- ChimeraX-users - RBVI Mailing Lists

color by conservation problem
by Elżbieta Wątor 05 Nov '23

05 Nov '23

Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator [cid:e1499547-d8cf-48a6-89cb-b2ea6e696097]

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Select truncated residues in PDB
by Vorländer,Matthias Kopano 05 Nov '23

05 Nov '23

Dear ChimeraX team, Is it possible to select all residues in a model that have been truncated to backbones rather build as a complete sidechain? Many thanks, Matthias

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installing plugin
by Dmitry Semchonok 04 Nov '23

04 Nov '23

Dear colleagues, Is anything happened with the website https://cxtoolshed.rbvi.ucsf.edu/ It seems to be still down. Kind regards, Dmitry

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mseries oscillate/loop ?
by vincent Chaptal 04 Nov '23

04 Nov '23

Hi again, it is possible to use vseries play #1 loop true, but the same command with mseries doesn't work. Same with oscillate or similar commands. I've also tried mseries #1.1-20-1 or mseries #1.20-1 but these 2 commands don't work. Is there a way to make the movement go back to the origin? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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ISOLDE and heparin
by Xuewu Zhang 04 Nov '23

04 Nov '23

Dear Tristan, Can ISOLDE handle heparin molecules now? I tried to simulate a heparin chain, it says one residue is not properly parametrized. I am using ISOLDE in Chimerax 1.6. Thanks, Xuewu

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UCSF Chimera 1.17.1
by hj_bowles＠sky.com 03 Nov '23

03 Nov '23

Good Evening, I need to download UCSF Chimera 1.17.1 for a examination, however due to the downtime on your website i am unable to do so. is there any way you can send me a link to download of get around this issue for me? I would be very grateful. Kind regards,Heather.

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fly command
by Sean Connell 03 Nov '23

03 Nov '23

Hello, I have a question about the fly command. I am trying to iterate over a series of saved views (p1-p6) using the fly command. The views are close-up views of residues because I am trying to make a movie similar to that made with resfit. The issue is that the cutting plans don't seem to update as it moves from view to view. Do you have a hint that could let me know what I am doing wrong? Thanks for any tips you have

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Show models from the same file, one by one into a movie
by vincent Chaptal 03 Nov '23

03 Nov '23

Hi, I have a PDB file with 20 models inside(#1.1 to #1.20)that I color as a rainbow. I would like to show them sequentially and make a movie showing one model at a time, back and forth (show #1.1, hide #1.1 and show #1.2, etc...). I've played with the morphing command but it is not what I want, and then with the Coordset command thinking it would be like a trajectory but I can't make it to work. I would appreciate a pointer to get me to the right direction. Thanks a lot. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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ChimeraX tutorial pages
by Kai Cai 03 Nov '23

03 Nov '23

Hi, Just noticed that the ChimeraX tutorial pages are not accessible. Are they temporarily down or permanently removed? Thanks, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Show models from the same file, one by one into a movie
by vincent Chaptal 03 Nov '23

03 Nov '23

Hi, I have a PDB file with 20 models inside(#1.1 to #1.20)that I color as a rainbow. I would like to show them sequentially and make a movie showing one model at a time, back and forth (show #1.1, hide #1.1 and show #1.2, etc...). I've played with the morphing command but it is not what I want, and then with the Coordset command thinking it would be like a trajectory but I can't make it to work. I would appreciate a pointer to get me to the right direction. Thanks a lot. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Middle mouse click to center and move to atom
by Adrián González López 27 Oct '23

27 Oct '23

Hi, I do not know if this is possible already (I could not find it), but is there a way in ChimeraX to set the middle click mouse button (or any other button) to center and orient the atom you click? Similar to what happens on PyMOL by default. This helps so much when navigating around a structure. I know you can do it in some other way, but it takes more time and it is not so user-friendly. If there is no way to do this, could it be implemented? Many thanks! Best, Adrián När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Cap clipped atoms or bonds
by Daniel Larsson 27 Oct '23

27 Oct '23

Is it possible to have atoms or bonds capped when they are truncated by a near clipping plane, similar to how surfaces can be capped. Currently, you can see the interior polygons when you clip the middle of a molecule. See the attached image for an example. I tried to search the mailing list and the documentations, but could not find anything. Regards, Daniel [cid:image001.png@01DA08BB.1559BC80] När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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ChimeraX for WSL: release request
by Dmitry Semchonok 27 Oct '23

27 Oct '23

Dear Elaine and Eric, Since the number of Windows WSL systems is increasing do you consider releasing the compatible version of ChimeraX? Thank you Kind regards, Dmitry

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Chimera(X) website and web services down Oct 30-31
by Elaine Meng 26 Oct '23

26 Oct '23

Dear users, Due to system upgrades, the Chimera and ChimeraX websites, associated web services hosted by the UCSF RBVI (Modeller, Blast Protein, etc.), and the ChimeraX Toolshed will be unavailable -- the estimated downtime is from Monday, Oct 30 8:00 am PDT through Tuesday, Oct 31 11:59 pm PDT. Please pardon the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: Selection with coordinates
by Tom Goddard 25 Oct '23

25 Oct '23

Hi Siyoung, The movie recording needs a "wait" command to actually render frames. If you have 300 frames in your coordinate set it would be perframe "open select_atoms.py" movie record coordset #1 wait 300 movie encode test.mp4 Also I would suggest that your python code not use "atom.hide". That is an obscure attribute for hiding backbone atoms with ribbon display. Instead use atom.display = True atom.display = False It might be possible to record the movie entirely in Python, but I've never tried it. I would not suggest trying that approach unless you want to waste a lot of time since the movie recording code was not designed to work in a Python script. Tom > On Oct 24, 2023, at 6:01 PM, Siyoung Kim <kkssy141(a)gmail.com> wrote: > > Thank you very much for the helpful information. I think I am very close to what I want to do. > > I would like to make a video of a molecular dynamics trajectory and want to show only the atoms whose x coordinates are smaller than 0. Here is what I tried. > > a) I made a python script that can be applied to each frame and named it "select_atoms.py" > --------------------------------- > from chimerax.atomic import all_atoms > atoms = all_atoms(session) > for atom in atoms: > if atom.scene_coord[0] < 0: > atom.hide = 0 > else: > atom.hide = 1 > ---------------------------------- > > b) I opened up a trajectory in ChimeraX. > > c) In ChimeraX, I executed > --------------------------------------------- > perframe "open select_atoms.py" > movie record > coordset #1 > movie encode test.mp4 > ---------------------------------------------- > > Interestingly, if I just move a frame by myself using a slider, perframe is applied well. i.e., only the atoms whose x coordinates < 0 are shown in EACH frame > However, if I record a video like the above or click a play button, perframe is not successfully applied. Only the atoms whose x coordinates < 0 in the last frame are shown in all frames. Updating a selection in each frame does not work with this approach. > I have attached the video. Would you please help me with this? Thank you. > > I would be also curious if it could be done inside a python script. In the above, I made a script that should be applied to each frame and then called this script using perframe in ChimeraX. Would there be something like RED in the below? Thank you very much! > > RECORDING A MOVIE > for s in all_atomic_structures(session): > for cs_id in s.coordset_ids: > s.active_coordset_id = cs_id > atoms = s.atoms > atoms.selecteds = atoms.scene_coords[:,0] < 0 > atoms[atoms.selecteds].hide = 0 > atoms[~atoms.selecteds].hide = 1 > SAVE THIS IMAGE > ENCODING A MOVIE > > > On Mon, Oct 23, 2023 at 11:52 AM Siyoung Kim <kkssy141(a)gmail.com <mailto:kkssy141@gmail.com>> wrote: >> Hi Eric, >> >> Thank you very much for the very helpful information! I learned a lot. >> >> Best, >> Siyoung >> >> On Fri, Oct 20, 2023 at 8:58 PM Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>>> On Oct 17, 2023, at 1:53 PM, Siyoung Kim via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> Hi Tom, >>>> >>>> Thank you for your help. I can confirm that making a text file, select.py, that contains the below and running "run select.py" in the ChimeraX command line works. >>>> >>>> from chimerax.atomic import all_atoms >>>> for a in all_atoms(session): >>>> if a.scene_coord[0] < 0: >>>> a.selected = True >>>> >>>> I am quite interested in learning more about the chimerax.atomix library. Would there be any helpful resources about this? >>> >>> There is automatically generated documentation, but I don't recommend it because it is poorly formatted and littered with rarely used constants and functions from base classes (e.g. Structure inherits from Model and Drawing and therefore documentation for first_intercept_children() [from Drawing] is included). Instead, I'd browse through the code for atomic class definitions themselves. The Cython class definitions for Atom, Element, and Bond are here: https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/atomic_cpp… . The definitions for the other classes are here: https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/molobj… . The latter only has the base class definitions for Structure and PseudobondGroup (StructureData and PseudobondGroupData respectively). The final definitions are in structure.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/struct…> and pbgroup.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/pbgrou…> . >>> >>> Another approach is to find a bundle that does something similar to what you want to do and look at its code to see how it does it. All the ChimeraX source code is in the repository linked to above (and the Python code is included in every ChimeraX installation). >>> >>>> Would it be also possible to loop over a molecular dynamics trajectory and select wanted atoms in this way? >>> >>> Yes. A structure that is a trajectory will have multiple "coordinate sets" (sets of coordinates for the atoms). Therefore you can loop through the trajectory like so: >>> >>> from chimerax.atomic import all_atomic_structures: >>> for s in all_atomic_structures(session): >>> for cs_id in s.coordset_ids: >>> s.active_coordset_id = cs_id >>> for a in s.atoms: >>> a.selected = a.scene_coord[0] < 0 >>> >>> It may also be useful to know that the value returned by s.atoms is an "Atoms" instance (see molarray.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/molarr…>) which in many ways can be treated as a vector for efficiency, which could definitely matter when processing a trajectory. So the above code could instead be: >>> >>> from chimerax.atomic import all_atomic_structures: >>> for s in all_atomic_structures(session): >>> for cs_id in s.coordset_ids: >>> s.active_coordset_id = cs_id >>> atoms = s.atoms >>> atoms.selecteds = atoms.scene_coords[:,0] < 0 >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>>> >>>> Thank you. >>>> Best, >>>> Siyoung >>>> >>>> On Tue, Oct 17, 2023 at 4:06 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>>> Oops. If you put this code in a file it needs to have a ".py" suffix, so call it select.py. The ".cxc" suffix is for ChimeraX commands. >>>>> >>>>> Tom >>>>> >>>>> > On Oct 17, 2023, at 12:58 PM, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > >>>>> > Hi Siyoung, >>>>> > >>>>> > Here is Python code to select all atoms with x < 0. >>>>> > >>>>> > from chimerax.atomic import all_atoms >>>>> > for a in all_atoms(session): >>>>> > if a.scene_coord[0] < 0: >>>>> > a.selected = True >>>>> > >>>>> > You can type this in the ChimeraX Python shell (menu Tools / General / Shell), or probably easier, put it in a text file "select.cxc" and open that in ChimeraX to run it. >>>>> > >>>>> > Tom >>>>> > >>>>> >> On Oct 17, 2023, at 9:04 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >> >>>>> >> Hello Siyoung, >>>>> >> Sorry no, I can't think of a way to do it with a ChimeraX command. Maybe you could do it by using the initial orientation of the structure (just opening and not rotating) and veerrryyy carefully using the mouse to select a rectangle (Ctrl-click drag) but that is probably too difficult. Also you would need to know where X=0 is from just looking at the structure. >>>>> >> >>>>> >> Certainly you could do it with Python, but somebody else would have to advise on that. >>>>> >> >>>>> >> Best, >>>>> >> Elaine >>>>> >> ----- >>>>> >> Elaine C. Meng, Ph.D. >>>>> >> UCSF Chimera(X) team >>>>> >> Department of Pharmaceutical Chemistry >>>>> >> University of California, San Francisco >>>>> >> >>>>> >>> On Oct 17, 2023, at 5:33 AM, Siyoung Kim via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >>> >>>>> >>> Hello, >>>>> >>> >>>>> >>> Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)? >>>>> >>> >>>>> >>> Thank you. >>>>> >>> Best, >>>>> >>> Siyoung >>>>> >> >>>>> >> >>>>> >> _______________________________________________ >>>>> >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>>> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>>> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> >> >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>>> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>>> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> > >>>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> > <test.mp4>

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crop the map
by Dmitry Semchonok 25 Oct '23

25 Oct '23

Dear colleagues, Could you advise on how to crop the map to the new 3D box size and save those changes? Thank you. Sincerely, Dmitry

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Fwd: [ccpem] Help with pairing RMSD in Chimera like COOT
by JAMES MICHAEL KRIEGER 25 Oct '23

25 Oct '23

Dear Rajnandani and all, I am adding in the chimerax users list (I don't know the plain chimera one) as I think this is a better question for people there. Just to clarify, by adjust the RMSD for the map, I guess you mean scrolling the cutoff value? Best wishes James ----- Mensaje reenviado de Alfredo Jose Florez Ariza <0000b1a72b269dbc-dmarc-request(a)jiscmail.ac.uk> ----- Fecha: Tue, 24 Oct 2023 11:49:00 -0700 De: Alfredo Jose Florez Ariza <0000b1a72b269dbc-dmarc-request(a)jiscmail.ac.uk> Responder-A: Alfredo Jose Florez Ariza <alfredo.florez(a)berkeley.edu> Asunto: Re: [ccpem] Help with pairing RMSD in Chimera like COOT Para: CCPEM(a)jiscmail.ac.uk You mean you wanna show just the density corresponding to certain region of the model? If so, you can use volume zone command. It will be something like: volume zone #X near #Y/Z: aaa-bbb range 3 X and Y are the ID numbers of your map and model. Z is the chain of your model and aaa and bbb are the residues you are interested in showing the map around. The range 3 can be modified accordingly to ‘how much of your map’ you wanna show around the model region, I guess. Alfredo On Tue, Oct 24, 2023 at 10:24 AM Rajnandani Kashyap < rajnandani.kashyap(a)health.slu.edu> wrote: > Hello Everyone > > I am at a stage of preparing figures for one of my manuscripts. And I was > wondering if we could adjust the RMSD for the map file (density) in chimera > as we do it in COOT. Basically, I want to show the electron density for a > flexible N-term residues for which I do observe the density at a lower RMSD > level in chimera. > > Any help would be greatly appreciated. > > Thanks, > Rajnandani Kashyap > Postdoc Fellow > > > ------------------------------ > > To unsubscribe from the CCPEM list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 > ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- Terminar mensaje reenviado -----

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ISOLDE error: Please remove “TER” card after the single residue
by Dmitry Semchonok 25 Oct '23

25 Oct '23

Dear colleagues, I have an issue with the validation website after working with my model in ISOLDE. More detailed: When starting the simulation in ISOLDE, I am running into the error: At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out. So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error: File upload failed. Please review the errors below and try again. Coordinates issues. ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again. Some more observations: Although MYR is the first residue in the ChimeraX sequence, it is not visible. At the same time, COOT can see it. Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE. Please let me know if you require a model/map file for the investigation. Thank you Kind regards, Dmitry

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Distinct clipping planes per model
by Dorien Pastoors 24 Oct '23

24 Oct '23

Hi, Thanks for maintaining such a nice software package! I'm still learning, and I'm currently stuck on clipping. I'm trying to clip models differently in ChimeraX. My aim is to have a global clipping plane to visualize two drugs binding to two domains (in the image in yellow/blue). Now I would like to offset the clipping plane slightly for surrounding protein (in beige). I would like to do this to increase the depth in my image and to emphasize that these domains are embedded in a bigger protein. As it is in fact a huge protein (its an alphafold predicted structure) making the entire protein transparent will still obscure the view on the compounds in their domains. As you can see, by using clip model I've been able to turn off clipping for the drugs in their binding pockets. However, with clip model I can only switch on or off the entire clipping plane , not offset it for a particular model. I've tried: clip model #2.3 front -10 clip model #2.3 offset -10 With clip model I can't specify an offset as it gives an error, I can only turn clipping off completely with "clip model #2.3 false", while "clip front -10" affects the total clipping plane, and I cannot specify a particular model for this clipping plane. (the beige protein model is #2.3) Hope this is clear enough and you have a solution! Thanks in advance! Kind regards, Dorien Pastoors

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Image rendering artifacts with silhouettes and pixelSize value
by Vorländer,Matthias Kopano 24 Oct '23

24 Oct '23

Dear ChimeraX team, I am having issues when using silhouettes and saving an image while specifying the pixel size, as I get the artefacts shown in the attached image. If I don’t use silhouettes or don’t specify the pixel size things look fine. I updated to the latest daily version and uninstalled Isolde and ArtiaX, but the problem persist. I work on a MacBook Pro under Mac OS Ventura 13.5.2. Any ideas for fixes? Many thanks, Matthias [A white structure with colorful strands Description automatically generated with medium confidence]

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Difference maps in chimerax?
by Francisco Murphy Pérez 23 Oct '23

23 Oct '23

When I open a map* in chimerax, how do I specify it is a difference density map? * maps are generated with `phenix.mtz2map finalpdb.pdb finalmtz.mtz` ... both files from the pdb-redo. Thanks

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Morphing problem
by Raphael Bader 23 Oct '23

23 Oct '23

Dear all, I would like to ask for some information/help for a problem I am facing at the moment: I am currently working on a pentameric protein (C5 symmetric) that undergoes a big conformational change (translational & rotational movement) and would like to utilize the morph function in ChimeraX to come up with a good animation for it. For one single protomer the animation works fine – however, for the full pentamer the subunits follow both directions, clockwise and counterclockwise, during their rotational movement which obviously leads to a lot of clashes and therefore does not look very convincing. Since I tried almost all options listed as parameters for the morph (linear & corkscrew method, cartesian true and false, rates, coreFraction, etc.) and it did not affect the direction of rotation at all, I was wondering whether there are additional values I could modify or any other trick that might equalize the movement? Thank you very much in advance! Best regards, Raphael P.S.: I would be happy to provide data if it might help solving the problem.

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Selection with coordinates
by Siyoung Kim 23 Oct '23

23 Oct '23

Hello, Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)? Thank you. Best, Siyoung

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Re: [Chimera-users] How to obtain transformation matrix between protein structures
by Elaine Meng 22 Oct '23

22 Oct '23

Hi Qiancheng Xia, Please use the chimerax-users(a)cgl.ucsf.edu address (CC'd here) for ChimeraX questions so that people don't get mixed up between Chimera and ChimeraX. Chimera does not have the reportMatrix option. As for ChimeraX, you didn't show the exact command that you tried so I can only guess what went wrong. My guess is that you need to include "reportMatrix true" not just "reportMatrix" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 20, 2023, at 4:39 AM, 夏前程 via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. > With Regards, > > Qiancheng Xia > > National Institute of Biological Sciences > > Beijing, China > > 2023/10/20 >

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Export Isolde residue paramters (xml) for phenix
by Sean Connell 21 Oct '23

21 Oct '23

Hello, Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement? Sean

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