- ChimeraX-users - RBVI Mailing Lists

Chimera-Animation equivalent utility/command
by Ray Y.-R. Wang 01 May '20

01 May '20

Dear all, I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt. Thanks so much! Best, Ray

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Missing segments
by Daniel Asarnow 01 May '20

01 May '20

Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug? Thanks and best, -da

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morph movie with secondary structure and dssp
by Joel Meyerson 30 Apr '20

30 Apr '20

Hi, I am making a morph between two PDB models representing two states of the same protein, and the overall secondary structure does not change much between the models. However, there is a region where the secondary structure does change. I would like to capture the secondary structure change in the morph and have a couple questions. 1. It seems the morph uses the secondary structure from PDB #1. Is there a way to use the two different secondary structure headers from the two PDBs to define the secondary structure endpoints on the morph? 2. If the above is not possible, is there a way to restrict DSSP to update only the region of interest (i.e. a residue range), and not change secondary structure throughout the molecule? Thanks, Joel

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addh and phenix
by Daniel Asarnow 24 Apr '20

24 Apr '20

Hi, Seems like with NAG glycans the addh result is incompatible with phenix real space refinement. It's easy enough to fix by deleting HD2 - the offending hydrogen - manually. I was wondering if anyone had an opinion about this, before I report a phenix bug. Error looks like: Number of atoms with unknown nonbonded energy type symbols: 5 "ATOM 2629 HD2 ASN A 362 .*. H " (4 more similar lines). Best, -da

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How to hide dashed lines?
by Steve Chou 24 Apr '20

24 Apr '20

Dear ChimeraX developers and users, I see a dashed line between an ion and a side chain when I display the side chain. Is there a way to hide the dashed line, either in command line or GUI? How to select all the atoms in residues (e.g., /A:10-100) except n, c, and o atoms? Many thanks, Steve -- Steve Chou

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displaying ribbon and tube simultaneously
by Joel Meyerson 23 Apr '20

23 Apr '20

Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles? Thanks, Joel

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Molecular Docking problem
by Estela Fernandes e Silva 23 Apr '20

23 Apr '20

Dears, Good night! I'm starting to use SwissDock to investigate new drugs. I'm having trouble viewing “the best result” through Chimera for Web (the browser cannot be configured) In the option “Download your predictions file” I can open all the ligands through ChimeraX (my computer's desktop) at the same time. But I would like to see only one ligand at a time. Would it be possible? Best regards Estela

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deleting sidechain in ChimeraX
by Joel Meyerson 22 Apr '20

22 Apr '20

Hi, What is the command or sequence of commands which can be used to delete the sidechain on an amino acid or range of amino acids? I reviewed the ChimeraX atom spec page but could not find a way to do this. Thanks, Joel

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Problem with showing 4 Fe-4S in pdb with chimerax
by Meinan Lyu 22 Apr '20

22 Apr '20

Dear chimerax-users(a)cgl.ucsf.edu, There is a 4 Fe-S in my structure, it shows a little bit funny when I open it with chimerax. It should only have links between Fe and S, but between 2Fe shows a link line two. Do you know how to show it normally like in pymol, or remove the links between 2Fe? I really want to draw some figures in chimerax. The attached are 4 Fe-S shown in chimrax,also shown in pymol. PDB id 2WDQ is also attached, which 4 Fe-S is in /B,F,J:303. Thanks very much. Be safe and Best, Meinan Postdoc from CWRU

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shape tool in ChimeraX
by Joel Meyerson 20 Apr '20

20 Apr '20

Hi, Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. Thanks, Joel

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Re: [chimerax-users] [EXT] Re: passing arguments to python scripts with command runscript
by Philipp Milkereit 15 Apr '20

15 Apr '20

Hi Eric, thanks for your fast help, works now as expected! Philipp Von: Eric Pettersen <pett(a)cgl.ucsf.edu> Gesendet: Mittwoch, 15. April 2020 22:19 An: Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Betreff: [EXT] Re: [chimerax-users] passing arguments to python scripts with command runscript Hi Philipp, In ChimeraX, the arguments will be in sys.argv — namely sys.argv[1:] since sys.argv[0] will be the name of your script file. --Eric Eric Pettersen UCSF Computer Graphics Lab On Apr 15, 2020, at 12:47 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de <mailto:philipp.milkereit@vkl.uni-regensburg.de> > wrote: Dear all, in Chimera 1 it was possible to pass arguments with runscript to python scripts which could be read out there by arguments[index]. In ChimeraX I am not anymore able to read passed values using arguments[index] in python scripts called by runscript. Was that feature dismissed or was there a change in the naming? Thanks for your help, Philipp _______________________________________________ ChimeraX-users mailing list <mailto:ChimeraX-users@cgl.ucsf.edu> ChimeraX-users(a)cgl.ucsf.edu Manage subscription: <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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passing arguments to python scripts with command runscript
by Philipp Milkereit 15 Apr '20

15 Apr '20

Dear all, in Chimera 1 it was possible to pass arguments with runscript to python scripts which could be read out there by arguments[index]. In ChimeraX I am not anymore able to read passed values using arguments[index] in python scripts called by runscript. Was that feature dismissed or was there a change in the naming? Thanks for your help, Philipp

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syntax on marker and marker link placement
by Joel Meyerson 12 Apr '20

12 Apr '20

Hi, I have a question about marker and marker link syntax. Suppose model #1 has chains A and B, and that chains A and B form a homodimer where each subunit has the same residue numbering. I would like to place a marker at the midpoint between alpha-carbons of position 10 on A and 10 on B. In turn, I'd like another marker at the midpoint between position 20 on each of the two subunits. I would then like to draw a linker between the two markers. I would expect the following syntax to work, but I get an error. marker #2 #1/a,b:10@CA color yellow radius 1 marker #2 #1/a,b:20@CA color yellow radius 1 marker link #2:1,2 color yellow radius 0.5 Gives the error: Missing or invalid "position" argument: Expected 3 floats or object specifier Any suggestions on how to fix the syntax, or is there an alternative approach? Thanks, Joel

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Move Z plane backside
by Aritz Roa Eguiara 09 Apr '20

09 Apr '20

Dear ChimeraX team, I would like to ask if there is any command to move the Z plane but not the front, but the back one, while recording a movie. I am familiar with clipping, however when recording a movie it directly appears, is there any way to do the same move z but for the far plane? Thank you in advance and happy Easter, Aritz

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How to do repetitive task using Python or command line in ChimeraX?
by 이서원 09 Apr '20

09 Apr '20

Hello, I think I'm good at dealing with the previous Chimera command line, and I'm learning Python coding and ChimeraX little by little. In Chimera, I was able to apply the Chimera command to a Python script using runCommand. So, I wrote some python scripts for Chimera, such as automatically coloring or cropping maps and/or models based on the target specification list in plain text. However, I think there's no python modules like runCommand, and I don't know how to repetitively input specifications by .cxc files. (Do I have to make as many .cxc files as many as the number of the variables?) Also I tried to understand the ChimeraX developer tutorial, but I failed to import color functions on chimeraX Python Shell. (I didn't understand how to import experimental API) Is there any fancy way to create a .cxc file that executes by sequentially inputting variables in the list? Or, How to import python modules such as color functions? (https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.ht…) Best regards, Seowon ______________________________________________________________________________________ 이 서 원 | Selcia Seowon Lee selcia20(a)snu.ac.kr Laboratory of Molecular Imaging , Ph.D. Candidate Department of Biological Sciences, College of Natural Sciences Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul 08826, Korea

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How to do repetitive task using Python or command line in ChimeraX?
by 이서원 08 Apr '20

08 Apr '20

Hello, I think I'm good at dealing with the previous Chimera command line, and I'm learning Python coding and ChimeraX little by little. In Chimera, I was able to apply the Chimera command to a Python script using runCommand. So, I wrote some python scripts for Chimera, such as automatically coloring or cropping maps and/or models based on the target specification list in plain text. However, I think there's no python modules like runCommand, and I don't know how to repetitively input specifications by .cxc files. (Do I have to make as many .cxc files as there are variables?) Also I tried to understand the ChimeraX developer tutorial, but I failed to import color functions on chimeraX Python Shell. (Experimental API Is there any fancy way to create a .cxc file that executes by sequentially inputting variables in the list? Or, How to import python modules such as color functions? (https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.ht…) Best regards, Seowon ______________________________________________________________________________________ 이 서 원 | Selcia Seowon Lee selcia20(a)snu.ac.kr Laboratory of Molecular Imaging , Ph.D. Candidate Department of Biological Sciences, College of Natural Sciences Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul 08826, Korea

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silhouette scaling and image dimension
by Joel Meyerson 08 Apr '20

08 Apr '20

Hi, I noticed that when I save images in ChimeraX with silhouettes on, the apparent width of the silhouette in the output image seems to scale inversely with the image dimensions. For example, these three commands give slightly different silhouette thicknesses. Images attached. save ~/Desktop/image1.png width 500 height 500 save ~/Desktop/image2.png width 1000 height 1000 save ~/Desktop/image3.png width 2000 height 2000 Is there a way to have a fixed silhouette thickness in output images? I'd also be interested to know why this happens. Thanks, Joel

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Making New Bonds between Protein & Ligand
by Gupta, Arun 08 Apr '20

08 Apr '20

Hi I followed similar " marker link " trick proposed by Tom for making new bonds between a selection of Serine residue of protein molecule with hydroxy group functionality of ligand molecule typing the below mentioned command in ChimeraX command line . marker link #1:54@OG #2:PNS@HOP1@SG radius 0.2 However, I am repeatedly getting following error. " TypeError: Cannot bond atoms in different molecules " Can you plz suggest the correct command or alternative way for making new bond between Protein & ligand molecules. Thanks Arun

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Making new bonds
by Mutum YAikhombA 07 Apr '20

07 Apr '20

Hi I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX. I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.htm… <https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.htm…>. Could you please help? Thanks Yaikhomba

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cartoon highlight color?
by Joel Meyerson 07 Apr '20

07 Apr '20

Hi, Is there a way to customize the highlight color of helices and strands? For example, here is how it appears in Pymol. https://pymolwiki.org/index.php/Cartoon_highlight_color Thanks, Joel

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cxc script does not execute 'surface dust' command
by Joel Meyerson 07 Apr '20

07 Apr '20

Hi, I am observing inconsistent behavior in the ‘surface dust’ command. When I launch ChimeraX and execute the following commands one-by-one at the command line everything works as expected. However, if I place the commands in a cxc script, then double click the script ChimeraX launches and the script executes, but the ‘surface dust’ command does not hide the dust. In addition, within that same session I can then enter the ‘surface dust’ command manually and it works as expected. I’m running ChimeraX Daily 0.93 (2020-04-04) on Mac OS 10.15.1. Do you know why the command is not working inside a script? close all open map.mrc turn x 90 volume erase #1 center 175,160,314 radius 100 outside true surface dust #2 size 40 Thanks for the help. Joel

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Command "mlp"
by Cosmin Stefan Butnarasu 06 Apr '20

06 Apr '20

Hello, Hope to find you doing well. I am a PhD student in Pharmaceutical and Biomolecular Sciences and I am writing this email because I would like to better understand the mlp command. First of all, I have to say that I am a very novice on ChimeraX, I discovered this software basically few days ago, so I will write concepts that maybe are not properly correct. I would like to calculate the surface hydrophobicity of a protein. I saw that the mlp command graphically displays the molecular lipophilicity potential, which I suppose is somehow close to the surface hydrophobicity. However, when mlp command is compute, in the Log panel are shown three values, a minimum, a mean and a maximum, which I have not completely understood what they are for (see the picture attached). I searched on ChimeraX manual and I found that the SES surface could stand for “solvent-excluded surface” but I’am not sure about this. If so, could the mean SES value be a measure of the surface hydrophobicity of the protein? If not, can you suggest me a method to obtain not only a graphical display but also a value of the overall molecular lipophilicity potential? Thank you in advance! Cosmin Stefan Butnarasu ********************************************************* Cosmin Stefan Butnarasu, PhD Student Department of Molecular Biotechnology and Health Sciences University of Torino Via Gioacchino Quarello 15, 10135 email: cosminstefan.butnarasu(a)unito.it *********************************************************

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Questions about ChimeraX
by Yuhua Fang 06 Apr '20

06 Apr '20

Hi Recently I transferred to ChimeraX from the old version. I found: 1. Some SMILE strings copied directly from ChemDraw cannot be recognized by ChimeraX, such as O=C1NC2=C(/C1=C3NC4=CC=CC=C4C/3=C\O)C=CC(Br)=C2 2. Correct me if I am wrong but ChimeraX seems not able to do molecule docking/ligand minimization like the old version, right? Thank you Joshua Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Show map only around certain selection
by Karim Rafie 02 Apr '20

02 Apr '20

Dear all, I was wondering how to show part of a map only surrounding certain residues, i.e. I have coordinates for a multiple-chain PDB but I only want to show the electron density surrounding one chain. Any help would be greatly appreciated. Best, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden

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ChimeraX equivalent to "Chimera web data"?
by Ben Webb 01 Apr '20

01 Apr '20

We have a number of web services and tools that generate web data (*.chimerax) files for legacy Chimera. (Typically they load in a PDB file and an alignment and apply some sort of custom view.) What would the equivalent be for ChimeraX? Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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