- Chimera-users - RBVI Mailing Lists

Four letter residue names
by Francesco Pietra 21 Apr '21

21 Apr '21

Hi all A pdb file deriving from a mmCIF file (with chimerax) and comprising both nucleotides and proteins, shows the protein residue names with four characters (i.e., using also column 21), such as ALAM in one subunit, or GLNm in another subunit. I read on passing somewhere (and I am unable to trace that back) that chimera accepts such four character names but was unable to find a description from chimera help. I also got lost in deciphering the intricacies of mmCIF files. What is the scope of the column 21 character? Could that simply be ignored, or deleted, for use with the CHARMM FF? Thanks for advice francesco pietra

2 1

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=…>

2 1

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

2 2

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

3 4

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

2 4

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

4 5

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

2 4

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

2 1

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

2 2

Query about adding charge to ligand
by Nirban Dey 19MSM0098 08 Apr '21

08 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

2 2

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 >

2 1

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)

3 4

ENQUIRY
by ogochukwu ngozi 05 Apr '21

05 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

2 2

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>

1 0

translation along x,y and z
by Ashok Nayak 01 Apr '21

01 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

2 2

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

01 Apr '21

3 3

count the selected residues in linux terminal
by Jayashree Chittari 31 Mar '21

31 Mar '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

1 0

Questions about probabilities in the Dunbrak library
by Moradkhan, Tiglath A 31 Mar '21

31 Mar '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

2 1

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

3 11

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

2 3

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

2 1

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.

3 2

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.

2 1

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

1 0

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

2 1