- ChimeraX-users - RBVI Mailing Lists

Making movie with crop function
by SHIQING LIAO 08 Jul '21

08 Jul '21

Hi there! I am trying to make movies with different cropped views in order to see the inside of my 3D model. I tried view name command and it cannot store the cropped information. The command seems to only work with rotation and translation. Any help would be appreciated! Best, Shiqing

2 1

fit map and bring other maps or models with it
by Alpay Burak Seven 07 Jul '21

07 Jul '21

Hi ChimeraX developers, I would like to fit one map to another and move some other maps with it using ChimeraX. This was possible with matrixcopy in Chimera. In ChimeraX, this type of translation/rotation is possible with matchmaker using "match #2 to #1 bring #3" I believe bring option is not available to "fitmap" command. Please let me know if there is a way. Would it be possible to implement the bring option to fitmap command or implement the matrixcopy command to ChimeraX? Kind regards, -- Alpay B. Seven Stanford University

2 2

Question about libLLVM
by Zhe Wang 07 Jul '21

07 Jul '21

Hi, We were trying to install ChimerX 1.2 on our Centos 8 system. It seems like ChimeraX 1.2 asks for libLLVM with version 10 which is not a default package that built in the rpm. The default one for CentOS 8 is version 9. Centos 7 does not provide and not available in EPEL either. Could ChimeraX provide the corresponding library for centos 8 and 7? Another question that I have is if the following is correct for ChimeraX 1.1: ChimeraX 1.1 is using the default libLLVM3.9-mesa.so for centos 8. And for centos 7, you have ChimeraX 1,1 using the libOSMesa.so.8.0.0 which ChimeraX provided, as I see ChimeraX 1.1 works fine one both, but not 1.2. Best, Zhe

3 6

Using ChimeraX as a Python Library
by James Loy 07 Jul '21

07 Jul '21

Hello! Thank you for creating such an amazing piece of software! I'm trying to use portions of ChimeraX for part of a CIF file processing pipeline. In order to automate the process, I'm building a docker image that has ChimeraX installed. Ideally, we would like to use the pieces of ChimeraX we need by importing the relevant python modules. Is this possible? If so, must I build ChimeraX from source? Additionally, I have tried several times to build v1.1.1 from source and I have not been able to. I am always prompted for a password when trying to rsync the dependencies: /bin/sh -c 'rsync -a $1 .' -- plato.cgl.ucsf.edu: /usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz user(a)plato.cgl.ucsf.edu's password: In order to build from source, do I need to register somewhere to get credentials? Just to be clear, this CIF file processing pipeline is for academic (UT Austin) use, not commercial. Thanks in advance! James -- James Loy, Ph. D. 614.915.9792 LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>

4 8

Toolshed server maintenance
by Yu Low 06 Jul '21

06 Jul '21

Hi ChimeraX, I encountered a problem accessing the toolshed in ChimeraX. I have attached a picture of the error message below. Is the server currently down? When would it be back up again? Regards, Yu Shang [cid:image001.png@01D7719E.469E4D30]

2 1

ChimeraX VR Feedback
by Gökhan Tolun 06 Jul '21

06 Jul '21

Hi, Thanks for all your hard work in getting ChimeraX going in VR and also for implementing a Meeting component. Here is some feedback after trying a VR meeting for the first time today: * Is it possible to have the same functionality of mouse-hover showing the labels, in VR? * Is it possible to add a button to the toolbar to turn labels for all residues on/off? * The VR cones do not show the correct controller layout while using a WMR controller (they still show the Vive controller layout). Is it possible to show the correct controller layout? * While using WMR controllers, the grip button is very easy to press by mistake, resetting the view. Can this be changed to a hold for X seconds behavior instead of being instantaneous? * While adding labels in VR, especially since the hover does not show the label (indicating youre at the correct place to add a label), a misplaced click removes all labels. May the removal all labels upon clicking to an empty area also changed to hold for X seconds or asking for a confirmation? Thanks, Gökhan

2 1

"Render by attribute" tool in ChimeraX
by Francesco Musiani 06 Jul '21

06 Jul '21

Dear ChimeraX developers, I would like to use one feature from the old "render by attribute" tool present in Chimera. My aim is to adapt the atomic radius of a series of atoms according to the value written in the B-factor column of the PDB file. Then I would like to calculate the molecular surface of the resulting molecule in order to calculate the surface volume. Chimera can do the first part by using "render by attribute" tool, but unfortunately it fails in the creation of the surface of the resulting molecule. How can I achieve the same result by using ChimeraX? Thanks in advance. Francesco

2 1

Python/Pip Inquiry - ChimeraX - Nathan Wood
by Nathan Wood 06 Jul '21

06 Jul '21

Dear ChimeraX With regards to the python and pip utilities organic to ChimeraX, is it possible to use the conda installed modules within the same script executed by ChimeraX? When running the script through ChimeraX I return an error that the module is not found. The module was installed using "pip install -e . " while in the conda environment. When I attempted this using the pip provided in ChimeraX Daily Release (22/06/2021, Generic X64 Linux) I return the error: /"/tmp/chx-develop.eKjBho/ChimeraX.app/bin/python3.8: bad interpreter: No such file or directory"/ This error can be resolved if I modify the /"#!"/ at the beginning of the pip in a text editor to the python3.8 found within ChimeraX, with pip installing correctly, but ChimeraX still returning that the module is not found. Furthermore I believe this method is not sound. Any assistance would be appreciated Very Respectfully, Nathan Wood

2 2

Is the toolshed server down?
by tolung.bio＠gmail.com 05 Jul '21

05 Jul '21

Hi, From https://cxtoolshed.rbvi.ucsf.edu/ I am getting Service Unavailable The server is temporarily unable to service your request due to maintenance downtime or capacity problems. Please try again later. _____ Apache/2.4.6 (CentOS) Server at cxtoolshed.rbvi.ucsf.edu Port 443 Is this something on my side, or a known issue that is being resolved? Is there an alternative way for installing the tools, when this happens? Best, Gökhan

2 1

how to change the radius of loop
by Wen-Jin Winston Wu 02 Jul '21

02 Jul '21

Hello, Does anyone know how to modify the radius of loops? I am trying to show structural difference between the three aligned proteins with the cartoon helices shown as tubes. However, when I reduced the helix radius from 2 to 1 ( "cartoon style modeh tube rad 1 sides 24"), the radius of a helix is only about twice that of a loop/coil. Also, what does the number "24" do in the "sides 24"?. I could not find the description on this on ChimeraX Any help will be appreciated. Thanks, Best wishes, Winston

2 3