- ChimeraX-users - RBVI Mailing Lists

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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