- Chimera-users - RBVI Mailing Lists

Unix download
by KEITH MUNSON 10 Sep '18

10 Sep '18

Hi Chimera, I downloaded chimera-1.13-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x8…> into my Dell desktop Downloads dir but there was no chimera-installer.bin included in the download. Where do I get the installer? Thanks, Keith Munson

2 2

Writing models in PDB only working via model panel, not via drop-down menu (UCSF Chimera 1.3)
by Jun Ha Song 10 Sep '18

10 Sep '18

Dear RBVI, I noticed that I could not write .cmm marker sets in UCSF Chimera as PDB file via drop down menu from main window, but that I could write it as PDB via Model Panel's side menu. Is this a bug? Best, Junha Song.

2 2

max density value using a script
by Tamas Hegedus 07 Sep '18

07 Sep '18

Hi, I subtract two electron density maps and I would like to get the min and max density values of the resulted map. I can see these values in the GUI, but I would like to get them running chimera without a gui using a python script. (Without saving the final map into an .mrc file and reading the header of that file.) Thanks for your help, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org

3 4

calculate density from an AA model
by Tamas Hegedus 06 Sep '18

06 Sep '18

Hi, Is there an option (command, tool) in Chimera to calculate the theoretical electrondensity map for an all atom protein model? Similar to the MDFF tool in VMD. https://www.ks.uiuc.edu/Training/Tutorials/science/mdff/tutorial_mdff-html/… Thanks, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org

2 2

Visualizing major and minor axes of inertia
by Felipe Vasquez 05 Sep '18

05 Sep '18

Dear all, I am interested in visualizing the major and minor axes of inertia of a ligand in a PDB structure by using UCSF Chimera. Once I calculate the axis of inertia by entering in command line: measure inertia sel I obtained the following info (in reply log): v1 = 0.985 -0.173 -0.013 a = 6.079 r1 = 2.103 v2 = -0.086 -0.553 0.829 b = 4.564 r2 = 2.765 v3 = -0.150 -0.815 -0.559 c = 1.127 r3 = 3.400 center = 38.682 56.595 62.547 However, I do not still know: 1- What are the major and minor axes of inertia? This info is given by the "a/b/c" or "r1/r2/r3" values? 2-How can I visualize the major and minor axes of inertia as planes (or arrows)? Thanks in advances for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* PhD candidate in Chemical Engineering Universidad de los Andes Bogotá, D.C., Colombia Carrera 1 #18A-12, Of. ML-754(26) +57 1 3394949 Ext. 1747

2 3

ChimeraX and crosslinks visualization
by Pascal Albanese 04 Sep '18

04 Sep '18

Dear Support Staff, first of all many thanks for developing Chimera! I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): - Is it possible to load different sets of distances/crosslinks (like with different IDs)? - is it possible to color code the distances with a cutoff (like red if >30 for instance)? - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) that's it, maybe something can be done writing the code but unfortunately it's not my job. Thanks a lot and looking forward to hear from you, Cheers, Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

3 2

Re: [Chimera-users] Mirror image proteins
by Chu Ji 04 Sep '18

04 Sep '18

Hi Eric, I was trying to get a mirror image of a PDB model and came across your thread. I know that you are typing in m = chimera.openModels.list()[0] for a in m.atoms: crd = a.coord() crd.z = 0 - crd.z a.setCoord(crd) in the Gen Control>IDLE section, but I also read on GitHub that I should change the [0] in openModels.list()[0]to the model specifier. What does that mean exactly? I tried to type in the PDB ID to replace the 0 but nothing happened…Could you show me an example? What if I want to flip Chain B of a certain model or just the entire model? Thank you so much for your help! Looking forward to hearing from you. Best, Nancy Sent from Mail for Windows 10

2 1

Chimera: Amber to PDB
by Boris TOUZEAU 04 Sep '18

04 Sep '18

Hi, I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei. I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues. Best wishes, Boris TOUZEAU

2 4

chimera error during AddCharge for MD preparation
by Waterbury, Amanda 04 Sep '18

04 Sep '18

Hi, I am attempting to perform MD stimulations with a protein containing an FAD cofactor, however, I keep receiving the following error message: Charge model: AMBER ff14SB Assigning partial charges to residue FAD (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.in.mol2 -fi mol2 -o /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 (FAD) (FAD) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (FAD) Referenced from: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (FAD) Reason: image not found (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (FAD) (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (FAD) Total number of electrons: 408; net charge: -2 (FAD) (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (FAD) Error: cannot run "/Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue FAD Check reply log for details Any help/suggestions would be much appreciate! Best, Amanda

2 1

Depicting entropy and mobility in pdb files
by George Tzotzos 27 Aug '18

27 Aug '18

Hi everybody, I’ve generated two pdb files which are of identical coordinates. Their only difference is that the b-factor column has been replaced with data indicating residue conservation (structure 1) and residue intrinsic mobility from normal mode analysis (structure 2). Below are indicative atomic coordinates. Structure 1 ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 2.87 N ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 2.87 N ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 2.84 N ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 2.84 C Structure 2 ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 1.35 N ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 1.35 N ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 1.73 N ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 1.73 C Is there a way to visualise these differences (e.g. by different thickness of ribbons or any other means e.g. colour of spheres). Thank in advance for any suggestions George

2 2

Re: [Chimera-users] UCSF Chimera Ribbon Question
by Elaine Meng 25 Aug '18

25 Aug '18

Hi Alex, The problem is not the ribbon style (and you don’t need supersmooth, simply smooth will do) but the “subdivision” graphics quality, which has apparently gotten set to some abnormally low value. Your ion isn’t particularly spherical in the image either, because this parameter also affects atom and bond display. See Tools… Viewing Controls… Effects, “subdivision” in the lower right area of the dialog. The factory default is 1.5 whereas your image looks something like 0.1. You can also control this value with the “set” command. This is discussed in the “Image Tips” under smoothness <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> …as well as the Effects and “set” documentation <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#subdivision> For future reference, we recommend sending questions to chimera-users(a)cgl.ucsf.edu (CC’d here) to better ensure that you get an answer. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 24, 2018, at 6:41 PM, Alex Yorn <alexyorn(a)yahoo.com> wrote: > > Elaine, > I'm having a little difficulty viewing ribbon models. I'm not sure what I did exactly, but I every time I open up Chimera, the default setting is this (see attached photo). This looks like a flat representation of the ribbon, but it's actually the supersmooth representation. I've tried double-checking the Cross Section in the Ribbon Style Editor, but everything looks normal (see attached photo). Can you help me with this? > Sincerely, > Alex Yorn

1 1

Tetramer using Chimera
by Bárbara Abrahim Vieira 24 Aug '18

24 Aug '18

Dear all, We wish apply in our research the Chimera system. Initially, we build our model (monomer) using ab initio and then, we will investigate the active site using docking. However, it is known that the protein is a tetramer. Then, we need to create a tetramer, without any pdb homologous, is it possible? Thanks for your time, ________________________________ Bárbara Abrahim-Vieira Modelagem Molecular ModMolQSAR Faculty of Pharmacy Federal University of Rio de Janeiro

2 1

some issues with download Chimera
by Zhu, Daming (NIH/NIAID) [E] 23 Aug '18

23 Aug '18

Hello, I have some issues with downloading Chimera. I can download and install it onto my computer, but it messed up my screens-I have two computer screens but only one works (with a terrible looking), and the other one cannot be connected. If I want both Chimera and my two computer screens working, what is the basic requirement for a computer? Thank you for your help. Best regards, Daming Zhu Daming Zhu Laboratory of Malaria Immunology and Vaccinology NIAID/NIH Twinbrook I, Room 1118 5640 Fishers Lane Rockville, MD 20852 Phone: 301-761-3993

2 1

Dropdown list of models in groups
by Yasser Almeida Hernández 23 Aug '18

23 Aug '18

Hello, I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. Best Yasser

4 6

Getting measure distance value
by al.kupczyk 22 Aug '18

22 Aug '18

Hi, I'm struggling with getting a value from runCommand in Chimera. I need to measure distance between an atom and a density map and keep it in a variable, so I'm trying to get a value from "measure distance" command in Python, but unfortunately with no results. Is there any way to somehow get it into a variable? Yours sincerely, Alicja

2 1

Changing chain ID for ligands
by Ahmad Khalifa 20 Aug '18

20 Aug '18

Is there a way to do it in chimera? Regards.

2 3

Chimera download
by Fengbiao Guo 17 Aug '18

17 Aug '18

Hello, My name is Fengbiao Guo, I work on Mercer University School of Medicine Savannah campus. I want to download the Chimera software, but I can’t open the page, so I want to ask how could I do can download this? Best regards, Fengbiao Guo

2 2

Measure the cross section of an EM map
by BuddySphinx 17 Aug '18

17 Aug '18

Dear Chimera users, I am trying to measure the diameter of my filament based on the EM volume. I am wondering which function I can use to measure the cross-section of it? Best, Yangqi Sent from Mail for Windows 10

2 2

CHIMERA liscence
by Lauer, Matthias 17 Aug '18

17 Aug '18

To whom it may concern. My name is Matthias Lauer. I am working for Pharma Research and Early Development at F. Hoffmann - La Roche Ltd. , in Basel, Switzerland. I would like to use Chimera for visualizing EM structures, as well as for modeling. I am heading a AFM laboratory, and I am closely collaborating with EM groups in academia. I belong to the drug discovery unit, and would need a written licence allowing me to use your software in our company. Your feedback would be highly appreciated, with kind regards from Basel, Matthias Lauer.

1 0

AutoVina Dock gives very different results running from GUI/command line tool
by Mariana Assmann 14 Aug '18

14 Aug '18

Hi everyone, I am trying to do docking using the command line tool in chimera. I found that when I use the GUI opening Tools > Surface/Binding Analysis > AutoDock Vina and following the docking window, I get very similar results for the docking pose and score every time I run the docking. However, if I do the same with the command line tool (with the same parameters, box size, local version of vina, same dock prep), I get very different results: the ligand is never in a good docking position, always on a different side of the pocket, and sometimes even intercepts strands of the protein. The docking scores are also off. I am using using Chimera 1.13 (build 41780), AutoDock Vina 1.1.2 (May 11, 2011), and the following command line for docking: vina docking receptor protein ligand #1.2 output /home/mariana/GTN/docking/keap1/docking_test13 search_center -7,3,-30.32 search_size 19,21,21 backend local location /home/mariana/bin/vina num_modes 9 I also found that the command line does not accept any of the vina receptor or ligand options (e.g. receptor_addh) and gives me error messages when including those ("Keyword 'receptor_addh' doesn't match any known keywords") Does anyone what the problems for those issues could be? Thanks, Mariana

2 1

Fwd: Bad number format Xplor file format
by Tom Goddard 13 Aug '18

13 Aug '18

Using single-precision for XPLOR output fixed the problem > > From: ISHWOR POUDYAL > Hello Tom, > > Many thanks! I changed the double precision to single-precision and it works. > > Ishwor > > > On Monday, August 13, 2018, 12:09:15 PM CDT, Tom Goddard <goddard(a)sonic.net> wrote: > > > HI Ishwor, > > The XPLOR format requires lines where the first 12 columns holds the first number, the second 12 columns holds the second number, … 12 columns per number. The example lines you provide do not use 12 columns per number. The software that wrote that file is not writing it in the correct format. My guess is that software fails because of the 3 digit exponents (e.g "E-166”) — probably the writing software only fails to follow the 12 columns per number rule when you have 3-digit exponents. In single-precision (32-bit floats) you would never get 3 digit exponents and perhaps the error is that the writing program was converted from single precision to double precision. > > Tom > > >> On Aug 12, 2018, at 7:51 PM, ISHWOR POUDYAL <ishwor_p_19(a)yahoo.com <mailto:ishwor_p_19@yahoo.com>> wrote: >> >> Hello All, >> >> I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines. >> >> ########################################################## >> 241 -120 120 241 -120 120 241 -120 120 >> >> 3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01 >> >> ZYX >> >> 0 >> >> 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00 >> >> 8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00 >> >> ############################################################# >> >> While I try to view the electron density in chimera it says >> "SyntaxError:Bad number format in line 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00" >> >> WOuld you please help me out >> >> Many thanks >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

1 0

Bad number format Xplor file format
by ISHWOR POUDYAL 13 Aug '18

13 Aug '18

Hello All, I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines. ########################################################## 241 -120 120 241 -120 120 241 -120 120 3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01 ZYX 0 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00 8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00 ############################################################# While I try to view the electron density in chimera it says"SyntaxError:Bad number format in line 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00" WOuld you please help me out Many thanks

3 2

Chimera for mac issue
by Yangfeng Li 13 Aug '18

13 Aug '18

Hello, I installed the latest version of chimera via your website on my mac (macbook air, 2013, hgih sierra). But it doesn't exist in my "application" file. And every time I need to double click chimera dmg file to launch it, which takss a very long long time verifying chimera. That process is different from Windows. I just wonder whether it's normal. Thanks, Yangfeng

2 1

Different center when display coordinates with bonds or ribbon
by 师扬 12 Aug '18

12 Aug '18

Dear chimera developers and users, Recently, I met a very strange issue about displaying coordinates in chimera. I found the helices were off-centered with the map, when I open a well refined PDB file and the map it was refined against, and keep an eye on the helices which is automatically displayed by Ribbon. But actually they are will aligned in COOT. And if I hide Ribbon and showed Atoms/Bonds, they were well-aligned. The attached files show the same region with different displaying modes. And I have tried several versions of chimera, the results were the same. Actually, I want to use Ribbon to display these helices. Does anyone know how to fix it? Thanks in advance! Yang

3 2

Animating peptide bond formation
by Alex Nazlidis 11 Aug '18

11 Aug '18

Dear Chimera users and staff, I've been thinking of ways to animate the formation of a peptide bond between two aminoacids but I haven't come up with a solution. Can you help me out here? :) Thanks in advance, Alex Nazlidis

2 1