- Chimera-users - RBVI Mailing Lists

Chimera Errors
by Henry Shook 18 Apr '21

18 Apr '21

Chimera Team, I have been using Chimera to test several Sialic Acid isomers on the Sars-CoV-2 spike protein over the past couple of months and a couple of days ago, I have been getting this error telling me that there was an "application stderr" and "application stdout". Previously to a couple of days ago, anytime I tried to run it during the day, this message would show up, however, I was able to run the docks from 9-12 pm at night without any problem, so I just worked on the docking during that time. Now, no matter what time I run the docks at, this message shows up. I have not changed any procedures from when I started until now. Is there a way I can fix this problem? I attached a screen recording of my procedures and how I arrived at the problem. Here is a link <https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=…> if the video does not load. Thanks! Henry Shook Screen Recording 2021-04-18 at 11.19.06 AM.mov <https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=…>

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ADP EM Chimera plugin
by Eric Pettersen 15 Apr '21

15 Apr '21

Hi Vilde, Since ADP EM is a third-party plugin, I don't know that I know that much more than you about how it works. Hopefully the plugin developers will get back to you. Nonetheless, I can offer some generic advice about seeing/finding the fitted structure. First, check the Model Panel (Favorites→Model Panel) to ensure that the structure model is shown (the "Shown" column for the structure model is checked). Second, type the 'window' command (Favorites→Command Line) to ensure the view is large enough to show the position of the structure. Third, click on the color well in the Volume Viewer panel (the square next to "Color") and adjust the 'A' component of the color (A = alpha, or opacity) so the the contour surface is semi-transparent, in case the structure is completely within a contour. --Eric Eric Pettersen UCSF Computer Graphics Lab > Hello, > > I’m trying to use the ADP EM molecular fitting tool (Chimera Plugin) to fit my PDB-models into a low resolution map. The plugin works as it should, but I’m having trouble visualizing the solutions. Once the fitting is finished (the table with all the coordinates is produced) and I chose for example solution 1, the PDB structure disappears in the Chimera Window. The EM map is still showing. If I click on the “Back to initial”-button, the PDB structure comes back, but in the initial position, of course. I have tried to save the solutions, but they are still not showing (the solutions are selected as “show” as a cartoon in the model panel). According to the description of the plugin developers, the solutions/fits should be visualized just by selecting one, no extra steps needed. > I’m doing something wrong in Chimera or is there a bug? > I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result. > > Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far. > > Best regards, > Vilde Leipart > PhD-student, > > Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences > Høgskoleveien 12, 1430 Ås, Norway > > Honey Bee Research Lab, Arizona Sate University > 427 East Tyler Mall, Tempe, AZ 85287

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Pixel size/box size and map display
by Cynthia Lee Page 14 Apr '21

14 Apr '21

Hi, I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. Can someone set me straight on this? Many thanks, Cynthia

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Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 14 Apr '21

14 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made. 1. Connection to 13.107.4.52 on tcp/80 (www.msftconnecttest.com) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 13 Apr '21

13 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made. 1. Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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combine models
by Francesco Pietra 11 Apr '21

11 Apr '21

Hi (1) I am faced by the coordinates for a nucleics/protein assembly being given in several bundle.pdb, while I need a sequential, continuous pdb file that comprises all nucleotides and proteins, not made of models (2) If I load all the bundles to chimera, I see all expected ligands around the small molecule. (3) With all models selected, copy/combine (adopting default first model as reference and allowing renaming chains) generates a new model. The new model laks some proteins that should lie near the ligand, as described at (2). I feel that I am missing something. Thanks for advice francesco pietra

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greeting and acknowledgement
by kajihara 09 Apr '21

09 Apr '21

Dear Prof. Ferrin, Dear stuff of Chimera, I am prof Yasuhiro Kajihara, Department of chemistry, Osaka University. Last April, Corona pandemic suddenly attack us, and our university closed in-person style classes. I needed to do online class of biochemistry. I recommended students to download UCSF Chimera for understanding protein structure and behavior. The Chimera soft wear was great help for us under the terrible Corona Pandemic and all students enjoy to deal with Chimera. They got unbelievable knowledge through the Chimera. I could not find a suitable word to express my thank. I thank you again for your great support and kindness to deliver it as free. Within a week 80 students will start download chimera. So, I need to send greeting e-mail to give my thanks. Sincerely Yasuhiro Kajihara, Ph. D. Department of Chemistry Osaka University Machikaneyama, 1-1, Toyonaka, 560-0043 Japan kajihara(a)chem.sci.osaka-u.ac.jp

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Where does Chimera copy command save images?
by Martti Tolvanen 09 Apr '21

09 Apr '21

I have tried to use the command copy on command line to save images, with a goal to do that in a script. The messages of rendering a high-res image and image saved come up, but the file is nowhere to be found. My guess is that the default save location is in the Chimera program folder, which would not be permitted, but Chimera just doesn't see it as a failed attempt. I do have a workaround of including the full path in a filename, but I'm just curious where the file would be going by default, and whether there is some command to change the working folder by a command. FYI it's Chimera 1.15 in Windows 10. Martti Tolvanen University Lecturer in Bioinformatics U of Turku, Finland

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Query about adding charge to ligand
by Nirban Dey 19MSM0098 09 Apr '21

09 Apr '21

Hello, I am a Masters student of VIT University India. I am using chimera to prepare my ligand. In the add charge option I noticed that if my ligand has negative or positive charge and I try to add AM1-BCC it gives error but I can add Gasteiger charge. Even if I set charge to +0 for the ligands that have charge like -1 or +1 and try to add AM1-BCC it gives error. I want to know what is the reason that Gasteiger charge can be added but AM1-BCC cannot be added..Kindly help me in this regard. Thanking You Nirban

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Re: [Chimera-users] Chimera-users Where does Chimera copy command save images?
by Susan 08 Apr '21

08 Apr '21

Hi there honey! I'm a 30 years old lonely housewife looking for an affair. I'm ready to try anything You can see my photos, you can see them right here <http://gallery.prince-ss.com?n=frfya&s=687474703a2f2f646174696e6773722e636f…> On Thu, Apr 8, 2021, at 5:41 PM, Chimera wrote: >Hi Martti, >I don't know the answer, but another thing you can do is use the Chimera cd command to change the working directory so that later in the same session, you no longer have to specify it in the filenames of files to open or save. (Alas, there is no Chimera pwd command to tell you what it thinks is the current working directory, however.) > > >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. >UCSF Chimera(X) team >Depa >

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rna model
by Divita Mathur, Contractor Code 6910, FN 06 Apr '21

06 Apr '21

Hello Chimera community I am trying to run the “rna model sequence #0” code but it is returning the following error: IndexError: list index out of range File “…path/RNALayout/rna_layout.py”, line 393, in place_residues rprev = rlist[0] See reply log for Python traceback. Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder. Regards, -- Divita Mathur, PhD Research Assistant Professor George Mason University & Center for Bio/Molecular Science and Engineering Naval Research Laboratory (202) 767-0687 (Office)

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ENQUIRY
by ogochukwu ngozi 06 Apr '21

06 Apr '21

Dear Concerned,I am a PHD student from University Putra Malaysia. This is my first time using Chimera, please I need your assistance. I want to use chimera to calculate RMSD values, could you direct me on steps to take please? Thanks as I await your kind reply.Ogochukwu Nwaefulu

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Re: [Chimera-users] ResProp Python code
by Elaine Meng 05 Apr '21

05 Apr '21

Dear Chittari Jaya Shree, I can't answer about python, but maybe you didn't know about the related feature that you can simply assign names to whatever you want. There is no need to use the ResProp tool if this is all going to be in a script anyway. For example, command: alias neutral :ile,val,leu,phe,cys,met,ala,gly,thr,ser,trp,tyr,pro,gln,asn ... will then let you use "neutral" in other commands, e.g. select neutral "alias" command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 5, 2021, at 4:54 AM, Jayashree Chittari <jayashreechittari27(a)gmail.com> wrote: > > Respected sir/ma'am > > Greetings for the day! > I want to make a new category named as neutral in which I would assign some amino acids to this category. So, in GUI we know that it could be done through tools-->structural analysis--> ResProp. > > My question is how to do the similar process in python, like how to assign certain amino acids to a new category and then perform the selection("select neutral")? > > Here is the attached ss of Residue category definition. I want to use this process in python where the new category contains assigned amino acids. > > Kindly help me in this issue, it would be very grateful if you suggest the code. > thank you, > > Regards > Chittari Jaya Shree > > <Capture.PNG>

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translation along x,y and z
by Ashok Nayak 02 Apr '21

02 Apr '21

HI Elaine, I want to know the rotation and translation components along x,y and z separately from the rotation matrix obtained from chimera reply log upon fitting a model into a map. Will it be possible to know? Matrix rotation and translation 1.00000000 -0.00000000 -0.00000000 1.83458738 -0.00000000 1.00000000 -0.00000000 1.15016978 -0.00000000 -0.00000000 1.00000000 -0.53835221 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis -0.53835221 thanks, Ashok

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identifying and counting selected residues
by Smit Patel 01 Apr '21

01 Apr '21

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count the selected residues in linux terminal
by Jayashree Chittari 01 Apr '21

01 Apr '21

Respected sir/ma'am Greetings for the day! I want to use chimera commands in shell scripting or python. So, my problem is how to count the residues using Chimera? in gui we know that there is a magnifying icon at the lower right portion of the window, but while running in linux terminal I'm unable to generate the same results. Here is the attached ss of inspect selection, so if I want to print this in linux terminal what steps should I follow to get to this result? I'm trying my best to search in the tutorials but unable to create a command related to inspect selection. Kindly help me in this issue, it would be very grateful if you suggest the code. thank you, Regards Chittari Jaya Shree

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Questions about probabilities in the Dunbrak library
by Moradkhan, Tiglath A 01 Apr '21

01 Apr '21

Hi I'm trying to understand the meaning of probabilities in the Dunbrak library. From what I've found, this parameter is a measure of how probable a particular rotamer is to be found within a given conformation. Is this what this is? Thanks Tiglath

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in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
by Lei Qian 31 Mar '21

31 Mar '21

Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei

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No MMTK name for atom "HD2" in standard residue ASN
by Sina Analoui 31 Mar '21

31 Mar '21

Hi All, I am currently attempting to minimize a large molecule (ACE2 alongside the RBM of a spike protein). I Dock Prep both chains (A chain is ACE2) and then go on to attempt to minimize them. However, I keep returning this error "No MMTK name for atom "HD2" in standard residue ASN" I have attempted to remedy this by rewriting parts of the PDB file and importing it back in and have had no success. Is there any way to either remove NAG that is associated with these residues or change this hydrogen to something feasible? This seems to be an issue for only the ASNs on the A chain and not elsewhere on the molecule Thank you in advance for your help

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Debug
by 안예림 29 Mar '21

29 Mar '21

Hi I have tried to make a movie of MD simulation by Chimera. I could be done one time, then for other MD’s it exits abnormally with the code -1073741819. Even I have decreased the size of .xtc file, it exits abnormally yet. Please check my capture picture. I have reinstalled chimera, but the problem did not resolve.What should I have to do ? I need your assistant. Thanksbe

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Can't open a VTK file in chimera
by Diego Amaya 24 Mar '21

24 Mar '21

Hello, I exported a surface in VTK format with the chimera extension but I can't open this vtk file back with chimera. This behavior is expected ? 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.

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how to generate different starting points to do md simulations
by Seera Suryanarayana 22 Mar '21

22 Mar '21

Dear chimera users, I have a small peptide of 20 residue length and I would like to do the simulations of this peptide at different starting points. How could one can generate the different starting points? Can I use the replica exchange MD simulations to generate the different starting points? I request you to please suggest me how to generate different starting points of peptide. Thanks in advance Surya Graduate student India.

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Re: [Chimera-users] select only side chains to calculate contacts
by Elaine Meng 21 Mar '21

21 Mar '21

> On Mar 20, 2021, at 10:03 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Hi Elaine, > > How do I calculate contacts among side chain atoms of a given category (aliphatic, hydrophobic, etc). Even when I select them, I cannot remove the main chain of them in the calculations. > > Thank you. > > Jackie Vitali Hi Jackie, Please send questions to chimera-users(a)cgl.ucsf.edu (CC'd here) rather than my individual address to clarify which program you're using and to ensure it gets answered. I'm assuming you are asking about Chimera. (If you're asking about ChimeraX, there is a different address: chimerax-users(a)cgl.ucsf.edu ...and the answer might be different.) You can use the "select" command and intersect your selection with sidechain only. It's explained in the command-line specification page: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#buil…> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#comb…> Examples: select hydrophobic & without CA/C1' select :phe,tyr & without CA/C1' (or "with" instead of "without" if you wanted to include the alpha-carbon) You can't see the difference if you are showing ribbons. You can only see the difference if displaying backbone atoms, e.g. menu: Presets... Interactive 2 (all atoms) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Visualizing Amber Trajectory in MD Movie
by Jatin Kashyap 17 Mar '21

17 Mar '21

Dear UCSF Chimera Community, I am trying to visualize an Amber NetCDF(.nc) trajectory in UCSF Chimera using a tutorial.[1] I have two trajectory files of the same system: first, the solvated system, and second I stripped the water molecules in the CPPTRAJ utility of AMBER. I am using the same .top file for both visualizations; however first one showing me the system, although the water molecules are missing. But the second one is throwing me an error, and nothing appears in GUI window.[2] Please help me find out my mistake in the process as I am a beginner-level user of UCSF Chimera. Thank you very much. [1] http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html [2] Assigning chain ID A to 306 residues, e.g. SER fillCoordSet: coordinates [arg 2] must be same length as atoms TclError Exception in Tk callback Function: <bound method ComboBox._resizeArrow of <_Pmw.Pmw_1_3_3.lib.PmwComboBox.ComboBox instance at 0x7fc164add170>> (type: <type 'instancemethod'>) Module: <module '_Pmw.Pmw_1_3_3.lib.PmwComboBox' from '/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py'> (line: 350) Args: (<Tkinter.Event instance at 0x7fc164ae65a8>,) Event type: ConfigureNotify (type num: 22) Traceback (innermost last): File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py", line 351, in _resizeArrow bw = (string.atoi(self._arrowBtn['borderwidth']) + File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget return self.tk.call(self._w, 'cget', '-' + key) TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848" ================================================ Event contents: char: ?? delta: 0 height: 24 keycode: ?? keysym: ?? keysym_num: ?? num: ?? send_event: False serial: 79507 state: ?? time: ?? type: 22 widget: .140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529344.140468594529488 width: 1194 x: 0 x_root: ?? y: 0 y_root: ?? TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848" File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget return self.tk.call(self._w, 'cget', '-' + key) See reply log for Python traceback. —— Jatin Kashyap Ph.D. Student Dr. Dibakar Datta Group Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435(a)njit.edu

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Orienting mol maps in space?
by Cynthia Lee Page 16 Mar '21

16 Mar '21

HI, I am a newbie with Chimera. I have learned a lot in this process of making reference maps for use in Relion, thanks to the tutorials and rich information available on this list and in the documentation for Chimera. I have followed this tutorial cool tutorial (https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html) for making 14 pf tubes (using EMDB 5194), 1JFF ( alpha/beta tubulin) plus the A chain of 3B6U (KIF3B) to represent the monomer of this motor protein. I made a 15 resolution mol map of the resulting model, then cropped off the ends to make the volume flush at the MT ends using the Subregion selection feature in the Volume Viewer. When I open this map in Chimera it does not open as other mrc files open. Specifically, instead of looking down the microtubule (considered Z axis, I believe) I am looking at the X-Y axis. “Centering" the map in Volume Viewer only centers it horizontally, “orienting” the file does nothing. Where as, if I orient any other reference files (including Relion generated 3D.mrc files) the map volume will orient so that the viewer is looking down the microtubule. Please see the attache image, the yellow volume centers/orients correctly, the pink volume is the one I made via the tutorial and doesn’t orient. I am guessing I am missing a coordinate system to align this volume in space but I haven’t been able to figure out how to add this information to my mrc file. I am also assuming that this orientation information is important to include in the mrc file formats. Any help or insight much appreciated! Thanks, Cynthia PS I did try to "vop resample onGrid” using pink onto the yellow models and learned that’s how you can create the same voxel size (!), but it did not change the orientation capabilities of the pink model. [cid:84AEE0E2-633C-4425-9B01-EA6207A3F276@colorado.edu]

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Occupancy clusters
by Yasser Almeida 16 Mar '21

16 Mar '21

Hello, I want to do an occupancy analysis of a rigid ligand in a MD trajectory. I used the MD Movie > Analysis > Calculate occupancy tool, and obtained the volume maps of each heavy atom of the ligand. To check, I also used the gmx spatial tool from GROMACS and the VolMap from VMD, to obtain the grids for the whole ligand, which have basically the same shape. This grid has a characteristic shape showing that particular orientations are stable through the MD run. I want to extract representative structures of these orientations, something like an "occupancy clustering". Note that I say orientations and not conformations. Since the ligand is rigid, there is no point to calculate the RMSD. So, what I want is to calculate clusters of orientations of the ligand in the binding site. Is this possible with Chimera? Thanks in advance, -Yasser

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Problem with nucleotide objects settings for 1d86
by svle＠tiscali.it 16 Mar '21

16 Mar '21

Hi, I have a visualization that seems not a correct one for 1d86 for DT 20.b when using Actions -> Atoms/Bonds -> nucleotide objects -> settings... . Settings: Show backbone as: Ribbon Show sides( .... ) as ladder Ladder Options: Ignore non-base H-bonds: false Shows stubs: false Rung radius: 0.45 Using existing H-bonds: true In the png file the problem. Where I'm wrong? Thanks Saverio Con Tiscali Mobile Smart 30 4G hai minuti illimitati, 100 SMS e 30 Giga in 4G a soli 8,99€ al mese. http://tisca.li/smart30

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render by attribute displacement of a NMA
by Giorgio Giardina 15 Mar '21

15 Mar '21

Hy, I have a pdb file containing the models (only CA atoms) describing the lowest mode from a NMA. I can easily generate a movie using the morphing tool, but I would like to visualize the mode as an image, using the render by attribute tool and with the displacement of each CA as value of the worm radius. How can I generate this attribute? Thanks in advance for you rhelp! Giorgio -- ------------------------------- Giorgio Giardina, Ph.D. Dep. of Biochemical Sciences (CU027) - Room T2 SAPIENZA - University of Rome Tel. +39.06.49910713 | Lab: http://www.macinmec.it/giorgio-giardina/ | Art: http://www.giorgio-giardina.com/ Art. 33 della Costituzione: *L’arte e la scienza sono libere e libero ne è l’insegnamento* -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.

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Failure Running ANTECHAMBER
by Mailyn Terrado 12 Mar '21

12 Mar '21

To whom it may concern: I am trying to use Chimera for protein Energy Minimization. I encountered a problem in running the program. Please find the attached screenshots of the error details. The problem seemed to be with the ligand BEF (beryllium trifluoride). Any help would be greatly appreciated. Many thanks, Mailyn

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ORCA XYZ FILES
by Rade Jibawi Rivera 10 Mar '21

10 Mar '21

Hello, I am a student from Nova Southeastern University, and I am conducting research where I am interested in utilizing your software "Chimera" for visualization of molecular dynamics. My concern is if your software will be able to create a movie of bond interactions with multiple time frames using ORCA XYZ output files. I would greatly appreciate it if you can give in some input. I hope to hear from you. Thank you for your time and consideration. Best regards, Rade Jibawi Rivera

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Regarding Chimera vina executable file
by Heshani Mudalige 10 Mar '21

10 Mar '21

Dear Elaine, Hi, hope you are doing well. I used Chimera for protein docking. But I got stuck in the last step when setting the local path. I downloaded the windows version and that installed to C drive program files and like this C:\Program Files(86)\The Scripps Research Institute But even after browse even it doesn't show any vina.exe file when setting the local path.Can you please tell me where I can find that? Or how to check whether that properly installed or not? Inside the Vina folder there are 3 files which two were applications files.But no exe file is visible I went many tutorials and heard after 2020 we need to install Auto dock vina to support Chimera. I did that as well.But still I can't properly debug this. Different you tube videos they mentioned inside Vina folder can fine vina.exe or inside bin can find vina.exe. Apperciate your help on this and your earliest reply.Thank you Kind regards Heshani

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Sidechain selection in Python
by achatz 10 Mar '21

10 Mar '21

Hello, I want to select a sidechain without CA in Python. The working command line select #0:30 & without CA/C1' is recreated in Python like this: chimera.selection.OSLSelection("#0:30 & without CA/C1'") But the lexer complains about an "illegal symbol in identifier" which is the apostrophe after C1. How do I solve this issue? Thanks Stefan

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Problem trying to download Chimera
by Elaine Meng 10 Mar '21

10 Mar '21

> From: Austine Gozie <austinegozieaustine(a)gmail.com> > Date: March 8, 2021 at 11:47:40 PM PST > > Good day sir/madam, > > I am trying to download the ucsf Chimera software for my ongoing project but its not responding. When i try to proceed to download icon, the next page displays "cant open page or refresh page, connection failed" I need your assistance in helping me with the download methodology or right website to enable me download the software. Thanks in anticipation for your kindest help. Hello Austine, I don't know what you mean by "proceed to download icon". In the download page, you would click on the link for the installer that you want: <https://www.rbvi.ucsf.edu/chimera/download.html> Then it shows the license, and if you agree, then click the "Accept" button at the bottom of the page to start the download. Occasionally the website is down, but as far as I can tell it is fine right now. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Scene transition is delayed in chimera animation
by Shanti Pal Gangwar 10 Mar '21

10 Mar '21

Hi All, I am trying to make scene based animation in chimera where every scene is rotated 360 by using action Roll 360. What I observe is that the scene transitions from 1 scene to another is extremely slow and not continuous also. For some scenes it is fast as well. How can I keep this transition minimum and fixed to all scenes to make a continuous animation. Thank you very much Shanti Pal

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Fwd: error code -1073741819
by Tom Goddard 09 Mar '21

09 Mar '21

Beni's problem with Chimera not starting was a graphics problem related to supersampling / super-resolution / multisampling. Not clear whether the fix was to change a graphics driver setting or the Chimera multisampling setting. Beni's email below. Tom > Begin forwarded message: > > From: Beni Sued <benisued(a)gmail.com> > Subject: Re: [Chimera-users] error code -1073741819 > Date: March 9, 2021 at 1:50:10 PM PST > To: Tom Goddard <goddard(a)sonic.net> > > > That's impressive knowledge! I was indeed using supersampling and superresolution (not sure if They are the same as multisampling but it worked) > Thanks so much! > solved > > On Tue, 9 Mar 2021 at 20:54, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Beni, > > The gzip message is just misleading. It is not an error and is explained here > > https://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011199.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011199.html> > > The real problem is almost surely that your graphics driver is broken since it gets to "Initializing graphics" and then dies. Updating the graphics driver was the right thing to try. > > One other remote possibility is that some Chimera preference setting is causing startup to fail -- like maybe you enabled multisampling in the past and the new graphics driver wipes out whenever you try to use it. The location of preferences is > > C:\Users\username\AppData\Roaming\.chimera\ > > (from documentation here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html>). You might rename that .chimera folder so Chimera starts with factory default preferences and try to start. > > Tom > >> On Mar 7, 2021, at 1:18 PM, Beni Sued <benisued(a)gmail.com <mailto:benisued@gmail.com>> wrote: >> >> Hey there >> I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: >> >> Cannot execute 'gzip': no automatic decompression of .Z files >> >> initializing general preferences >> loading Tix >> initializing graphics >> Return code: -1073741819 >> Press return or enter to to exit >> >> precisely like this gentleman: >> https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html> >> and this >> https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html> >> >> my dxdiag info is attached, nothing wrong jumps to me. >> >> What I've tried: >> - uninstalling and reinstalling Chimera >> - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ <https://sourceforge.net/projects/gzip-for-windows/> ) >> - updating drivers (graphics drivers and chipset drivers) >> - getting the alpha version of the program >> - going to and fro compute mode in the the graphical settings >> >> I'm using Chimera 1.15 and this is my hardware >> chipset b550m >> ryzen 5600x >> RX 590 >> >> in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow >> >> thanks so much, let me know if I missed any info >> <DxDiag.txt>_______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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error code -1073741819
by Beni Sued 09 Mar '21

09 Mar '21

Hey there I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* precisely like this gentleman: https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html and this https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html my dxdiag info is attached, nothing wrong jumps to me. What I've tried: - uninstalling and reinstalling Chimera - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ ) - updating drivers (graphics drivers and chipset drivers) - getting the alpha version of the program - going to and fro compute mode in the the graphical settings I'm using Chimera 1.15 and this is my hardware chipset b550m ryzen 5600x RX 590 in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow thanks so much, let me know if I missed any info

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renseignements
by Camelia Hamadouche 09 Mar '21

09 Mar '21

je n'arrive pas a télecharger votre logiciel meme si je clique sur accepter on me dirige vers une fenetre disant quelle partie vous ne voulez pas accepter? alors que j'ai bien cliqué sur accepter

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each rotation of the molecule in chimera will unexpectedly add an extra "c" at command line
by xiaoyu liu 03 Mar '21

03 Mar '21

Hello, I'm Xiaoyu Liu, a chimera user. Thank you for developing and sharing this powerful software. I have a problem now and bothered me for a while when using chimera. I'm wondering if you know how to solve it. I downloaded chimera-1.15-mac64.dmg <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…> from "https://www.cgl.ucsf.edu/chimera/download.html" for my Mac OS Catalina(10.15.5). When I rotate the molecule with left mouse button, an extra character "c" will be automatically added in command line. Each rotation will result in adding one "c". Here I have some screen shot to show more clearly. [image: image.png] [image: image.png] [image: image.png] I tried to restart my computer. It is helpful within the first 10 minutes after the restart, but later it has the problem again. Please let me know if you know how to solve it. Many thanks! Best, Xiaoyu

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problem with pdb file saved from chimera-autodock vina analysis
by Amol Ghodke 03 Mar '21

03 Mar '21

Hi, First of all thank you so much for making such a wonderful tool and sharing it freely with scientific community. I have been using chimera for sometime now and performed docking analysis using autodock vina. I recently come across a problem. After exporting pdb file with desired docking pose, I tried to run protein ligand interaction analysis on PLIP<https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index> server. But ligand in my file does not get recognised for analysis. I opened pdb file in a text editor and upon looking care fully I see chimera saves receptor and ligand as separate model like this ATOM 7453 HD2 PRO A 462 15.986 11.983 20.450 1.00 0.00 H ATOM 7454 HD3 PRO A 462 16.532 10.334 20.885 1.00 0.00 H ENDMDL MODEL 2 HETATM 1 S1 CGT A 1 9.051 5.106 43.099 1.00 0.00 S HETATM 2 C6 CGT A 1 8.150 3.680 42.370 1.00 0.00 C After comparing it with the pdb file from pbd database I removed “ENDMDL” and “MODEL 2” and re-ran the PLIP analysis. This time it works but PLIP also mentions that – [cid:image001.png@01D7103D.5D0AB030] Analysis went well but the .pse file that I get from PLIP server does not allow me to show ligand in stick format in Pymol software. I suspect this is due to the original pdb file format. I also noticed that pdb file when opened in pymol shows ligand and receptor as different states which is not correct (if I am right). I have attached both original pdb file that I saved from Chimera-autodock vina and pse file from PLIP analysis. May I request to help me resolve this issue? Please let me know if you need any further information or clarification. Thanks for your time and support Amol --------------------------------------------------------------------------------------------------------------------------------------------------------- Dr Amol Bharat Ghodke | Post-Doctoral Research Fellow Queensland Alliance for Agriculture and Food Innovation Level 3, Queensland Bioscience Precinct [#80] Room 3.318, 306 Carmody Rd, St Lucia The University of Queensland St Lucia, Brisbane Qld 4072, AU E. a.ghodke(a)uq.edu.au<mailto:a.ghodke@uq.edu.au>

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active/non active
by Ana Andreea ARTENI 03 Mar '21

03 Mar '21

Dear all, I want to fit a pdb structure into a cryoem map. Accordingly to the youtube tutorials I open both, place the correct pixel size, centre, and then I want to zoom only on the pdb file, but inactivating the cryoem map doesn't work: both maps zoom together. What am I doing wrong? Best regards, -- Ana Andreea ARTENI, PhD ******************************** UMR 9198 Institut de Biologie Intégrative de la Cellule Platforme de cryo-microscopie électronique Bâtiment 14B (RDC. pièce 111) 1 avenue de la Terrasse 91198 Gif-sur-Yvette Cedex, FRANCE Phone: + 33 (0)1 69 82 38 56 Fax: +33 (0)1 69 82 43 08 E-mail : ana-andreea.arteni(a)i2bc.paris-saclay.fr Site web: http://www.i2bc.paris-saclay.fr/spip.php?article277

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editing session file
by Olivier Bignucolo 02 Mar '21

02 Mar '21

Dear Chimera-users, I am new to Chimera. I saved a session.py file that manages the appearance of, say, folder1/proteinA.pdb. I would like to apply exactly the same formats, colors, etc... to proteinB.pdb located in folder2. I edited session.py but was unable to find out how to do it. It seems that the python script does not contain any line like: "open("filename","r") or anything similar. How can I reuse session.py for a new pdb file? Thanks Olivier

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Hydrophobicity extensions
by Sam Hopgood 26 Feb '21

26 Feb '21

Hello, I'm currently studying at Imperial to complete my final year project for my MSci in Chemistry, but due to remote working I have to take on more of a computational project rather than something lab based and I'm not too experienced in the area and neither is my group. I have been told to use chimera to model the hydrophobic surface of proteins and determine a value for the surface hydrophobicity that can be later linked to data collected from HIC studies. I've been told to use chimera to model this but even basic visualisation of the hydrophobic surface does not work for proteins as large as rubisco. I know this is a big ask and an open ended question but are you aware of any extensions available to use to mitigate this issue? Or are you aware of any techniques I could use utilising the software to calculate an actual value for the surface hydrophobicity? I hope you are all keeping safe and well, and thank you for any insight! Best, Sam

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Re: [Chimera-users] Chimera-users Digest, Vol 214, Issue 8
by Khurram Shahzad 26 Feb '21

26 Feb '21

My username and password incorrect plese help me On Thu, Feb 25, 2021, 7:11 PM <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: (no subject) (Thomas Cheatham) > 2. MD analysis of ion position (Elaine Meng) > 3. Re: Chimera Visualization Tool (Ela Ka) > 4. Chimera help submission (David Leeming) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 Feb 2021 21:06:55 +0000 > From: Thomas Cheatham <tec3(a)utah.edu> > To: K Jan <10dunajkr(a)gmail.com>, "chimera-users(a)cgl.ucsf.edu" > <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] (no subject) > Message-ID: <6bbb12c3268847adbbf93577d9f4313a(a)utah.edu> > Content-Type: text/plain; charset="us-ascii" > > > The program CPPTRAJ can bin ion densities on a grid which can be > visualized with chimera... > > See: > https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-s… > > CPPTRAJ is available in AmberTools or via GitHub - > https://github.com/Amber-MD/ > > Also AmberHub may have a tutorial related - > https://amberhub.chpc.utah.edu/making-a-3d-histogram/ > > --tec3 > > ________________________________________ > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of K > Jan <10dunajkr(a)gmail.com> > Sent: Wednesday, February 24, 2021 1:53:36 PM > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] (no subject) > > Hello, > > I`ve just finished a simulation on DNA with K+ ions and I would like to > get images of the average ion location at different points in the > simulation. > > I was wondering how I could find the average location of K+ ions ( because > right now they`re scattered around the DNA) at different points of the > simulation.? > > Thanks > > > > ------------------------------ > > Message: 2 > Date: Wed, 24 Feb 2021 13:22:02 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: K Jan <10dunajkr(a)gmail.com> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] MD analysis of ion position > Message-ID: <870D7C13-E4ED-49DB-8AA0-5E503A94DCA9(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Thanks, I agree that CPPTRAJ is a great solution for analyzing > trajectories. Looks like it can read several formats: > <https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/> > > Alternatively: > In Chimera, if you can view your trajectory in the MD Movie tool, you can > also use that tool to calculate and display an occupancy map. I think > that's essentially the same thing that Tom mentioned, a density map on a > grid that can be viewed as isosurfaces. > > MD Movie help, click "Occupancy Analysis" in the left hand links: > < > https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie… > > > > Occupancy analysis is also covered in the last section of this Chimera > tutorial: > < > https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html… > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 24, 2021, at 1:06 PM, Thomas Cheatham <tec3(a)utah.edu> wrote: > > > > > > The program CPPTRAJ can bin ion densities on a grid which can be > visualized with chimera... > > > > See: > https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-s… > > > > CPPTRAJ is available in AmberTools or via GitHub - > https://github.com/Amber-MD/ > > > > Also AmberHub may have a tutorial related - > https://amberhub.chpc.utah.edu/making-a-3d-histogram/ > > > > --tec3 > > > > ________________________________________ > > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of K > Jan <10dunajkr(a)gmail.com> > > Sent: Wednesday, February 24, 2021 1:53:36 PM > > To: chimera-users(a)cgl.ucsf.edu > > Subject: [Chimera-users] (no subject) > > > > Hello, > > > > I`ve just finished a simulation on DNA with K+ ions and I would like to > get images of the average ion location at different points in the > simulation. > > > > I was wondering how I could find the average location of K+ ions ( > because right now they`re scattered around the DNA) at different points of > the simulation.? > > > > Thanks > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 24 Feb 2021 22:18:45 +0330 > From: Ela Ka <e.kashani.a(a)gmail.com> > To: Chimera User Help <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Chimera Visualization Tool > Message-ID: > < > CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Elaine, > > Thank you very much. I appreciate your consideration. Sure, we'll take care > of the credit and other considerations. > > Best Regards > Elaheh Kashani-Amin > > On Wed, Feb 24, 2021, 10:13 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > Dear Elaheh Kashani-Amin, > > Thanks for asking. Yes, it would be acceptable to use Chimera (free > > version) to create images for your slides, providing that Chimera is > > credited for the images in these materials. > > > > However, if you were going to use Chimera interactively as part of the > > paid educational sessions, your group would need to license the software > as > > described here: > > <https://www.rbvi.ucsf.edu/chimera/commercial_license.html> > > > > Best regards, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 24, 2021, at 2:40 AM, Ela Ka <e.kashani.a(a)gmail.com> wrote: > > > > > > Dear Madam/Sir, > > > > > > We are a group of researchers who try to prepare educational contents > in > > different aspects of protein molecular modeling for the students. Access > to > > these educational content is not free. We need to prepare some pictures > of > > proteins, ligand-receptor interaction, etc. for the slides. Can we use > the > > Chimera software (free version) to prepare some pictures for the slides? > > Though, we won't use the tool, itself, for those educational sessions. > > > > > > Thank you for your consideration > > > > > > Best Regards > > > Elaheh Kashani-Amin > > > PhD, Bioscience > > > > >

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Chimera help submission
by David Leeming 25 Feb '21

25 Feb '21

Dear Chimera users, I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html The script I have is as follows: rc('surface') # defines areaSES of residues rc('defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0') # define attribute using areaSESgxg.txt for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for r in m.residues: r.relSESA = r.areaSES/ r.areaSESgxg However, when I run this script, I am receiving this error: [cid:39cc50d4-a627-494c-b0f5-411a7785a9a2] When I run the process using the UI I can successfully calculate relSESA By using the command: "surface" Then using the assign attribute function to assign areaSESgxg.txt Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI. Kind regards, David

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(no subject)
by K Jan 24 Feb '21

24 Feb '21

Hello, I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation. I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.? Thanks

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Chimera Visualization Tool
by Ela Ka 24 Feb '21

24 Feb '21

Dear Madam/Sir, We are a group of researchers who try to prepare educational contents in different aspects of protein molecular modeling for the students. Access to these educational content is not free. We need to prepare some pictures of proteins, ligand-receptor interaction, etc. for the slides. Can we use the Chimera software (free version) to prepare some pictures for the slides? Though, we won't use the tool, itself, for those educational sessions. Thank you for your consideration Best Regards Elaheh Kashani-Amin PhD, Bioscience

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No mmcif module in ChimeraX 1.0?
by Yangqi Gu 23 Feb '21

23 Feb '21

Dear Chimera Developer, I am trying to use an external python script to run some calculations. I am using ChimeraX 1.0 and the script requires the import of mmcif module but apparently it is not installed in ChimeraX 1.0? How should I install this module? I also downloaded a newer version 1.1, but it is a precompiled version. Do I need to remove ChimeraX 1.0? Because the older version was installed in /usr/bin with an executable file, but for the newer version, I assume I need to add the path for the executables? I also need to run some ISODLE refinement with my gpu, will ChimeraX configure gpu automatically? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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volume position/placement question
by Chen Mu 23 Feb '21

23 Feb '21

Hi Dear List, I am new to Chimera and I have a question using the volume viewer: I have three volumes (reconstructions from different tomographic reconstruction algorithms) to compare. They are in the same size and structure as saved in the .mrc files. I will rotate one volume and adjust the volume viewer and view it. And I then will create an animation video by adding 'roll' in timeline. But the question is, how can I make sure that when I open the other volumes, all of them are in the same starting position/placement, in order to compare and each frame in the animation video to make it possible to compare, because they should start at exactly the same volume position/placement. How can I set up this placement of the volumes to be the same? Thanks very much in advance! Best, Chen

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On pdb structure match or align
by Smith Lee 23 Feb '21

23 Feb '21

Dear All, With chimera I open A.pdb abd B.pdb. A.pdb contains domain a and doain b, B.pdb contains domain b and domain c, which is to say, the 2 structures share a common domain b. Will you please tell me the chimera specific command to align or match the 2 structures based fully on the common domain b in each structure, without consideration of the domain a and domain c for calculation of the alignment? Best wishes, Smith

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on chimera mask
by Smith Lee 22 Feb '21

22 Feb '21

Dear All, When I use command "mask ones #0" to get the mask for #0 image and use the mask.mrc for further processing by other program, it says the mask.mrc got was not in the "cube volume" format. Will you please explain what is the "cube volume" format mrc, and is any way to convert the above mentioned 'non-cube volume" format mask.mrc to "cube volume" format mask.mrc? Best wishes, Smith

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