved with view name p1 view name p2 Thanks in advance, Greg -- Gregory Martin, PhD. Staff Scientist Lab of Andrew Ward Department of Integrative Structural & Computational Biology The Scripps Research Institute La Jolla, CA 92037

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Inquiry: Map sequence conservation onto a protein structure
by Gomez Barillas, Andrea 13 Jan '23

13 Jan '23

Dear ChimeraX developers, I am trying to map sequence conservation onto a protein structure. I am using ChimeraX version (version 1.4 (2022-06-03). For this purpose, I was trying to use a tutorial from 2014 for Chimera for Mapping Sequence Conservation onto Structures (Showing Sequence Conservation in Chimera (ucsf.edu)<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html>). It seems that some the tools mentioned in this tutorial are no longer available, or maybe work differently. Specifically, the tutorial's "Case 4" (calculating values outside of Chimera but showing them in Chimera) has you set an attribute, and then render/color the structure based on the attribute. The Tools > Structure Analysis > Define attribute mentioned in the tutorial is no longer available. I was as able to assign values directly to structure residues in a text file and read it in using the command defattr instead. The next step would be to use the tool Render by Attribute for coloring but I cannot find this option anymore. Is there a different command I can use for this step, or a new functionality built into ChimeraX I could use for my purpose of mapping sequence conservation onto the structure? One relevant point is that I already have my sequence identify values calculated from another program, and I want to import those values. Thank you in advance for your help, Andrea Showing Sequence Conservation in Chimera<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html> Example 2B Chimera session: ConSurf-1hd2-chimera19.py [show this last!] (result of submitting 1hd2 to the ConSurf server and choosing to show results in Chimera; alignment has 150 sequences including that of the query, 1hd2) . Given a protein structure, the ConSurf server estimates the evolutionary conservation of amino acid positions based on the phylogenetic relations between homologous ... www.cgl.ucsf.edu

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