- ChimeraX-users - RBVI Mailing Lists

problem with color by conservation option
by elzbieta.wator＠doctoral.uj.edu.pl 06 Nov '23

06 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

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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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Re: Movie Record/Encode with GPU?
by Tom Goddard 20 Oct '23

20 Oct '23

No. The only way to show multiple frames of a trajectory in ChimeraX is to open them as separate models. Tom > On Oct 18, 2023, at 9:37 AM, Alexander Hung Lee <Alexander.Lee(a)uga.edu> wrote: > > Oh, and I forgot to ask… Is there an option in command line to show all the hbonds in a trajectory concurrently, even if the bond shows up at a different point in time but not current frame? >

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Surface calculation in ChimeraX
by Dennis Dannecker 20 Oct '23

20 Oct '23

Hello Chimera/ChimeraX team I recently asked already a question regarding the saving/exporting of vertices generated during the surface calculation in ChimeraX and the associated parameters with this surface generation. On a related note, I wanted to ask whether it is possible to also extract the surface (SESA and/or SASA) on a per atom basis. MSMS calculates not only the vertices for each atom (usually several vertices per atom) but it also calculates the SESA and SASA on a per atom basis. Now, I was wondering whether something is possible in ChimeraX too. As I was parsing through the docs, I was wondering whether ChimeraX calculates the surface no longer using MSMS. The vertices density supported by ChimeraX is considerably higher than what I can get with my standalone MSMS program (at least factor 6). So, if ChimeraX does not longer employ MSMS, what else does it use? With "MEASURE CONVEXITY" I get the surface vertex positions, normals, convexity values, and triangles. Unfortunately, the association with the corresponding residue is lost (however, can be regained with a little bit of work I guess, simply using euclidean distance). Question: Is there something similar for the SESA or SASA of the different atoms in the model/chain. In theory, this information should be available, at least the SESA. I am just wondering whether there is a way to write this out as a raw txt file in ChimeraX The closest I found in the save command is the .obj or .vtk format. However, both are semi-satisfying in that that they both do not provide the data looked for and are in somewhat special formats, at least the vtk. The .obj file is much much bigger than what MSMS or "measure convexity" generates, and not really handy for then working with the data in other programs, mainly python. As always, I very much appreciate any help and wish to thank the team for their contributions to the field. Best regards Dennis

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ChimeraX Help
by Bani Kaur 20 Oct '23

20 Oct '23

Hi, I hope you are well! My name is Bani Kaur and I am a ChimeraX user. I wanted to ask you about how I can specify labels on ChimeraX, specifically with finding the names of the residues on a protein. Additionally, how does info residues work and info resattr. I would appreciate any help and guidance! Thanks! Best, Bani Kaur

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ChimeraX fading?
by Elaine Meng 19 Oct '23

19 Oct '23

> On Oct 19, 2023, at 4:21 AM, Carl Johan Hagstromer <carl.johan.hagstromer(a)ki.se> wrote: > > Would love fading options, like in PyMOL > Hi Carl, We aren't Pymol users so we don't know exactly what you are referring to, but it may well be possible in ChimeraX if you could give more detail. We can put this discussion on chimerax-users(a)cgl.ucsf.edu (CC'd here) so that more folks can weigh in. ChimeraX can do: depth cueing (fading front->back), gradual fading in/out of structures and/or 2D labels by increasing or decreasing transparency over a number of image frames, and/or color modification (e.g. increasing whiteness of all current colors). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Isolde usage in Chimera
by Dmitry Semchonok 19 Oct '23

19 Oct '23

Dear colleagues, How to drag the structure, preserving the secondary structure (alpha-helix and beta-sheet) geometry in Isolde? Can I set up certain restraints to keep the correct geometry of the structure while dragging it? Many thanks! Kind regards, Dmitry

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Uncaught bounce notification
by postmaster＠cgl.ucsf.edu 18 Oct '23

18 Oct '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: command for moving atomic models in ChimeraX Date: October 18, 2023 at 5:51:07 PM PDT Dear All, I have a set of 8 proteins forming a mega complex that we are working on. The density map of the mega complex has a resolution of 2.7Ang. The atomic structures of the proteins were determined. Out of the 8, proteins 3 have C5 symmetry. I am trying to generate potential models using the atomic structures where these pentameric proteins can be expanded out (kindly see the schematic diagram S1 to S2). Is there a command (move command ??) to do so? Thanks Stay safe & 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 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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Movie Record/Encode with GPU?
by Alexander Hung Lee 18 Oct '23

18 Oct '23

Hi everyone, I have another question about scripting. I decided to use the morph command over a trajectory with 200 frames (imported as separate pdb's) to make a really smooth movie. Currently, my .cxc has matchmaker #2-200 to #1; morph #1-200 frames 8 same true play false; close #1-200 (< 5 mins) hbonds #201:UNL restrict :UNL :< 5 reveal true interModel false cacheDa true coordsets true (< 5 mins) movie record supersample 4; perframe "~label; label hbondatoms" ; coordset #201 1,1593; wait 1593; ~perframe; movie encode output movie.mp4 bitrate 6000 framerate 25 (> 1 hr) The output is buttery smooth, and the hbond calculation only takes 3-4 mins even with 1600 frames. However, I have a problem with the speed of recording/emcpdomg... it's more than an hour. I found it strange since if I played the trajectory from morph using coordset/slider, it barely takes any time and is very smooth. I was wondering if there was a way to make this recording/encoding faster or to switch from cpu to gpu if that was possible (and if it would help any)? On another note, I'm experimenting with smooth_md.py script but with trajectory files instead of pdb's. I'll see which one looks better/is faster Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Open small molecule cif
by Jaremko, Matt Joseph 18 Oct '23

18 Oct '23

Hello, How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: [cid:image001.png@01DA0026.3D6BC080] Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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memory questions
by Tintos-hernandez, Alonso A 17 Oct '23

17 Oct '23

Hi i was trying to do some modeling using the alfafold colab but it says that i need to buy more memory to run more modeling, hos should i do that ? Jesus Tintos Childrens Hospital of Philadelphia Senior scientist II

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model becomes invisible behind the map when color with hexadecimal color codes
by Kai Cai 17 Oct '23

17 Oct '23

Hi, I've got this weird bug that hope you can help me with. When I try to color a selected protein model with nonmajor hexadecimal color codes (e.g. #f17d21cc), the selected model will become invisible behind the map it was fit with. The map is set as transparent surface. Once it becomes invisible, it won't come back no matter how I change the color. This appears to be a recent issue. Not sure if it's a bug caused by recent macOS update. I am running the most recent ChimeraX daily update on a macOS 14.0. Here is an example if you would like to test it: open 25428 fromDatabase emdb open 7sth transparency 50 select #2 color sel #f17d21cc Thanks, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Opening series of pdb's in incorrect sequential order
by Alexander Hung Lee 13 Oct '23

13 Oct '23

I have a series of pdb's in a folder numbered 1 - 500 (so 1.pdb ... 500.pdb). I'm opening them in ChimeraX using *.pdb. I'm expecting 1.pdb to have ID1 and 2.pdb to to be ID2, but it appears ChimeraX is only looking at the first digit and not the whole number. Is there a way around this? For now, my work around is to use 001, 002 ... 500 instead [cid:d19d2d17-71bb-430f-8a09-65921a0ca962] Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Gaussian surface visualization of a subset of residues
by Stefano Pellegrini 13 Oct '23

13 Oct '23

To whom it may concern, I am a PhD student at the Biomedical Genomics Lab at the Institute of Biomedicine of Barcelona. I am using ChimeraX to produce figures for the publication of an in-house recently developed tool for cancer driver gene discovery. I am new to using ChimeraX, so I am sorry if my question might seem very naive to you. Anyway, I can't find this information anywhere else. My problem is simple: I want to show the surface (or volume) occupied by the atoms of a selected number of residues within a chain. I can easily achieve this by using the Gaussian surface (GS) by adding the parameter "resolution" to the "surface" command as "surface :10-20 resolution 6" The problem is that the surface visualized in this way has "gaps" where it overlaps with other atoms that are not from the selected residues. As expected, these gaps get larger when using a greater resolution. Now, I would like to show the complete surface around these residues, without gaps. Could you please provide any suggestions? Thank you in advance, and best regards, Stefano Pellegrini -- *Stefano Pellegrini, **PhD student* Barcelona Biomedical Genomics Lab Institute for Research in Biomedicine (IRB) Carrer de Baldiri Reixac 10, 08028, Barcelona, Spain http://bbglab.irbbarcelona.org

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About saving alphafold2 predictions
by Luz Cristina Vallejo Garcia 12 Oct '23

12 Oct '23

Hi there! I have a problem using ChimeraX. I tried to use the aphafold2 tool to predict a large protein structure. The process to predict the structure of my protein was successfully completed, but the downloading of my results failed. I observed that the folder for the prediction was created but is empty. So my questions are: Why did the program fail to download my results? Is there a possibility to obtain my results without to re-run the process? Thanks in advance Cris Vallejo IBt, UNAM, México <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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saving alignment in ESP format using chimerax
by Ferreira Ramos, Ana Sofia 11 Oct '23

11 Oct '23

Hi, I would like to save a sequence alignment in ESP format but in my chimerax the option "Save EPS" is not present in the menu of the sequence viewer. The menu is only show if I right click inside the sequence viewer and I do not have all options there: [cid:55913c6a-a21d-45c9-b616-c60bdb4a6b4a] Please, could you let me know how can I save the alignment in the ESP format? Is there a way to do it through the command line? Thank you very much for your attention. Kind regards, Ana

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Re: [Chimera-users] ChimeraX Redistribution Policy Question
by Tom Goddard 10 Oct '23

10 Oct '23

Hi Pat, The ChimeraX license does not allow redistribution. But we have sometimes given permission for that, for example the Structural Biology Grid Consortium (SBGrid). The main issue is our project is funded almost entirely by grants and we have to document how widely the program is used to continue to get funding. Could you explain more details about your distribution? In what way does it use ChimeraX? Can ChimeraX visualization use desktop graphics rendering accelerated by the graphics card within in a Docker image? In general we recommend using ChimeraX on laptop/desktop computers, not containerized, not remotely displayed, because the interactive 3D rendering is often slow or broken in virtualized setups. Let's continue this discussion on the ChimeraX mailing list, not the Chimera mailing list. Tom > On Oct 8, 2023, at 5:53 PM, Patrick Rynkiewicz (RIT Student) via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello! > > I am a co-developer on a molecular dynamics software package that relies on UCSF ChimeraX, and am looking to package this software in a docker container. It's unclear to me from the licensing process what the policy is for ChimeraX redistribution, such as including the .deb package in a docker build. Can you please clarify if I would be able to cite and redistribute ChimeraX 1.6, Ubuntu 22.04 to non-commercial users in my software package, or does each individual user need to accept the non-commercial license agreement separately? > > Thanks! > > Pat Rynkiewicz > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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ChimeraX- protein protein interaction parameter
by Elaine Meng 05 Oct '23

05 Oct '23

Hi Ali, My colleague shared your question with me and I will try to answer it here. For the future, please send your ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time) so that other users can benefit, unless you are including data that needs to be kept private. Sorry, ChimeraX does not calculate binding affinities (binding free energy) or predict their changes when you mutate the protein. You can only get a an approximate, first-order impression of whether they appear to improve or disrupt favorable interactions by measuring things like the surface area in the interface or the number of hydrogen bonds or clashes (bad packing) between the binding partners. See command "measure buriedarea" and the tools "Hbonds" "Contacts" and "Clashes" : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> The picture that you get from these tools might still be incorrect if any of the 3D structures are predicted inaccurately (wrong sidechain conformations, wrong binding interface, wrong fold, etc.). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Ali Aljasser <aljassera(a)cua.edu> > Subject: ChimeraX- protein protein interaction parameter > Date: October 5, 2023 at 5:12:46 PM PDT > > I am part of Dr. Choy's group at the Catholic University of America. I work on studying the protein-protein interaction for two kinetochore proteins. Based on alpha fold prediction, we utilized Chimerax to predict the strength of the interaction of these two proteins. We also added some mutations that are known to influence the interaction. However, I still struggling with how to find parameters such as delta G that would help me to predict the strength of the interaction and whether the mutations affect the interaction. > > Please let me know if you can assist me in this regard. Thank you for your time and I am looking forward to hearing from you soon. > Regards, > Ali

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Saving Looking Glass shots and movies
by tolung.bio＠gmail.com 05 Oct '23

05 Oct '23

Hi, Once I open a structure, create a scene and adjust the depth in the Looking Glass display, is there way to save that in a format that can then be imported into the Looking Glass Studio to be displayed in the stand-alone mode of the display? It is possible to do the same thing with animation, such as a 360 rotation or rocking? Thanks, Gökhan

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Surface representation - Dots
by Dennis Dannecker 04 Oct '23

04 Oct '23

Hello, I would like to ask a question regarding the surface representation of protein molecules in ChimeraX. I remember from Chimera that one could very customize the surface representation in terms of probe size, vertices density, and dot size used in the dot surface representation. While ChimeraX also allows to show dot surface representation, does it also allow for setting these attributes? But the more important question of mine is, can one export/extract the coordinates (spherical or cartesian) of the dots generated during dot surface representation. I would be interested in a file that holds the coordinates of these dots/particles around the molecule. In principal that should be possible, but as always, how amenable is that data? Thank you very much. Cheers Dennis

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Showing CAVER channels and tunnels
by Tom Goddard 03 Oct '23

03 Oct '23

I wrote a brief tutorial on how to show channels and tunnels computed by CAVER using ChimeraX. https://rbvi.github.io/chimerax-recipes/caver/caver.html Tom

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worm plots?
by Gabriel Lander 03 Oct '23

03 Oct '23

Is it by any chance possible to do b-factor worm plots in ChimeraX yet? I recall this was going to take a lot of effort since the code for ribbon depiction would have to be overhauled, but hoping maybe there's been some progress. If not I'll keep exporting from Chimera. thanks, -gabe

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Speeding up commands from cxc
by Alexander Hung Lee 02 Oct '23

02 Oct '23

Hello everyone, I'm working to automate making movies from 10,000 frame trajectories. Currently, my cxc contains the following commands windowsize 1920 1080 set bgColor white view zalign ligand inFrontOf #1 sel protein surface; surface color salmon; transparency protein 60 target s sel :UNL color sel dark slate gray; color sel byhetero sel :SIA color sel dim gray; color sel byhetero sel :UNL hbonds :UNL reveal true surface zone #1 nearAtoms ligand distance 15 select zone ligand 15; select add ligand select ~sel ~cartoon sel delete sel ~sel view ligand movie record supersample 4 perframe "~label; label hbondatoms" ; coordset #1 1,10000,50; wait 200; ~perframe movie encode output hbond.mp4 bitrate 6000 framerate 4 The above takes ~ 30 mins, and it's something I would like to do for whole libraries I'm screening. I think the longest process is "hbonds :UNL reveal true" while second longest is movie record and perframe. Is there a way to speed this up? Is there a way to take advantage of multi-threading if it isn't already enabled? If multi-threading is already being used, what can I change to be more efficient? I deleted the parts that I didn't need "delete sel" since they're not involved in the binding site, and I thought it would help speed up surface calculations while recording. Regards, Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Bright light while using fly command
by Haselbach,David 02 Oct '23

02 Oct '23

Hi, I am trying to make a fly movie in which I move from one rotation state of the molecule to the next. Unfortunately, the lighting during the flight is not nice. The light goes very bright while moving and in the end jumps back to normal. However, if I do the turn life with mouse the light is fine. I am using soft lighting. Find attached an example movie. What could I do? Can anyone help? Best, David

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ChimeraX Alphafold Question
by Vincent Candela 02 Oct '23

02 Oct '23

Hello, I am an undergraduate researcher at McGill University using the Alphafold feature of ChimeraX to study the role of tau on microtubule dimers, and I was wondering if you could point me to detailed documentation on the energy-minimization feature of Alphafold. I’ve been looking at the ChimeraX documentation and couldn’t find an in-depth documentation on what it does. Thank you so much, Vincent Candela

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Color info
by Margulies, David (NIH/NIAID) [E] 29 Sep '23

29 Sep '23

If I color, say, “bychain” how do I get the info on what the displayed color is. Is there an info color command? David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892 Email: dmargulies(a)niaid.nih.gov<mailto:dmargulies@niaid.nih.gov>, dhm(a)nih.gov<mailto:dhm@nih.gov> Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd “Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-o…<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.federalregister.go…> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender’s own and not expressly made on behalf of the NIAID by one of its representatives.

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