- Chimera-users - RBVI Mailing Lists

Capping in VRML
by Greg Williams 02 Nov '20

02 Nov '20

When I export a vrml file to process in my Cinema 4D application, the ends of the helices, coils and sheets are capped at the ends with a material that is different then the material I use to color the secondary structure features. In Cinema 4D, I have to change every capped end individually. Where do I change the vrml export settings so that the individual objects are capped with the right material? Thanks!

4 4

Accessible surface area calculation
by Martino Benvenuti 02 Nov '20

02 Nov '20

Good morning, I would like to know if it is possible to calculate with Chimera the accessible surface area for a selected amminoacid of a protein. May you help me to figure it out? Thank you for having developed such a great program! Have a nice day, Martino Benvenuti. -- Martino BENVENUTI Ph.D. in chemistry. <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

Screenshots for publication?
by Gustaf Olsson 02 Nov '20

02 Nov '20

Would it be acceptable to include screenshots of the Chimera GUI in publications as long as chimera is being cited as suggested? Best regards // Gustaf

2 1

Select multiple files and open in the same instance
by Ahmad Khalifa 30 Oct '20

30 Oct '20

I used to have Chimera configured to select multiple files, click open, and have them all open in the same instance. After I reinstalled it, now it opens an instance for every file, how can I change it back? Regards.

3 3

Chimera: Per-model clipping and contour level
by Selenschik, Philipp 30 Oct '20

30 Oct '20

Hello, I really enjoy working with Chimera (version 1.14), however I encounter two problems: I fitted the X-ray based crystal structure of apoferritin to my cryo-EM density map, determined the symmetry and based on that the algorithm fits 24 subunits to the map. Really nice. Now I would like to show a "sliced" image of both map and structure. I tried doing so by "Side view", enabling "clip". That works, but I would like to rotate the clipped object. Then I tried per-model-clipping. Here I can clip the map and structures separately. However, I have to choose all fitted (e.g. 12 out of 24) substructures and the clipping works only partially. What am I doing wrong? Also, I tried to figure out the best contour level setting. It seems there is no guide as to which is ideal? Based on a tutorial, I assumed 1 A³/Da for a globular protein, which turns out to be around 620*10³ A³ for my protein. The problem here is: If I slide beyond approx.. 550*10³ A³ all that remains is a square. What's wrong? I hope you can help me out :) Kind regards Philipp

2 4

Help with something really simple
by M. Elizabeth Stroupe 29 Oct '20

29 Oct '20

Hi ChimeraX team, I need to measure a simple angle between three atoms, two within one model and the third in another model to describe a domain motion. In Chimera I could do this from the Structure Analysis tab but now it seems you can only measure distances. I tried the following command(s) and they both gave me an error. I also tried including commas between the angles. What am I doing wrong? angle #1/A:602@C7m,:222@CB,#17/A:602@C7M measure angle #1/A:602@C7m #1/A:222@CB #17/A:602@C7M Thank you! Beth

2 1

MD Simulation on Chimera
by Samiha I Amer 27 Oct '20

27 Oct '20

Please may I know the ideal system specification to run a successful molecular Dynamics simulation on Chimera? Thank you Sent from Yahoo Mail on Android

2 1

REGARDING CHIMERA SESSION FILE
by ASIF JAHAN SHUVRO 26 Oct '20

26 Oct '20

Dear concern, this is Asif from BRAC University, Biotechnology program. I hope you're in good health. I need a little help from you. Recently, I have joined two peptide fragments by forming a peptide bond between them using your standalone UCSF Chimera software. The file has been saved as a Chimera session fle. However, I'm not finding any clue on how to convert it into an entire pdb file. I'm not being able to do any other modification to it since a pdb file is required for this purpose. Could you please help me out on this regard? kindly let me know how can I generate a pdb file from that session file format. I wish to hear your reply. Thanks in advance! Regards, Asif Jahan Shuvro Biotechnology Program Department of Mathematics & Natural Sciences BRAC University

2 2

Morphing PDB
by Reza Khayat 26 Oct '20

26 Oct '20

Hi, Is it possible to morph multiple chains serially? I have a trimer in two different conformations, I would like to morph Chain A in conformation 1 to Chain A in conformation 2. Then, I'd like to do this with chain B and finally chain C. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

Running Chimera on X server
by Ahmad Khalifa 26 Oct '20

26 Oct '20

The refresh rate of Chimera running on a linux server is very slow. I'm connected to the server with an ssh client with X server. I wonder if it's because Chimera is not configured properly or possibly the X server. I also tried to make some movies but they are always blank (black screen). Any suggestions?

2 1

Query on selecting one water molecule
by Izzati Mokthar 26 Oct '20

26 Oct '20

Hi, I am Izzati. I would like to ask how to select only one water molecule in chimera? Thank you

2 2

(no subject)
by Yasser Almeida 22 Oct '20

22 Oct '20

Dear Anabel, As others pointed out, you can just represent the beads as balls, points, or wire, and remove all the pseudbonds. On the other hand, how did you obtained your pdb? If you used GNOM in the ATSAS package (GUI version), it writes pdbs with a bigger bead size, which Chimera fails to represent by default. But if you use GNOM in the command line, it writes pdbs with a smaller bead size, which are more compact, smoother, and better for representation in Chimera, and others. Best, Yasser Dear Chimera team, > I am a user from your software and I would like to have a > superimposition of some crystallographic structures in a recent saxs > pdb model I obtained. However, I cannot visualize the saxs pdb file > with Chimera. Would you have any tips or inputs how can I do this? > Thank you very much in advance for all your help, > Kind regards, > Anabel

1 0

Broken links, system requirements
by Calvin Dodge 21 Oct '20

21 Oct '20

Hello, I have been trying to find out what the hardware requirements are for Chimera. For example, how can it be run in a cluster environment with CUDA cards, but no Nvidia graphics cards? My search for information has been hampered by an apparent failure or reorganization of the main site -https://www.cgl.ucsf.edu/chimera/ Every internal link from that page (like to Downloads) is broken. Will the broken links be fixed? Is another page the preferred one for Chimera? Do I need the OSMesa version to run without graphics cards? Thanks, Calvin Dodge Calvin Dodge Systems Analyst Office: 832-271-7148 Email : cdodge(a)x-iss.com<mailto:ellorente@x-iss.com> http://www.x-iss.com<https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> [cid:image001.png@01D5DB72.2E9C2F40]<http://www.x-iss.com/> Smart Management and Analytics for Clusters

4 4

Re: [Chimera-users] Broken links, system requirements
by Greg Couch 21 Oct '20

21 Oct '20

Your university might want the regular version of Chimera to remotely display data. In that case, you should set up VirtualGL as well. And a RDP solution, like x2go. It doesn't perform as well as Chimera running locally on the desktop, but it might be sufficient. -- Greg On 10/21/2020 11:21 AM, Calvin Dodge wrote: > > Greg, > > Thanks for your reply _/I/_ don’t want to run Chimera in a cluster > environment, but the university I’m doing the install for does. I’ll > install the headless version. > > Sincerely, > > Calvin Dodge > > */Calvin Dodge/*/ > Systems Analyst/ > > /Office: 832-271-7148/ > > / > /Email : cdodge(a)x-iss.com <mailto:ellorente@x-iss.com> > > http://www.x-iss.com > <https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> > > <http://www.x-iss.com/> > > Smart Management and Analytics for Clusters > > *From: *Greg Couch <mailto:gregc@cgl.ucsf.edu> > *Sent: *Wednesday, October 21, 2020 12:24 PM > *To: *Calvin Dodge <mailto:cdodge@x-iss.com>; > chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > *Subject: *Re: [Chimera-users] Broken links, system requirements > > (We're working on the web site issues.) > > So the real question is why do you want to run Chimera in a cluster > environment? > > Chimera is not designed to run in a cluster environment, it is > designed to run a user's desktop computer using 3D graphics. Chimera > does not use CUDA. That said, there is a headless version for Linux > that uses a software implementation of OpenGL to create images that > you could use in a cluster, so no graphics card is needed. > > ChimeraX, our successor to Chimera, can take advantage of CUDA in some > circumstances, but it is not required. ChimeraX also only works > headless on Linux, with a software implementation of OpenGL. The > headless operation is included in every Linux version. So no graphics > card is needed there either. We are investigating ways to take > advantage of the graphic card's performance when running headless, but > we're not there yet. > > HTH, > > Greg > > On 10/21/2020 9:24 AM, Calvin Dodge wrote: > > Hello, > > I have been trying to find out what the hardware requirements are > for Chimera. For example, how can it be run in a cluster > environment with CUDA cards, but no Nvidia graphics cards? > > My search for information has been hampered by an apparent failure > or reorganization of the main site -https://www.cgl.ucsf.edu/chimera/ > > Every internal link from that page (like to Downloads) is broken. > > Will the broken links be fixed? Is another page the preferred one > for Chimera? Do I need the OSMesa version to run without graphics > cards? > > Thanks, > > Calvin Dodge > > */Calvin Dodge/*/ > Systems Analyst/ > > /Office: 832-271-7148/ > > / > /Email : cdodge(a)x-iss.com <mailto:ellorente@x-iss.com> > > http://www.x-iss.com > <https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> > > <http://www.x-iss.com/> > > Smart Management and Analytics for Clusters > > > > _______________________________________________ > > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

issues with visualization of saxs models in chimera
by Anabel Pacios Michelena 20 Oct '20

20 Oct '20

Dear Chimera team, I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this? Thank you very much in advance for all your help, Kind regards, Anabel

3 2

Writing residues coordinates and COMs
by Yasser Almeida 20 Oct '20

20 Oct '20

Hello, I am writing a python script to iterate through all the residues of my model and write the residue coordinates and its correspondent center of mass. I tried with 'runCommand' with the command 'write' but it only accepts a model to be written, not a specific residue. Any thoughts? Thanks in advance. Yasser

2 2

Query about energy minimisation
by Izzati Mokthar 19 Oct '20

19 Oct '20

Hi, I am Izzati. I have a few queries on UCSF Chimera. I need your guide to use the tools. I have two questions. Below are the questions: 1.I would like to do energy minimisation for protein structure with PDB ID: 2J9F. I click Structure editing > Minimize Structure. To be honest, I don't know how to set the settings. I used the default setting and a warning pops up as the attached picture. Do you have any suggestion of reference that I can refer to, to do the energy minimisation? [image: 5.png] 2. I need to also do molecular dynamics for my research. May I know whether I can use chimera to run molecular dynamics as well. If yes, where can I refer to the tutorials? Thank you in advance for your response. Regards, Izzati.

2 4

atom ID
by Francesco Pietra 18 Oct '20

18 Oct '20

Dear all Which is the quickest way to identify the atom ID? As visualized in the context of a multimer, where three identical subunits, distinct by chain name, bind the same peptide, also distinct by chain name. Atom IDs are needed to build a QM-MM simulation. thanks francesco pietra

2 2

PyChimera addCharge
by Matas Tiskus 16 Oct '20

16 Oct '20

Hello, I was looking for ways to add charges to protein structures in a python script and write a .mol2 file. I believe it is possible to do with importing pychimera into the script, but i can't seem to make it work. How would the code for this purpose look like? Matas

2 3

Re: [Chimera-users] [chimera-dev] Building a dimeric protein model
by Elaine Meng 15 Oct '20

15 Oct '20

On Oct 15, 2020, at 1:41 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > Hi > I've built a monomeric model using Chimera's MODELLER interface. I was wondering whether it's possible to use this model in Chimera to create a dimer. The dimer of the protein that I'm studying is composed of two antiparallel symmetric monomers. > Thank you > Tiglath > Hi Tiglath, Sure, but you would need to know the proper positioning of the two monomers in the dimer. There is nothing in Chimera to figure that out automatically. If there is a known dimer structure of a related protein and you think your modeled protein forms a similar dimer, you can simply (1) save your new monomer model as a PDB file (2) start a new Chimera, open that new PDB file two times so that you have two copies open (3) open the known dimer structure of the related protein, let's say it has chains A and B (4) superimpose one copy of your monomer model onto chain A of the known dimer structure, and superimpose the other copy of your monomer model onto chain B of the known dimer structure. Different methods of superimposing structures are discussed in the link below. Probably the easiest is to use the Matchmaker tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (4) close the known dimer structure, and what you have left is the approximate dimer with two copies of your model, which can be saved as a session, or combined into a single model (see "combine" command) and then saved as a PDB file. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Alternatively if you have a dimeric template structure you can use Modeller to make a dimeric comparative model directly, but to do that you would have to use the Modeller interface in our newer program ChimeraX. The one in Chimera only allows modeling monomers. Modeller interface in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> This chimera-dev e-mail address is mostly for programming questions. For general user questions like this (for future reference) a better address to use is chimera-users(a)cgl.ucsf.edu CC'd here, and there is also a similar address for ChimeraX: chimerax-users(a)cgl.ucsf.edu 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

kill graphics windows after crash
by Dieter Blaas 15 Oct '20

15 Oct '20

Hi, please forgive me when this question is not directly related to Chimera: Sometimes Chimera becomes unresponsive because of a slow network connection. When I then try exiting it or killing it with <ctrl> c from the terminal I used to start it or killing the chimera-related process as shown with ps -ealf|grep UCSF or grep chimera the chimera windows remain and I cannot remove them. Any way of doing so? Thanks for hints, best, Dieter ----------------------------------------------------------------------- Dieter Blaas, Max Perutz Labortories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

4 9

how to get specific view
by Shuo 15 Oct '20

15 Oct '20

Dear sir or madam, I wonder how to get specific view parameter in Chimera, just like command get_view in Pymol. So that next time I can easily adjust the view in Chimera. Best Shuo

2 1

Modelling missing residues in a protein
by Edmund Marinelli 14 Oct '20

14 Oct '20

Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD

4 4

MOLE 2.5 plugin
by Reza Khayat 13 Oct '20

13 Oct '20

Hi, I'm receiving the following error when launching the MOLE 2.5 plugin from Chimera. The plugin was installed as suggested by the developers: Favorites -> Preferences -> Add -> Select directory The plugin's icon appears in my tool bar. However, launching it generates the following error in the Reply Log. Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1rc\share\chimera\toolbar.py", line 26, in _guard func() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 954, in <lambda> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 76, in display dialog = find(name, create=1) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 61, in find return d() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' Error in toolbar callback: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: See reply log for Python traceback.? Any help is appreciated. Best wishes, Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

Help on using Modeller interface
by Moradkhan, Tiglath A 09 Oct '20

09 Oct '20

Hi I'm currently trying to use the Modeller interface but I'm having difficulties. I am trying to model a monomeric protein but one of the templates is a homotetramer containing chains A, B, C and D. I only need to use chain A to model the protein but I'm not sure how to do it. Whenever I use the Modeller interface, it uses all of the chains which is not what I want. Unfortunately, this is the only template that I can use since the others are either structures that have since been refuted or don't really correspond to the protein I'm studying. I would be very grateful for your help. Thanks Tiglath

2 3

Help for Chimera please
by EMILIE MONTELLIER 09 Oct '20

09 Oct '20

Hello, I have just downloaded your Chimera software. It looks great! I would like to map a list a specific amino acid on p53 protein and I struggle to find a way to do it. I have downloaded the PDB file of 1TUP TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA (at [ https://www.rcsb.org/ | https://www.rcsb.org ] ). For exemple what would be the command to hightlight amino acid 175 + 248 + 273 + 282 on p53 protein? Thanks by advance for your help, Regards, Emilie Emilie Montellier, PhD Postdoctoral Researcher Institute for Advanced Biosciences Team Tumor Molecular Pathology & Biomarkers Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

2 1

Latest nightly broken on Mac (10.15.7)
by Oliver Clarke 09 Oct '20

09 Oct '20

Hi, In the notes for the latest nightly Chimera build, it states "Many user-interface problems on Mac fixed by upgrading the Tk windowing toolkit to version 8.6.10" - this sounds great, but it seems to have broken basic functionality, at least on my system. See screen recording here: https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0 <https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0> Many UI elements are not responsive any more (including the "Report a Bug" dialog, hence why I am reporting here). This is using Mac OS X 10.15.7 on a macbook pro 16", using the trackpad. Cheers Oli

3 4

AutoDOCK plugin for UCSF Chimera
by James Starlight 08 Oct '20

08 Oct '20

Dear Chimera users! Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb

3 2

matchmaker and MSA
by arrafzaher＠campus.technion.ac.il 06 Oct '20

06 Oct '20

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

2 14

Volume eraser accelerator not working properly
by Ahmad Khalifa 01 Oct '20

01 Oct '20

As I keep clicking "es", the shadows / lighting keep changing, but after clicking 10 times or so, it finally erases. Is this something I'm doing? How can I change to a more easier accelerator?

2 1

bound ligand's are exposed to solvent. Current calculations do not protect surface of ligand embedded in protein
by Anne-Frances Miller 01 Oct '20

01 Oct '20

Dear Chimera, I see on-line advice on calculating areaSAS and areaSES, however Chimera is calculating these for my bound flavin as if the protein were not there. I would like to assess the area exposed outside the protein, not total area (on an atom-by-atom basis). Indeed, the show surface command produces two surfaces, one for the FAD and a different one for the protein, even though both are chain A. Can I edit the pdb file to cause Chimera to create a single surface for both chains including both bound FADs, so that SASA calculated will represent the extent to which the FAD protrudes from the protein? (My protein is a heterodimer with two bound FADs, my Chimera version is 1.13.1 running on Mac OS 10.15.6) Thank you, Anne-Frances Novel Meritorious Research (and teaching) —————————————— A.-F. Miller, Ph. D. Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin Chair, Div. of Biological Chemistry, American Chemical Society

2 2

Undo for volume eraser
by Ahmad Khalifa 30 Sep '20

30 Sep '20

Is there a way to undo a recent erasing that I did? Also, are there ways to use custom shapes, or other surfaces to erase density?

2 1

scipy
by Hernando J Sosa 29 Sep '20

29 Sep '20

Is scipy installed with Chimera? If not how can it be installed? Thanks Hernando >From Chimera idle: >>> import chimera >>> import scipy Traceback (most recent call last): File "<pyshell#1>", line 2, in <module> ImportError: No module named scipy ___________________________________

2 1

Re: [Chimera-users] Troubleshooting request for help
by Cain, Cheryl A 29 Sep '20

29 Sep '20

Hi Tanuja, I've added chimera-users(a)cgl.ucsf.edu to this email as they should be able to help you there. Thanks, Cheryl Cheryl Cain cheryl.cain(a)ucsf.edu Operations Coordinator, Department of Pharmaceutical Chemistry Accreditation Project Coordinator, School of Pharmacy UCSF ________________________________ From: Saswat, Tanuja (NIH/NCI) [F] <tanuja.saswat(a)nih.gov> Sent: Friday, September 25, 2020 9:56 AM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Cc: Goins, Jerquan (NIH/NCI) [C] <jerquan.goins(a)nih.gov> Subject: Troubleshooting request for help Hi, I am a researcher at the NIH who uses this software to complete analysis. But as of recently some of the features that I usually use have not been able to access them. Can you guys assist me in finding a resolution. I’ve CC’s my IT support in case there was something above my cresds level. Regards -- Tanuja Saswat, Ph.D. Postdoctoral Research Fellow Laboratory of Dr. Laurie T. Krug HIV and AIDS Malignancy Branch (HAMB) Center for Cancer Research National Cancer Institute tanuja.saswat(a)nih.gov<mailto:tanuja.saswat@nih.gov> Building 10, Room 4A08 Ph:240-858-3201 NCI Website<https://urldefense.proofpoint.com/v2/url?u=https-3A__ccr.cancer.gov_HIV-2Da…>

4 6

vop subtract removing too much of my map
by Ahmad Khalifa 29 Sep '20

29 Sep '20

I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1! how can I get precise subtraction?

3 7

clustering models of a single pdb
by Subhrangshu Das 29 Sep '20

29 Sep '20

Dear sir, I have 100 pdb files. named as output.1.pdb to output.100.pdb what i do manually for clustering is as follows 1. select 100 pdbs -> open in chimera -> golto *File *-> *save PDB.. *-> *Save Multiple Models as PDB File *(renamed as all.pdb) 2. open chimera -> goto *Tools *->* MD/Ensemble Analysis *->* MD Movie* 3. in *Get Ensemble Info *dialogue box set -> *Trajectory format :* *PDB* *PDB frames contained in:* *single file* * Browse *to select File <all.pdb> *Use frames **first **through * *last* 4. on click *OK,* a dialogue box pops out, *MD Movie: PDB trajectory from all.pdb*, in which, goto *Analysis -> Cluster...*5.. on click* Cluster,* a dialogue box pops out,* Get Clustering Parameters,* in which I set *Cluster trajectory *as: *Starting frame: * *1* *step size: **1* *Ending frame:* * 100* *Cluster based on current selection, if any: * *true* *Ignore solvent and non metal ions: true* *Ignore hydrogens: * *true* *Ignore metal ions: * *alkali* 6. on click *OK, *after some RMSD calculation, i get the *Clustering* result, which I save to a text file <cluster> Now, as I need to do this for multiple times, I want to automate these steps by a python script. Can you please help with a scipt or some command help for the aforesaid tasks. Any help will be helpful in these regard. -- Thanks & Regards, Subhrangshu Das Junior Research Fellow, CSIR-IICB Department of Structural Biology & Bioinformatics Contact - IICB TRUE Campus, CN-6, Salt lake, Sector V, Kolkata-700091 *+919804938813*

3 3

tile from command line
by Dieter Blaas 28 Sep '20

28 Sep '20

Hi, I am trying to use the command line command TILE as given here: Usage <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/usageconvent…>: *tile* /models/ [ columns /N/ ] [ spacingFactor /f/ ] [ independentRotation true|false ] [ viewAll true|false ] [ label true|false ] I tried (following the syntax of e.g. "vol all level 0.02": "tile vol all columns 3" or "tile all columns 3" or "tile models all columns 3" or "tile #0, #1, #2, #4, #5, #6 columns 3" but none works can you please give me an example! Thanks, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 1

Is RTX support planned?
by Gokhan Tolun 25 Sep '20

25 Sep '20

Hi Tom, Are there any plans to implement RTX (real-time ray tracing) support to ChimeraX (and even better, allow the use of physically modelled materials and textures)? Thanks, Gökhan Gökhan Tolun<https://scholars.uow.edu.au/display/gokhan_tolun>, M.S., Ph.D. Senior Lecturer School of Chemistry and Molecular Bioscience<https://www.uow.edu.au/science-medicine-health/schools-entities/school-of-c…> | Faculty of Science, Medicine and Health (SMAH)<https://smah.uow.edu.au/index.html> | Room 125 / Building 18 Molecular Horizons Research Institute<https://www.uow.edu.au/molecular-horizons/index.html> Illawarra Health and Medical Research Institute<https://www.ihmri.org.au/researchers/gokhan-tolun/> University of Wollongong NSW 2522 Australia T +61 2 4221 3365 uow.edu.au<http://uow.edu.au/> | Facebook<https://www.facebook.com/UOW> | Twitter<https://twitter.com/uow> | Instagram<https://www.instagram.com/uow/> | LinkedIn<http://www.linkedin.com/edu/school?id=10255> NOTICE: This email is intended for the addressee name and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Please consider the environment before printing this email.

2 1

X-PLOR format, finding a maximum
by Gustaf Olsson 25 Sep '20

25 Sep '20

Hello Chimera users This might be a somewhat “of-topic” question though I thought that this would be a good place to start. When loading density maps (particularly the X-PLOR format density maps) into Chimera the 'volume viewer’ window provides a maximum number of gridpoints for the map. My question has to do with the format of the XPLOR files. The documentation regarding this format is rather sparse and my I have not been keeping my knowledge regarding matrices up to date. Is there a way to identify this maximum value by just inspecting the content of these files? I have a lot of these files and as I en up presenting results only for ligands with grids visible above a specific cut-off, I though it would save me a lot of time and headache if I could just load the density maps with maximum densities above the cutoff. My though was to just parse the files through AWK or similar to find files with a x > a and then only load these. Sadly, I keep looking at the content of these files and I am not able to make much sense of what I am looking at. Any solutions, suggestions or suggested reading to be able to find a way to create a solution would be greatly appreciated. Best regards // Gustaf

2 1

Error reading multiple models
by Francesco Pietra 25 Sep '20

25 Sep '20

In my hands CHIMERA can't read multiple models as in .trj.xyz provided by ORCA software in QM calculations Error reading 5-sulf-min_trj.xyz: Coordinate line of XYZ file '/home/francesco/work_AGAs/VITTORIO/5-sulf-min_PBE0_OPT_FREQ_SMD/ 5-sulf-min_trj.xyz' is not element,x,y,z: '36' That is no problem for Jmol, however I would be interested in opening the models with also CHIMERA (which can open these models as a single-model-file. thanks for advice francesco pietra

2 1

Open .mrcs stack in chimera
by Ahmad Khalifa 24 Sep '20

24 Sep '20

Can I open a .mrcs stack in chimera? What file type should I pass to Chimera in order to do that?

2 1

Re: [Chimera-users] Stereo Red Cyan
by Greg Couch 24 Sep '20

24 Sep '20

Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book. -- Greg On 9/21/2020 11:43 PM, Michael Elbaum wrote: > Red-cyan, sorry. No, I didn't look for stereo at all, just to > reproduce the condition posted that one channel appears in red and the > other in gray. Is that normal? > Michael > ------------------------------------------------------------------------ > *From:* Greg Couch <gregc(a)cgl.ucsf.edu> > *Sent:* Tuesday, September 22, 2020 4:57:50 AM > *To:* Michael Elbaum <michael.elbaum(a)weizmann.ac.il> > *Subject:* Re: [Chimera-users] Stereo Red Cyan > > Are you wearing red-cyan glasses to see the stereo? It doesn't work > without them. > > > -- Greg > > > On 9/21/2020 1:08 PM, Michael Elbaum wrote: >> >> I'm confirming the problem with a different dataset (optical >> deconvolution in tif format). Red-green shows red and gray, >> green-magenta shows green and gray. This is with version 1.14 on linux. >> >> regards, >> Michael >> >> >> >> ------------------------------------------------------------------------ >> *From:* Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf >> of Angus McDonald <amcdonald(a)boisestate.edu> >> *Sent:* Monday, September 21, 2020 9:46:24 PM >> *To:* chimera-users(a)cgl.ucsf.edu BB >> *Subject:* [Chimera-users] Stereo Red Cyan >> I am looking at some cryo em data. When I try to view a a 3D stack of >> em dat with the Red-Cyan stereo setting I seem to only get Red and >> grayscale. The data is in 32-bit floating point and is in MRC2014 >> header format. I cannot figure out what I am doing wrong. Is anything >> obvious? >> >> Thanks for your time. >> >> >> >> -- >> Angus McDonald >> amcdonald(a)boisestate.edu <mailto:amcdonald@boisestate.edu> >> >> _______________________________________________ >> Chimera-users mailing list:Chimera-users@cgl.ucsf.edu >> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

4 4

electrostatic interactions
by Ruchika 23 Sep '20

23 Sep '20

Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika

2 5

Fitting structure in rescaled map
by Ahmad Khalifa 23 Sep '20

23 Sep '20

Hello, How to fit an atomic model after downscaling my map (map shrinks)? Are atomic models built to scale?! Regards.

2 3

Writing a SINGLE pose (with ligand and protein) to a PDB file
by Edmund Marinelli 22 Sep '20

22 Sep '20

Hello: I used ViewDock to open a pdbqt file generated by use of AutoDock Vina. The ligand was shown in the graphics window. Then I opened the protein pdb file that was used in the docking experiment. The ViewDock dialog lists the poses obtained and I can select each and view the resulting pose in the graphics window fine. I opened the Model Pane. I selected from the list of models the first pose (#0.1) and the protein (#1) in the list. I assumed that saving these two into a file would give a file that contained only the protein and the ligand bound as in the best pose . I want to save the best pose as a pdb file wherein the protein and ligand are present. I gave a filename Test.pdb . Chimera returned the following error message: "You must provide a filename that contains either $name or $number , which will be changed to the model name or model number (respectively) in the final saved file name." I do not understand what this means. I tried using the pose number and also the protein name but it gave the same error. I don't understand what is meant by $name and $number - what do they refer to ? What do I need to do to save a single pose containing protein and the ligand to a unique file not containing other poses? The screenshot below is what I see: Note that in the models list I selected the best pose #0.1 and also the protein, which is at the bottom of the list, hence it is not visible in the picture. What is the filename syntax that I need to use to save a pose with protein to a single PDB file? Stated more plainly: Can you give a viable example of what I need to enter as a filename that will allow saving of the file? Or am I going about this all wrong? Sorry for the verbose email. [image: image.png]

3 3

Stereo Red Cyan
by Angus McDonald 21 Sep '20

21 Sep '20

I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious? Thanks for your time. -- Angus McDonald amcdonald(a)boisestate.edu

3 2

Using iBabel to convert Chimera's pdb to pdbqt
by Jatin Kashyap 19 Sep '20

19 Sep '20

Dear UCSF Chimera Community, I am trying to minimize a complex[1] and saving it in a pdbqt format. I minimize it in Chimera and saved in pdb[2], followed by using iBabel (GUI of open babel for Mac) to convert pdb into pdbqt. Here are two things: first, if I convert without using any flag then output gives me pdbqt file with BRANCH information which is not supported by Vina. To solve it I am using -XR flag in iBabel to trim the BRANCH information so that resulting pdbqt file can be read by Vina. But in that case iBabel is giving me weird looking structure and upon inspection of pdbqt file[3] I realized the complex was split into different models. I had successfully followed the same workflow for other minimization code i.e. YASARA. Can anybody please help me to fix it. I am attaching files below with corresponding citations. Thank you. [1] [2] [3] —— 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 2

Setting a pathway/trajectory for a molecule
by Rani Wiswedel 18 Sep '20

18 Sep '20

Good day, I am an honours student attempting to set up my first molecular dynamics simulation, and am having some trouble trying to understand how to set a pathway for a substrate through a pore in Chimera. I am very unsure of how to do this, and was wondering if you could provide some help. I tried following the Trajectory and Ensemble Analysis tutorial, but essentially cannot get past the first step of downloading leap.top etc. I am also not sure if this is the correct tutorial to follow for what I am looking to do? Any advice would be greatly appreciated, I am in way over my depth. Thank you Kind regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

2 4

Re: [Chimera-users] alpha carbon atom as sphere
by Elaine Meng 18 Sep '20

18 Sep '20

On Sep 18, 2020, at 1:58 PM, Ruchika <Ruchika(a)ucsf.edu> wrote: > Hi Elaine > I am trying to select just alpha carbon on the atom and show it as a sphere, but I am having hard time doing that. When I select the atom, and go to actions and sphere, I must show the side chain and then going to sphere, shows the whole side chain as a sphere instead of just alpha carbon as sphere. Could you please help me with this issue ? > Thanks a lot !! > Regards > Ruchika Hi Ruchika, Assuming you are using Chimera, we recommend sending such questions to chimera-users(a)cgl.ucsf.edu (CC'd here) or else they may fall through the cracks. It doesn't make sense to me that you would need to show the sidechain. I can only guess that maybe you're showing ribbon and that is causing the confusion. If you are showing ribbon, you cannot see or select the alpha-carbon with the mouse, because ribbon normally hides the backbone atoms. If you select the ribbon it selects the whole residue. If you want to show backbone atoms at the same time as ribbon, use command "ribbackbone" or alternatively, just hide the ribbon, and then show whatever atoms you want. Select only the CA and then change it to sphere. Explanation of "ribbackbone" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> Example commands: open 1gcn ribbackbone show :5@CA repr sphere :5@CA I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Backbone RMSD
by Zhang, Bixia 18 Sep '20

18 Sep '20

Hi, I am trying to get the backbone RMSD between two structures. However I tried selecting backbone and use matchmaker, it gives me same value with the whole protein. So there must be something wrong. Could you please teach me a command that can do this? Thank you so much for helping! Best, Bixia

2 7