- ChimeraX-users - RBVI Mailing Lists

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>

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How to access ChimeraX remotely from macbook (OS mojave)?
by Rayees Mattoo 22 Jul '21

22 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

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Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)?
by Tom Goddard 22 Jul '21

22 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>

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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

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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

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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

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scale_bar
by Dmitry A. Semchonok 09 Jul '21

09 Jul '21

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Making movie with crop function
by SHIQING LIAO 07 Jul '21

07 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

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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

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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

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Using ChimeraX as a Python Library
by James Loy 06 Jul '21

06 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/>

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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]

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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

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"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

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Python/Pip Inquiry - ChimeraX - Nathan Wood
by Nathan Wood 05 Jul '21

05 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

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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

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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

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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.

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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

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Python API Inquiry
by Nathan Wood 29 Jun '21

29 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

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Fit crystal structure into mrc
by SHIQING LIAO 29 Jun '21

29 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!

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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.

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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

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Global Fit List and Model Seperation
by Christian Tüting 28 Jun '21

28 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

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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> >

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