- ChimeraX-users - RBVI Mailing Lists

question
by 王镐锋 26 Jul '21

26 Jul '21

Dear guys, Sorry to disturb you guys. When I use the UCSF ChimeraX, I try to define the second structure for part of model. I type the command like "dssp (#1 & sel) energy cutoff 0.5 minheliexlen 3", it works for the whole model instead of what I choose specially. Could you please help me? Thanks so much! Best, Haofeng Wang Ph.D student Tianjin University, China

2 3

measure volume in ChimeraX
by Andrew Blyth 24 Jul '21

24 Jul '21

Hi, I am having trouble getting the ‘measure volume’ and ‘measure area’ command to work in chimera. I have been trying the command: measure volume #3/A:457 for the structure that I have been using, however, nothing happens when I execute this command. Could you please provide me with an example command that will work for measuring the volume or area of a residue? Thanks, Andrew Blyth PhD Candidate Medical Biochemistry - Flinders University Room 6E109 Flinders Medical Centre | South Australia 5001, Australia Phone: +61 8 8204 5098 | E: andrew.blyth(a)flinders.edu.au<mailto:andrew.blyth@flinders.edu.au>

2 1

Model missing residues in Chimera X
by He, Amy 23 Jul '21

23 Jul '21

Dear Chimera X community, I’m a new user of Chimera X and I have a question about the built-in Modeller function in Chimera X Previously in Chimera 2, we use the “Model/Refine Loop” function to model missing residues in the experimental structure, before any further calculation or simulations. The “Model/Refine Loop” function uses Modeller and the function provides modeled, complete structures in which the non-missing residues do not move. In Chimera X, a similar function is “Modeller Comparative” but it works differently. The “Modeller Comparative” performs a modeling for the full structure with the given sequence. Is possible in Chimera X to model the missing residues, without moving the existent residues? Thank you for your kind advice in advance! Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768(a)osu.edu<mailto:he.1768@osu.edu>

2 2

How to access ChimeraX remotely from macbook (OS mojave)?
by Rayees Mattoo 23 Jul '21

23 Jul '21

Hi, I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help! Best Rayees

3 2

Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)?
by Tom Goddard 23 Jul '21

23 Jul '21

Hi Rayees, Mac Air graphics is pretty slow for running ISOLDE. But Tristan Croll who develops ISOLDE added a nice option "Sim Fidelity" to the ISOLDE panel in the middle -- by default it is set to "High" and setting it to "Quick" will make the simulations run much faster. Here is what Tristan told me about what it does: "The latest ISOLDE release has new “sim fidelity” radio buttons on the “Sim settings” tab. The “quick” mode (no implicit solvent, nonbonded cutoff tightened to 9 Å) runs about 4x faster on my MacBook Air and still gives reasonable results in good density. Still not *fast*, but I think definitely usable." This is in ISOLDE 1.2.2. If you need to update ISOLDE use ChimeraX menu Tools / More Tools.... If this is still too slow, I'm afraid it is a limitation. You have to use faster hardware. The realtime dynamics simulations used by ISOLDE need fast graphics - the molecular dynamics is done with OpenMM using OpenCL or CUDA GPU accelerated computation. CUDA is fastest and needs Nvidia graphics and the CUDA driver installed -- Macs don't support Nvidia gpus. The macOS OpenCL implementation is very slow, almost as slow as just running on the CPU. Tristan has ISOLDE benchmarks on different hardware here https://isolde.cimr.cam.ac.uk/performance-benchmarks/ Tom > On Jul 22, 2021, at 6:03 PM, Rayees Mattoo <rmattoo(a)stanford.edu> wrote: > > Hi Tom, > Thanks for responding. Actually, I wanted to run ISOLDE from chimeraX and already tried it running on Mac with my 500KDa protein complex. It was very slow, wanted to try on linux machine and ran into the OpenGL problem. Do you have any suggestions how to run ISOLDE faster on mac? > > Best > Rayees > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, July 22, 2021 5:32 PM > To: Rayees Mattoo <rmattoo(a)stanford.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu>; chimerax-bugs(a)cgl.ucsf.edu <chimerax-bugs(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)? > > Hi Rayees, > > I guess you have X Windows (XQuartz) running on your Mac and are hoping that X remote display from Linux to the Mac will work with ChimeraX. Unfortunately X Windows remote display of 3D OpenGL graphics has not worked reliably since the days Silicon Graphics computers in the 1990s. It is possible to get it to work between two Linux machines with identical OpenGL drivers. But it would be a near miracle if the XQuartz implementation of X Windows on Mac could handle the OpenGL from a Linux machine. > > The sensible approach is to run ChimeraX directly on your MacBook Pro. We don't recommend remote display even when it works because rendering speed is likely to be poor. > > Tom > > >> On Jul 22, 2021, at 1:31 PM, Rayees Mattoo via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hi, >> I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". >> My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help! >> >> Best >> Rayees >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

1 0

Re: [chimerax-users] python loop with ChimeraX
by Rangarajan, Amith 21 Jul '21

21 Jul '21

Hi, I am new to chimeraX , i want to loop through a set of biological assemblies measuring SASA of selecting residues and write them to a file. I need some help with starting on this .How to include this into the .cxc script? is there a example somewhere? please share your tips and suggestions, thanks everyone ! warm regards, Amith

4 8

Hide dust tool & threshold of the map
by Dmitry Semchonok 20 Jul '21

20 Jul '21

Dear colleagues, I would like to ask you for the common practice in showing the threshold of the 3D map and usage of the "hide dust tool”. Am I allowed to use the “hide dust tool” when making the figures for the paper? And if yes, if/how shall I specify that in the description to the figure? Thank you Sincerely, Dmitry

2 1

Moving labels
by Maciej Basczok 15 Jul '21

15 Jul '21

Dear ChimeraX staff, I have a problem with moving 3D labels. I would like to move them in the z-axis, but I cannot find how to do it. My version is 1.2.5. In some earlier release it could be done with the right mouse button + ctrl, but it seems to be changed. I have also tried to find a solution in archive messages, but the hint to click favourites and preferences also appears to be no longer an issue. Under favourites, there are no preferences or mouse settings. I would be extremely grateful for any suggestions. Kind regards, Maciej

2 3

scale_bar
by Dmitry A. Semchonok 10 Jul '21

10 Jul '21

4 7

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

Re: [chimerax-users] Generating surfaces from a specific selection
by Eric Pettersen 01 Jul '21

01 Jul '21

Hi Diego, If there are interior voids within the structure your main surface is enclosing, there will be "bubbles" like what you're seeing, where solvent (or possibly larger things) could theoretically be contained. If you want to only create the outermost surface and not any of the interior void surfaces then add "visiblePatches 1" to your surface command, and only the single largest surface will be created. --Eric > On Jun 30, 2021, at 8:32 AM, Diego Amaya <diaamayaram(a)unal.edu.co> wrote: > > Hi Eric, > > Thanks for your fast reply. The script works but I identify a "weird behavior" in some surfaces. In some cases, you can find "isolated spheres" and if you superimpose them with the corresponding entire surface, these spheres are buried in the structure. All the pdb files have the same atom order and there are no waters, ions or other molecules. The structure is composed of two protein chains. I tried several probeRadius and gridSpacing values but the problem stays. Any suggestions ? > > Best regards, > > > > > El mar, 29 jun 2021 a las 22:58, Eric Pettersen (<pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>>) escribió: > Hi Diego, > It's impossible to be 100% certain without knowing exactly which line it crashed in, but my strong suspicion is that the long atom spec you generate overran some limit in the atom spec or command parser and resulted in a crash. I will be investigating in more detail later, but working off that assumption I would change your script to directly select the atoms in Python rather than via a command. I'm going to assume the atoms in your PDB files are always in the same order, and that the structure is the only model open. If so, change these lines in the 'if' block: > > cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers > for a in cur_sel: > list_atoms.append('@@serial_number='+str(a)) > sel_atoms = ' | '.join(list_atoms) > > to: > > selected = session.models[0].atoms.selecteds > > and these lines in the 'else' block: > > rc(session, 'sel {}'.format(sel_atoms)) > rc(session, 'surface {} enclose #1'.format(sel_atoms)) > to: > > session.models[0].atoms.selecteds = selected > rc(session, 'surface sel enclose #1') > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Jun 29, 2021, at 10:00 AM, Diego Amaya via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hello, >> >> I have a pdb trajectory of 50 frames (in separated pdb files). I want to generate only the solvent accessible surface around amino acid 31 within a radius of 15 A. I want to use the same set of atoms when generating each surface with respect to the first frame of the trajectory. I'm using the python script here below but it doesn't work, I get a segmentation error in the else block. It works if I use "rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius))" in the else block but in that way I don't use exactly the same atoms each time. Any suggestions? >> >> Thanks in advance. >> >> Here the code : >> >> ########################################################### >> from chimerax.core.commands import run as rc >> >> def get_surfaces(resid, radius): >> from chimerax.core.commands import run as rc >> from chimerax.atomic import selected_atoms >> >> with open('list_pdbs.txt', 'r') as list_pdbs: >> flag = 0 >> for pdb_file in list_pdbs: >> if flag == 0: >> list_atoms = [] >> rc(session, 'open ' + pdb_file.strip()) >> rc(session, 'sel :{} @<{}'.format(resid, radius)) >> cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers >> for a in cur_sel: >> list_atoms.append('@@serial_number='+str(a)) >> sel_atoms = ' | '.join(list_atoms) >> rc(session, 'surface #1 enclose #1') >> rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius)) >> rc(session, '~ribbon') >> rc(session, '~disp') >> rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) >> rc(session, 'surface close') >> rc(session, '~sel') >> rc(session, "close all") >> flag = 1 >> else: >> rc(session, 'open ' + pdb_file.strip()) >> rc(session, 'sel {}'.format(sel_atoms)) >> rc(session, 'surface {} enclose #1'.format(sel_atoms)) >> rc(session, '~ribbon') >> rc(session, '~disp') >> rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) >> rc(session, '~sel') >> rc(session, 'surface close') >> rc(session, "close all") >> >> resid = 31 >> radius = 15 >> >> get_surfaces(resid, radius) >> rc(session, "quit") >> ############################################################# >> >> >> -- >> Diego A. Amaya Ramírez >> >> Aviso legal: El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>. Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad. >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> > > > > -- > Diego A. Amaya Ramírez > > Aviso legal: El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>. Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

2 1

Having multiple marker files
by SHIQING LIAO 30 Jun '21

30 Jun '21

Hi! I’m trying to have multiple marker files because I would like them to have different radius and coloring distance. I figured out that I can create new marker files by “marker #5 1,1,1 radius 100”, for example. However, if I add new markers, the new marker always goes to the first marker file, instead of the selected marker file that I want. Any help is really appreciated! Best, Shiqing

3 9

Python API Inquiry
by Nathan Wood 30 Jun '21

30 Jun '21

To Whom it May Concern, My name is Nathan Wood and I am currently a Google Summer of Code Intern with the OpenChemistry Group. Currently I am currently in the process of replacing Visualizing Molecular Dynamics (VMD) with ChimeraX as a means to visualizing computationally generated electrostatic potential diagrams. To accomplish this I am having to use the Python API in a script. However, I am having difficulties enabling the Python API. When I execute a Tutorials example found in the online developer's documentation, I receive the error: /ImportError: No module named chimerax.core.commands// / which suggests that the python modules were never installed properly. I also recieve similar errors when attempting to import the toolshed. Otherwise, the ChimeraX GUI and its shell work properly and I am unsure how to resolve the API error. I am currently using the Generic Linux 64 Bit Daily Release and can provide more information if necessary. Any assistance would be greatly appreciated ------------------------------------------------------ Very Respectfully, Nathan Wood Undergraduate Year 3, GSOC Intern University of Florida

3 2

Fit crystal structure into mrc
by SHIQING LIAO 30 Jun '21

30 Jun '21

Hi, I am trying to build an illustration using marker/color zone. I successfully colored my mrc file. Now, I want to fit a crystal structure I downloaded from pdb into the mrc. But they apparently have different sizes. I tried voxelSize to scale up my mrc, but then all my markers don’t fit with the enlarged mrc. However, voxelSize doesn’t seem to work with the crystal structure (.pdb1) as I got an error message “no volumes specified” when I indeed wrote “volume #5 voxelSize 2”. I am wondering is there any function like voxelSize to scale down the crystal structure? Thank you!

3 3

Generating surfaces from a specific selection
by Diego Amaya 29 Jun '21

29 Jun '21

Hello, I have a pdb trajectory of 50 frames (in separated pdb files). I want to generate only the solvent accessible surface around amino acid 31 within a radius of 15 A. I want to use the same set of atoms when generating each surface with respect to the first frame of the trajectory. I'm using the python script here below but it doesn't work, I get a segmentation error in the else block. It works if I use "*rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius))*" in the else block but in that way I don't use exactly the same atoms each time. Any suggestions? Thanks in advance. Here the code : ########################################################### *from chimerax.core.commands import run as rcdef get_surfaces(resid, radius): from chimerax.core.commands import run as rc from chimerax.atomic import selected_atoms with open('list_pdbs.txt', 'r') as list_pdbs: flag = 0 for pdb_file in list_pdbs: if flag == 0: list_atoms = [] rc(session, 'open ' + pdb_file.strip()) rc(session, 'sel :{} @<{}'.format(resid, radius)) cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers for a in cur_sel: list_atoms.append('@@serial_number='+str(a)) sel_atoms = ' | '.join(list_atoms) rc(session, 'surface #1 enclose #1') rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius)) rc(session, '~ribbon') rc(session, '~disp') rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) rc(session, 'surface close') rc(session, '~sel') rc(session, "close all") flag = 1 else: rc(session, 'open ' + pdb_file.strip()) rc(session, 'sel {}'.format(sel_atoms)) rc(session, 'surface {} enclose #1'.format(sel_atoms)) rc(session, '~ribbon') rc(session, '~disp') rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) rc(session, '~sel') rc(session, 'surface close') rc(session, "close all") resid = 31radius = 15get_surfaces(resid, radius)rc(session, "quit")* ############################################################# -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

2 1

Accessing Chain IDs
by Diana Lee 29 Jun '21

29 Jun '21

Hi team! I have what I hope is an easy question. I'm accessing ChimeraX commands via python script, and I need a list of the Chain IDs. I'm currently getting the number of chains using the num_chains property. I've done quite a bit of digging through documentation and can only find ways to rename, or view interfaces, but I can't seem to find any specific command to list them. I feel as though it must be so basic, no one has needed to ask. :) Thanks for your help, Diana Lee Graduate Student Luque Lab, SDSU VII

3 2

Global Fit List and Model Seperation
by Christian Tüting 29 Jun '21

29 Jun '21

Dear ChimeraX-Team & MailingListUsers, My question is actually two different questions: I would like to perform a global fitting in ChimeraX and seperate all fitting solutions into independent models. I loaded the map (#1) and a dimeric model (#2) into ChimeraX and perform the global fitting by: fit #2 inMap #1 search 50 My map represents a homo-oligomeric model with 40+ monomers (20+ dimers), so multiple fitting solutions are probably correct solutions. This is the log of the fitting: "Found 41 fits. List window not yet implemented." which matches with my assumption. I would like to now (a) inspect all fittings, but the list window is not implemented yet. Can I access the fitting solutions via console commands? And (b) I would like to save each fitted solution as an indepent object, reconstruction the entire model in the map for furhter refinement. Again, could this be done via commands like: "fit #2 inMap #2 search 50 saveFit fittings.pdb", which results in a multi-state pdb? The "Save PDB" button is probably only available in the List windows, which is not implemented yet. Thanks in advance Best Christian

2 2

Fwd: Problem with preset original command in Chimerax 1.2.5
by Tom Goddard 28 Jun '21

28 Jun '21

Saverio reports his problem where ChimeraX "preset original" hung was solved by updating his graphics driver. Tom > Begin forwarded message: > > From: svle(a)tiscali.it > Subject: Re: [chimerax-users] Problem with preset original command in Chimerax 1.2.5 > Date: June 26, 2021 at 1:21:04 AM PDT > To: Tom Goddard > > I have upgraded the graphics driver by a program from AMD website and now it seems that all is working fine and the graphics operations are more responsive and faster. > The picture is very nice. > I have used the Report a Bug before and after the driver upgrading to give driver version information. > > Many thanks. > Saverio > Il 25.06.2021 21:05 Tom Goddard ha scritto: > >> These commands work fine for me in ChimeraX 1.2.5 on Windows 10. It is likely a bug in your graphics driver. Updating your graphics driver might fix it. You can use ChimeraX menu entry Help / Report a Bug and then we will see what graphics card and driver you are using which may give us further ideas. >> By the way maybe you will like preset cylinders/stubs shown below. >> Tom >> >> >>> On Jun 25, 2021, at 12:34 AM, svle--- via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> I have a problem with Chimerax 1.2.5 on windows 10. >>> In the command line I use the following: >>> >>> open 5u1c ( ok ) >>> preset riboon (ok) >>> preset original >>> >>> After the last command the application freezes and I must to kill it. >>> >>> What I can do? >>> >>> Thanks >>> >>> Saverio >>> >>> >>> >>> >>> Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70 <http://tisca.li/Smart70> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > > Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70 <http://tisca.li/Smart70> >

1 0

saving coordinates with respect to map in ChimeraX
by khaja faisal tarique 28 Jun '21

28 Jun '21

Hello everyone While doing rigid body fit we know that after placing the coordinate to its correct position we can save it with respect to the map. Does anyone know if a similar feature exists in ChimeraX ? Is there a way where the coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ? Thank you -- Faisal Tarique Khaja

2 1

Problem with preset original command in Chimerax 1.2.5
by svle＠tiscali.it 25 Jun '21

25 Jun '21

Hi, I have a problem with Chimerax 1.2.5 on windows 10. In the command line I use the following: open 5u1c ( ok ) preset riboon (ok) preset original After the last command the application freezes and I must to kill it. What I can do? Thanks Saverio Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70

2 1

access to current selection
by Diego Amaya 25 Jun '21

25 Jun '21

Hello everyone, I would like to find the equivalent to chimera expression "chimera.selection.currentAtoms()" in ChimeraX. Any idea ? Thanks in advance. Best regards -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

2 1

Chimerax 1.2.5/CentOS-7 Rizen cpu: WARNING: RDRND generated: 0xffffffff 0xffffffff 0xffffffff 0xffffffff
by Tru Huynh 25 Jun '21

25 Jun '21

Hi I have just installed the centos7 rpm (and rpm2cpio into our NFS shared software installation tree). tru@sillage ~]$ chimerax WARNING: CPU random generator seem to be failing, disabling hardware random number generation WARNING: RDRND generated: 0xffffffff 0xffffffff 0xffffffff 0xffffffff is diplayed upon startup on my desktop: /proc/cpuinfo: model name : AMD Ryzen 9 3900X 12-Core Processor stepping : 0 microcode : 0x8701012 .. fpu : yes fpu_exception : yes cpuid level : 16 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc art rep_good nopl nonstop_tsc extd _apicid aperfmperf eagerfpu pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_l2 cpb cat_l3 cdp_l3 hw_pstate sme retpoline_amd ssbd ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsave opt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave _vmload vgif umip overflow_recov succor smca ... No error is shown on other machines equipped with: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz Cheers Tru -- Tru Huynh (PhD) | mailto:tru@pasteur.fr | tel +33 1 45 68 87 37 https://research.pasteur.fr/en/team/structural-bioinformatics/ Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

2 1

Your site is not working
by Moradkhan, Tiglath A 24 Jun '21

24 Jun '21

Hi, I'm trying to download a daily build of ChimeraX but when I try to access the UCSF ChimeraX website it seems to be down. Also when I try to access user guides, I'm also not able to access them. Are you experiencing some system-wide issue today? Thanks Tiglath

2 1

Open a PDB-formatted file and a MTZ file
by Wen-Jin Winston Wu 23 Jun '21

23 Jun '21

Hi, I am trying to inspect electron density of X-ray data. I have the PDB-formatted coordinate file a.pdb (not been submitted to PDB yet) and a mtz file (a.mtz). I have downloaded Clipper to Chimera X (1.2.5) running on Window 10. I have opened my a.pdb, and I then tried to open my a.mtz file from the File-Open and I specified the file type with "*.mtz", and opened the a.mtz file, but I then got the error message: "Must specify a structure model to associate with crystallographic data". I know that I was not doing it correctly (e.g. not typing proper commands with correct syntax.). I looked into the description in the URL below. However, I just could not get it work. Any help will be appreciated. Thanks! http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper Best wishes, Winston

4 7

Chimerax 1.2.5 Ubuntu 16.04 failed to start
by Zhou, Bing-Rui (NIH/NCI) [E] 22 Jun '21

22 Jun '21

Hello ChimeraX developer, I am trying to update ChimeraX from v1.1 to v1.2.5 on a Ubuntu 16.04 Linux machine, but Chimerax v1.2.5 failed to start with the following error message: > sudo apt-get install ~/Downloads/ucsf-chimerax_1.2.5_amd64.deb >chimerax qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007f5866636700 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 87 in _run_code File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted (core dumped) I could downgrade to ChimeraX v1.1 and it works fine, just wondering what has changed in v1.2.5 and if there is a fix for this issue. Thanks, Bing-Rui

2 2

Ball-and-stick model modification
by Volodymyr Dvornyk 21 Jun '21

21 Jun '21

Hello, I wonder whether it is possible to modify the ball-and-stick model shape, i.e., change color, ball diameter, stick length, etc. Right now, the only available presentation style is like one in the attachment. Maybe there is some way to modify it but I was unable to find. Thank you, Volodymyr ________________________________ DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While "Alfaisal University" has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.

4 7

Fwd: Troubles when saving a map
by Tom Goddard 18 Jun '21

18 Jun '21

Stephane's problem with the MRC map written by ChimeraX looking like noise in Coot was because the map origin was not correct. Tom > Begin forwarded message: > > From: Stéphane ROCHE > Subject: RE: [chimerax-users] Troubles when saving a map > Date: June 18, 2021 at 5:37:12 AM PDT > To: "Vadim Kotov" , "Tom Goddard" > > Thanks to both of you for your help ! > > I have finally understood what was happening, the origin of my map was changed and it was a very long way from its old position given that the box was quite large. So basically, when if I was looking around for densities, I was only scrolling inside the solvent. > > Thanks again, > Stephane Roche > > > On 17.06.21 10:07, Stéphane ROCHE via ChimeraX-users wrote: >> Dear Mr/Mrs, >> >> I am new to ChimeraX (v 0.7) and I have a trouble when saving a map. >> >> I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that. >> - Opening the map is fine. >> - Then I change the pixel voxelsize which is also fine. >> - I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format). >> - However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created >> >> Do you know what I could do to solve this problem ? >> >> Thanks, >> Stephane Roche >> Institut de Biologie Intégrative de la Cellule >> 91198 Gif sur Yvette >> France >>

1 0

Assistance
by Priyanka Abeyrathne 18 Jun '21

18 Jun '21

Hi, Could someone assist me to sort out the following? In Chimera, we can save PDB relative to the electron microscopy density map. Can we save the electron microscopy density map relative to the PDB? Any suggestion? Thank you. Priyanka

2 1

Troubles when saving a map
by Stéphane ROCHE 18 Jun '21

18 Jun '21

Dear Mr/Mrs, I am new to ChimeraX (v 0.7) and I have a trouble when saving a map. I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that. - Opening the map is fine. - Then I change the pixel voxelsize which is also fine. - I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format). - However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created Do you know what I could do to solve this problem ? Thanks, Stephane Roche Institut de Biologie Intégrative de la Cellule 91198 Gif sur Yvette France

3 2

listing all-by-all atom distances
by Elaine Meng 15 Jun '21

15 Jun '21

> On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina(a)gmail.com> wrote: > > Hi Elaine, > I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. > Thanks! > Juliana Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.) One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances. You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection. In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command: name frozen blah sel See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like contacts #1/A:55 restrict blah overlap -1000 log true The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers: 1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...] The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance. The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 4

Adjusting coil width
by Edgar A Hodge 15 Jun '21

15 Jun '21

Hello, I'm struggling to adjust the coil width. This seems easy to do using the "cartoon style" command, but I can't seem to figure it out with coils. Thanks! Eddie

3 4

align peptide to model sequence
by Lagerwaard, I.M. (Ilse) 15 Jun '21

15 Jun '21

Hi everyone, I want to write a script that can align the sequences of peptides to a model sequence and return the identical residues. Because I am new to programming, I could really use some help to get started. Could I use the search() method of the Sequence class for this? And if so, how could I go about this? Kind regards Ilse Lagerwaard

2 1

Mesh resolution/smoothness
by Saren Tasciyan 15 Jun '21

15 Jun '21

Hi, I am trying to generate STL files out of protein models. Often the problem is that the mesh doesn't as smooth as the models (see pics below). I wonder if this is an artifact of rendering in ChimeraX or the mesh is actually hard coded to have certain resolution, which makes it look like this? I tried to find out why and ended up in custom_x3d function but didn't notice anything. Post-export smoothing is an option but I wonder, if that's the optimal approach? Perhaps, smoothing can create collisions between 2 STL models, where a higher resolution export may avoid this. Best, Saren -- Saren Tasciyan /PhD Student / Sixt Group/ Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria

3 3

dual conformation
by Wen-Jin Winston Wu 15 Jun '21

15 Jun '21

Hi, I am trying to use Chimera X to display an amino acid with dual side chain conformations (PDB code: 7a5v) together with its cryoEM density map (EMDataResource: <https://www.emdataresource.org/EMD-11657> EMD-11657). For example, Tyr 66 have two side chain conformations, however using the command below, it only showed one conformation. resfit /a:66 map #1 (a very nice command, by the way) I then used Chimera 1.15 to view the PDB coordinate, and it showed two side chain conformations for Tyr66 (as I saw in PyMol); on the other hand, Chimera X only shows a single conformation. Is there any way to display the two alternative conformations using Chimera X? Thanks a lot for your time, and possible help! Best wishes, Winston ************************* ATOM 495 N ATYR A 66 124.799 162.717 112.222 0.50 11.67 N ATOM 496 N BTYR A 66 125.017 162.760 112.080 0.50 12.99 N ATOM 497 CA ATYR A 66 124.008 162.914 110.998 0.50 12.05 C ATOM 498 CA BTYR A 66 124.035 162.916 111.002 0.50 14.20 C ATOM 499 C ATYR A 66 124.638 164.062 110.190 0.50 11.84 C ATOM 500 C BTYR A 66 124.433 164.115 110.140 0.50 13.40 C ATOM 501 O ATYR A 66 125.008 165.077 110.788 0.50 11.86 O ATOM 502 O BTYR A 66 124.411 165.246 110.660 0.50 14.99 O ATOM 503 CB ATYR A 66 122.562 163.249 111.355 0.50 13.02 C ATOM 504 CB BTYR A 66 122.666 163.125 111.624 0.50 17.22 C ATOM 505 CG ATYR A 66 121.759 162.139 111.997 0.50 14.56 C ATOM 506 CG BTYR A 66 121.542 163.315 110.654 0.50 21.09 C ATOM 507 CD1ATYR A 66 121.860 161.839 113.348 0.50 16.21 C ATOM 508 CD1BTYR A 66 120.718 162.258 110.325 0.50 25.90 C ATOM 509 CD2ATYR A 66 120.832 161.436 111.248 0.50 17.74 C ATOM 510 CD2BTYR A 66 121.189 164.579 110.209 0.50 29.25 C ATOM 511 CE1ATYR A 66 120.974 160.942 113.960 0.50 18.53 C ATOM 512 CE1BTYR A 66 119.590 162.443 109.543 0.50 32.51 C ATOM 513 CE2ATYR A 66 119.990 160.494 111.824 0.50 18.57 C ATOM 514 CE2BTYR A 66 120.067 164.784 109.421 0.50 27.89 C ATOM 515 CZ ATYR A 66 120.076 160.228 113.177 0.50 20.29 C ATOM 516 CZ BTYR A 66 119.252 163.714 109.107 0.50 30.80 C ATOM 517 OH ATYR A 66 119.241 159.287 113.722 0.50 24.21 O ATOM 518 OH BTYR A 66 118.168 163.886 108.291 0.50 39.05

3 9

using pandas
by Lagerwaard, I.M. (Ilse) 11 Jun '21

11 Jun '21

Hello everyone, Is it possible to use the pandas package in ChimeraX? I tried opening a Python script containing the line 'import pandas', but I get the error: 'ModuleNotFoundError: No module named 'pandas''. Kind regards, Ilse

4 7

Independent centres of rotation
by Shahid, Taha (Dr.) 10 Jun '21

10 Jun '21

Hi, Is there a method, even if an indirect one via a long command or a series of commands, to set independent rotation centres for a series of (cryo-EM) maps that would then turn together. This could be easily achieved by 'set independent' in the original Chimera, and is much missed by our group of structural biologists. Kudos otherwise on a wonderful upgrade to the program. Many thanks, Taha

3 3

Re: [chimerax-users] saving multiple .obj files from a morph
by Elaine Meng 09 Jun '21

09 Jun '21

On Jun 9, 2021, at 3:38 AM, Brett Murrah <murrahx5(a)att.net> wrote: > I’m trying my best to use the perframe command to save each frame / model out from a morph and slider animation after morphing some pdbs. It is exporting something.. but only 1k files. I’m not sure what I’m doing wrong. Any help? My command is this: > > perframe "save D:/Projects/OBJs/model$1.obj model #3.$1" frames 10 > > PS, I put model #3 because the ID’s for 1 and 2 are the models I used for the morphs. The final morph is #3. If I export each slider frame by hand.. that seems to work. Trying to automate it best I can. > > Thanks you for any help! > Brett Hi Brett, I'm guessing you meant to send this to chimerax-users(a)cgl.ucsf.edu (CC'd here, the recommended address for questions). The morph #3 is a trajectory model. It does not have the frames as submodels #3.1, 3.2, ... so your save command doesn't make sense. I don't know what you mean by "1k files" either... do you mean it makes 10 files but they are too small? You would use "perframe" in combination with "coordset" to replay the existing morph trajectory. E.g. put something like this into a command file (plain text named something.cxc) and then open it in ChimeraX: perframe "save D:/Projects/OBJs/model$1.obj models #3" coordset #3 1,10; wait 10 ~perframe <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> The reason I say to put it in a command file is to make the commands execute instantly one afer the other. I expected it to work when I entered them all as one long line in the command line (with semicolon separators) but then I got a parsing error, possibly due to a bug. E.g. I tried entering this as one long line (the mail tool may choose to break it up): perframe "save D:/Projects/OBJs/model$1.obj models #3"; coordset #3 1,10; wait 10; ~perframe ... but that gave an "incomplete quoted text" error which I will report as a bug. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 2

Change default volume display settings?
by Oliver Clarke 08 Jun '21

08 Jun '21

Hi, Is there any way in ChimeraX to change default volume display settings? For example, I would like to set all volumes to "step 1" by default - in Chimera I can set these defaults in the Volume Viewer menu but I can't see an equivalent in ChimeraX. Sort of related - I wonder if it would be possible to have the option to set default display preferences for molecules or maps? Or more generally, have a script that executes when a file of a particular type is loaded - similar to how the startup commands are executed when ChimeraX is started, but triggered by the opening of a particular filetype and applied to that particular model? Cheers Oli

4 6

Surface Coloring
by Juliana Glavina 07 Jun '21

07 Jun '21

Dear All, I am moving from Chimera to ChimeraX and I am trying to reproduce some of things that I used to do in Chimera. I managed to colour the surface by the kdHydrophobicity scale. However, the coloring is discrete with sharp edges between the residues. I was wondering if it was possible to smooth the edge between two different colors on the surface - similar to mlp but with customized attributes. Thank you very much in advance UCSF ChimeraX version: 1.2.3 (2021-05-13) Ubuntu 20.04 Juliana

2 2

Re: [chimerax-users] Unit cell orientations
by Elaine Meng 04 Jun '21

04 Jun '21

> On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh <silva228(a)llnl.gov> wrote: > > Hi Elaine, > Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. > Thanks! > -chinthaka Hi Chinthaka, (CC to chimerax-users(a)cgl.ucsf.edu ... please use that address for ChimeraX questions) Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/unitcell.html> The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

4 10

Consultation about developing plug-ins in ChimeraX
by Chen, Xiang 28 May '21

28 May '21

Dear Sir or Madam, I am a graduate student in the Department of Computer Science at the Memorial University of Newfoundland. I am currently engaged in developing and researching VR applications to visualize biological microstructures. I learned that Chimerax is a relatively mature piece of software, containing many excellent functions and features. So I'd like to know: 1. Is ChimeraX completely open-source and free? I will only use it for research and non-profit purposes. 2. If ChimeraX is open source, is there a description or summary of the structure/principles of the source code? (In order to learn what features are implemented by each code file.) 3. May I develop new plug-ins/bundles/modules based on ChimeraX's VR mode to implement one or more new features/functions? Could you please briefly describe the feasibility of developing it? Best regards, Xiang Chen --- Xiang Chen, M.Sc. # 201992538 Department of Computer Science Memorial University of Newfoundland St. John's, NL, Canada T (709) 219-2960 / E xiangc(a)mun.ca

2 1