- Chimera-users - RBVI Mailing Lists

command line > vol all surface level 0.1 colour gradient
by Dieter Blaas 20 Jan '21

20 Jan '21

Dear Elaine, please forgive me for asking again, I cannot find your previous mail and my notes: How can I, in command line, do the following, i.e. what is the correct syntax? vol all style surface level 0.1 colour by gradient colours 5 palette rainbow set I have a number of volumes loaded and want to colour their surfaces, at level 0.1 by 'volume data gradient norm' with 5 rainbow colours setting them to the full range Thanks a lot, 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

Coloring peptide bonds in Chimera
by Tynan A. Becker 19 Jan '21

19 Jan '21

Good afternoon, I have been trying to figure out how to color just a single peptide bond between 2 residues in a protein. What I have figured out so far is to show chain trace under actions|atoms/bonds. Then invert the selection (whole protein). This shows the bonds. I can select a residue and color the bond on both sides. But I want to color the bond between 2 residues. If I pick the bond by manual selection, the action|color|choice doesn't work. The manual tantalizingly suggests using the "halfbond" setting or "bondcolor" for the command line. The problem that I encounter is that I can't figure out how to tell the program which bond I want. I've read the "atom specifications" page of the manual and tried every logical combination I can figure to tell the program which bond I want to color. But each time, I get the "mangled atom specifier" error. I was told today that there is a way to do this, but I'm stuck. Any input is welcome. Thank you, Tynan

2 6

Problem with electron density
by Elaine Meng 14 Jan '21

14 Jan '21

Dear Francesco, Probably you just need to use "vop cover" as described in these previous posts: <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html>> <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html>> Details on the "vop cover" command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>> For future: the recommended address for questions is chimera-users(a)cgl.ucsf.edu (CC'd on this message) ... since I'm not the expert in everything (or might be sick or away from work), it's helpful if more people see the question! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Francesco Papi <Francesco.Papi(a)iit.it> > Subject: Chimera: Problem with electron density > Date: January 14, 2021 at 3:03:55 AM PST > To: "meng(a)cgl.ucsf.edu" <meng(a)cgl.ucsf.edu> > > Dear Elaine, > I am using Chimera to get a picture of a small molecule (cif file) in an electron density map (xplor file). My issue deals with the position of some atoms of the molecule in an adjacent unit cell (see attached image) which prevents me to see some atoms within the map. I thought to simply expand the map beyond the cell boundaries and eventually crop the map, but it didn’t work. I have checked different tutorials and the chimera mailing list for troubleshooting but I haven’t found a solution to this problem. Is there something you can think of? > Thank you. > Regards, > Francesco Papi > > Francesco Papi, PhD > PostDoc > Center for Nanotechnology Innovation@NEST > Istituto Italiano di Tecnologia > Piazza San Silvestro, 12 > 56127 Pisa, Italy > Phone: +39 050 509 495 > E-mail: francesco.papi(a)iit.it <mailto:francesco.papi@iit.it> > Skype: francesco.papi.89 >

2 1

Can't open large .bild files
by Hannah Bridges 13 Jan '21

13 Jan '21

Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

4 5

APBS
by mailman-bounces＠cgl.ucsf.edu 12 Jan '21

12 Jan '21

From: benjamintam <benjamintam(a)um.edu.mo <mailto:benjamintam@um.edu.mo>> Subject: APBS Date: January 11, 2021 at 7:28:44 PM PST To: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> Dear All, I can see that we have to run the APBS locally, however, which default execute file that I need to select in the Chimera in order to run APBS? Best, Ben

2 1

view along a crystal axis
by Michael Elbaum 11 Jan '21

11 Jan '21

Hi. I would like to view a lattice of molecules generated by "Unit Cell" along a given axis. Is there a way to set the view accordingly, say along a, b, or c axis? Other than showing the I'm showing the outline box and eye-balling, but probably there's a more precise way to do this. thanks for your help, Michael

3 6

Identifying type of interaction
by nitya yerabandi 09 Jan '21

09 Jan '21

Hi, I'm using UCSF Chimera right now to analyze the contact residues between two proteins, Hsp70 and BAG3. I have created a distance monitor table on chimera that shows residues, atoms, and the distances between them. I am now trying to identify the type of interaction between each pair of atoms, like polar, nonpolar, hydrogen,etc. However, I am having difficulty doing this. I was wondering if you could assist me with this. Thank you, Nitya Yerabandi

2 2

command line "vol all style surface plane z,60,8
by Dieter Blaas 08 Jan '21

08 Jan '21

Hi, I am trying to display a volume (128 px box) sliced through the middle as seen down the z axis but 8 slices thick instead of just one. I can render a single slice with "vol #0 style surface plane z,64" but I could not find out how to make it e.g. 8 slices thick. In VolumeViewer there is the parameter 'Depth' but it is not accepted as parameter in the command line! Rater, adding one more number at the end of the command starts playing a movie of one slice after the other.... Thanks a lot for hints, bw 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 ------------------------------------------------------------------------

3 3

Make a new pdb model from a part of pdb file
by C.J. 07 Jan '21

07 Jan '21

Hi, I have a pdb with a A chain of 1000 amino acids. How can I make a new model with a part of A chain (i.e. 500 amino acids) using command line? Thank you! Best, Jianhao

2 2

(no subject)
by Hemapriya Kumar 07 Jan '21

07 Jan '21

While clicking on the fetch, its getting like certificate no verified as command -- With Regards Hemapriya Kumar

2 1

RMSD after superimposition
by Subhabrata Majumder, PhD 07 Jan '21

07 Jan '21

Dear Support, I have recently started using chimera_ucsf. I was trying to look at Calpha RMSD list after superimposition two conformation of a particular protein. Do you know where should I get the list after superimposition? Thanks, Subhabrata -- Subhabrata Majumder, PhD Assistant Professor Biophysics & Structural Genomics Saha Institute of Nuclear Physics HBNI Sector 1, Block AF Saltlake Kolkata -700064 India Email subhabrata.majumder(a)saha.ac.in ; subhabrata.sinp(a)gmail.com

2 2

Deleting lipid molecules
by Moradkhan, Tiglath A 04 Jan '21

04 Jan '21

Hi I've built a lipid particle containing 252 molecules and I'm trying to randomly delete 20 lipid molecules. Does the delete command allow this? I've tried using it but it doesn't seem to work for this case. Thanks Tiglath

2 1

Re: [Chimera-users] betacavity web and chimera
by Elaine Meng 03 Jan '21

03 Jan '21

On Jan 2, 2021, at 10:42 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Hi Elaine, > is there a way to incorporate in chimera the option to read cavities from betacavity web (Nucleic Acids Res 2015 vol 43 W413-W418) ? Right now you do it for CASTP. > Please let me know. > THank you. > Jackie Vitali > Cleveland State University Hi Jackie, Unfortunately we don't have resources to provide visualization capability for the many useful web servers that exist. A related server with Chimera visualization capability is MOLEonline: <https://mole.upol.cz/> I hadn't heard of betacavity before. In general it would be useful to say or give examples of what outputs they do provide, to give some idea of whether it might be possible... I had to run it myself to figure that out. Looks like they just give Jmol visualization in the web browser and a script for Pymol. Maybe you could ask the authors of betacavity if they would also provide a Chimera script too, but it's probably unlikely. I also see they give lists of atoms on the right side of the results page, but not in PDB format. You could try manually showing surface for those atoms in Chimera (with a Chimera command) but it would be (1) tedious, and (2) just the molecular surface of those atoms, so there may be jagged edges and bits sticking out, not a nice enclosed blob as in their Jmol visualization. Our Castp visualization has this same issue. E.g. for 2gbp I get in the betacavity results: VOID 3 VOID-VOLUME 8.468 A^3 VOID-BNDRY-AREA 41.050 A^2 VOID-DEFINING-ATOMS 27 ATOM 131 CE1 PHE A 16 0.064 A^2 ATOM 689 CA ASN A 91 0.978 A^2 ATOM 691 O ASN A 91 3.921 A^2 ATOM 695 ND2 ASN A 91 1.857 A^2 ATOM 705 N GLU A 93 0.796 A^2 ATOM 709 CB GLU A 93 1.116 A^2 ATOM 713 OE2 GLU A 93 1.118 A^2 ATOM 829 CE2 TYR A 107 0.001 A^2 ATOM 831 OH TYR A 107 5.812 A^2 ATOM 840 CA GLY A 109 0.897 A^2 ATOM 843 N THR A 110 0.696 A^2 ATOM 846 O THR A 110 1.145 A^2 ATOM 848 OG1 THR A 110 2.830 A^2 ATOM 849 CG2 THR A 110 2.985 A^2 ATOM 863 OG SER A 112 2.918 A^2 ATOM 1174 CE1 HIS A 152 0.504 A^2 ATOM 1180 CB PRO A 153 2.424 A^2 ATOM 1182 CD PRO A 153 0.061 A^2 ATOM 1183 N ASP A 154 0.007 A^2 ATOM 1188 CG ASP A 154 1.146 A^2 ATOM 1189 OD1 ASP A 154 3.493 A^2 ATOM 1190 OD2 ASP A 154 1.781 A^2 ATOM 1944 OD1 ASN A 256 0.193 A^2 ATOM 1945 ND2 ASN A 256 0.811 A^2 ATOM 1982 OE1 GLN A 261 2.372 A^2 ATOM 2240 OH TYR A 295 0.069 A^2 ATOM 2356 O1 BGC A 310 1.045 A^2 ...and then in Chimera I could open 2gbp surf :16@ce1:91@o,nd2:93@n,cb,oe2:107@c32,oh:109@ca:110@n,o,og1,cg2:112@og:152@ce1:153@cb,cd:154@n,cg,od1,od2:256@od1,nd2:261@oe1:195@oh:310@o1 ...where the surf command is all one line although the mail program may break it up. (Or you could have multiple surf commands for subsets of those atoms.) 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

Accession number
by Yasmeen Nasr 31 Dec '20

31 Dec '20

Hello there, This doesn’t seem very much chimera related but I hope someone could help me out. I’m trying to use phD-SNP server and SNP&GO server and they require a Swiss prot code and a uni-prot accession number respectively. Does anyone know where I retrieve such numbers for SNPs? Thank you in advance. Yasmeen Abdulhadi Sent from my iPhone

1 0

Clustering saving PDB
by Lorena Roldán 28 Dec '20

28 Dec '20

Good afternoon, I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name) which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. However, this script is not working, and I would greatly thank any help you could provide me with. Lorena. -- <http://www.uab.cat> Lorena Roldán Martín *PhD Student in Bioinformatics* Departament de Química Unitat de Química Física Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 690799431 www.uab.cat <http://www.uab.cat> <https://orcid.org/0000-0002-6902-8285><https://www.linkedin.com/in/lorena-roldan-biomedica/>

3 4

Density map tranformation
by Ahmad Khalifa 22 Dec '20

22 Dec '20

Hello, When I fit two maps into each other, I get the transformation matrix in the reply log, but what if the moving map doesn't converge by fitmap and require some initial manual alignment, how can I calculate the transformation matrix for that? Best regards.

2 3

Movies and Symetries
by Stéphane DUQUERROY 21 Dec '20

21 Dec '20

Hi, I generated a set of coordinates in a single PDB file for a movie (coord flanked by MODEL / ENDMDL tags) I can read it and play it with MD movie menu The PDB File has also BIOMT matrices set for displaying the biological assembly My question is how can I play the movie with multiscale model? How Can use automatically the color zone tool to color various protomer instances for all intermediate conformations? (The only way I know for doing that is to generate and select all sym instances but they moved with each of the models!) S Duquerroy -- -------------------------------------------- Duquerroy Stéphane, PhD, Assistant Professor, Univ Paris Saclay Structural Virology Unit, Institut Pasteur 28 rue du Dr Roux, 75015 Paris - France 33 - (0) 140 613 575 --------------------------------------------

2 1

Holiday greetings from the ChimeraX team!
by Elaine Meng 18 Dec '20

18 Dec '20

The Chimera(X) team at the UCSF RBVI wishes you a safe and happy holiday season! Our holiday card is virtual this year: =-=-=-=-=-= Atoms of Apoferritin At a miraculous 1.22 Å resolution, the electron microscopy map of mouse apoferritin (right, EMDB 11638) can be mistaken for an atomic model (left, PDB 7a4m), with each atom standing out. The map from Nakane et al. (2020 Nature 587:152-156) shows glimpses of the lightest atoms, hydrogen, directly revealing the hydrogen-bonding network. Ferritin stores iron, as many as 4500 ions (Fe3+), as crystallites within its shell of 24 proteins. Apoferritin, ferritin without its iron cargo, has rock-like stability, making it ideal for divining the limits of electron microscope resolution. The images were made with UCSF ChimeraX, using ambient-occlusion lighting, coloring to delineate trimeric subunits within the dodecahedral shell, and curved helix tubes. Best wishes for a happy and healthy 2021! Conrad, Greg, Elaine, Tristan, Tom, Scooter, Eric and Tom =-=-=-=-=-= Full-resolution image: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png>> Gallery of previous cards back to 1985: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html>>

1 0

Create an atom object
by Yasser Almeida 15 Dec '20

15 Dec '20

Hello, How can I create an atom object, with a given xyz coordinates, via command or python? Thanks in advance, Yasser

3 2

Volume information from segmentation data
by Juleen Dickson 14 Dec '20

14 Dec '20

Good Morning Everyone, I fear the answer to my question is probably 'no' but I wanted to ask the experts first. I have segmentation of vesicles that I did from a cryo-EM tomogram that I did in EMAN2. I can open the segmentations and view them in chimera, however, I wanted to find a way to extract volume and surface area data on the segmentations so I can do statistics on them. If I use the Volume--> Measure and color blobs, the individual blob information will show up in the log. I am not sure if this information is accurate. Is there away to do this for all of the vesicles and download the data, maybe with the volume--> Segment map? If so, how do I do it? Thanks for your help. Cheers, Juleen "Never interrupt someone doing what you said couldn't be done." *--Amelia Earhart, American aviator* "Friends... they cherish one another's hopes. They are kind to one another's dreams." *-- Henry David Thoreau* *“Life isn’t about waiting for the storm to pass. It’s about learning how to dance in the rain…” -Vivian Greene*

2 1

Can't open IMOD .mod file
by Luiza Mendonça 12 Dec '20

12 Dec '20

Good morning, Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help. Best, Luiza Mendonca Zhang Lab University of Oxford

3 3

scaling models
by Rani Wiswedel 12 Dec '20

12 Dec '20

Good day, Is there any way to ensure that the scale you are looking at is kept constant when taking images of different models? I would like to include photos of pores from my structure, but each pore is saved in a different file, so I have to re-open Chimera and adjust the view each time. I have the scale bar open and the projection set to orthographic, but I am struggling to manually adjust the view so that the scale bar looks the same length in each picture (attached below is my manual attempt (pic1)). Is there any way to set the scale each time chimera is opened so that I don't end up with pictures that have scale bars that appear to be different sizes?(example of what I would like to achieve is in the second image(pic2)) Thank you! 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 1

Using UCSF Chimera inside python environment
by Jeff Saxon 10 Dec '20

10 Dec '20

Dear Chimera Users, I would like to use chimera to do some calculations on PDB filles (mainly I am interesting to cluster conformations in multi-model PDB using Ensemble cluster) Could you explain to me how I could install chimera (I am using python3 with conda) in order that I could use some of Chimera's functions directly inside of my python scripts? I have already tried install package pychimers but did not succeed conda install -c insilichem pychimera nsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0'] - pychimera -> python[version='3.4.*|3.5.*'] Your python: python=3.8 May I use chimera with my python using alternative ways of installations? Thank you in advance! J.

3 3

Chimera and All-in-One system tune up tools
by Nagy Milan 09 Dec '20

09 Dec '20

Hello, how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. Greetings Milan

2 4

Failure Running ANTECHAMER
by Eric Choi 04 Dec '20

04 Dec '20

To whom it may concern, My name is Eric Choi and I am currently a student at Ithaca College doing research about virtual ligand screening where I utilize programs like Chimera and Dock6. In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC database) by adding hydrogens (using the "steric only" method and "unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program, which predicts potential binding geometries and interactions of a molecule to a target protein. When I add hydrogens and charges to individual ligands (downloaded from the ZINC database), it works fine. However, when I downloaded different subsets of molecules (containing 100 ligands to 2000 ligands), an error message popped up saying that ANTECHAMBER failed to run (please see screenshots below). What does this mean? Is there any way that I can fix this issue? If a certain ligand is causing this problem, is there a way to see which one it is? Thank you very much for your time and help. Sincerely, Eric Choi

3 2