- 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

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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.

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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

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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

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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

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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>

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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

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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

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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

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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

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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

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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

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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

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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

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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

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

20 Aug '18

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

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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

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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

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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.

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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

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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> >

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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

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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

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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

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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

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problem with electron density map
by kesgin-schaefer＠chemie.uni-hamburg.de 07 Aug '18

07 Aug '18

Dear all, I have a problem with my electron density map: if I load the map in chimera, it will only show a subregion of the map and after "fit to model" the model will not be completely covered (see attachment). Any suggestions about how to solve the problem would be much appreciated. Thanks Steffi

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Problem with FIndHBonds
by Nawel Mele 07 Aug '18

07 Aug '18

Dear Chimera Users I am using hbond command to determine hydrogen bonds between a receptor and multiple compounds with different conformations from a docking simulation. I used a cmd script to automatise the process however I am facing and error that I am not sure to understand. I just pasted follow the part of the reply log where the problem appeared. The problem here is that when I load the compound with the different docked conformations separatly it is not always the same conformation taht has this error so I don't know what is the real problem. Many thanks for your help. Nawel *Finding intermodel H-bondsFinding intramodel H-bondsConstraints relaxed by 0.4 angstroms and 20 degreesModels used: #0 Representative_confo_site_active_minimum_distance_state001.pdb #1 DB08734_1|LigPrep_output_named|sdf|8330|dock5H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):#0 LYS 73.A NZ #1 UNK 1 O1 no hydrogen 2.924 N/A#0 ASN 76.A ND2 #1 UNK 1 N4 no hydrogen 2.398 N/A2 hydrogen bonds foundDB08734_1|LigPrep_output_named|sdf|8330|dock6 openeddonor: #0 ASN 76.A ND2 acceptor: #1 UNK 1 N4Traceback (most recent call last): File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimera/__init__.py", line 1919, in open models = func(filename, *args, **kw) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/ChimeraExtension.py", line 35, in func processCommandFile(cmdFile) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 108, in processCommandFile _processFile(f, emulateRead, filename) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 143, in _processFile if makeCommand(line): File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/ChimeraExtension.py", line 33, in cmdHBonds specInfo=[("spec", "models", "molecules")]) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 451, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 940, in createHBonds interSubmodel=interSubmodel, cacheDA=cacheDA) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args):TypeError: accPhiPsi() takes exactly 8 arguments (9 given)Error while processing chimera_input_step2_bug.cmd:TypeError: accPhiPsi() takes exactly 8 arguments (9 given) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args):See reply log for Python traceback.* -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK)

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Re: [Chimera-users] from govinda - How to save coordinates after rotation and translation fitted in cryo em map
by Elaine Meng 05 Aug '18

05 Aug '18

Dear Govinda, Please see the User’s Guide page on saving your data, and the links therein: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> …including Save PDB <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> ...write command <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> …saving after fitting <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’d here). You can also use Chimera menu: Help… Search Documentation. 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 4, 2018, at 11:22 AM, Govindasamy, Lakshmanan <lgovin(a)pennmedicine.upenn.edu> wrote: > > Dear Dr.Meng, > > How to save the coordinates in chimera after fitting into cryo em map. > i am having difficulty in save the coordinates > Please educate me how to save coordinates. > > thanks > govinda

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question
by 许东 04 Aug '18

04 Aug '18

Dear editors: thank you for your excellent work. I had a problem. After i built my protein model, it was shown in software as:but when i tried to save the result, the output was displayed as so could you tell me how to solve this problem? look forward to your reply, thank you

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Error from running headless Chimera
by Zhe Wang 03 Aug '18

03 Aug '18

Hi, I am trying to using headless Chimera on RedHat linux server 7.3 to produce some images. But I end up with a segmentation fault. Does anyone have an idea how it comes to this? The headless chimera is from https://www.cgl.ucsf.edu/chimera/download.html (64-bit daily build). The test code was taken without changes from https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html. Any ideas will be appreciated. Best, Zhe PS: OSMesa 11.2.2 has been installed. Executing chimera_surface.py... Processing 6c7m.pdb Opening 6c7m.pdb... #0, chain A: kemp eliminase KE07 6c7m.pdb opened Center of rotation: 0.867528 -1.77985 11.157 /software/chimera_headless/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 2 12 connected surface components Total solvent excluded surface area = 10612 component areas = 10035.4, 126.971, 97.9893, 90.9594, 38.157, 36.4953, 34.1487, 33.7557, 32.681, 30.3253, 29.9037, 25.222 Total solvent accessible surface area = 11324.6 component areas = 11265.5, 25.8506, 19.8737, 10.3135, 0.685134, 0.778238, 0.522429, 0.365982, 0.314644, 0.177358, 0.178001, 0.00214196 Surface 6c7m.pdb, category main has 12 components /software/chimera_headless/bin/mscalc 1.400000 10.000000 1 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags RESTART FROM TRI: 1 radius of atom 5 goes from 1.880000 to 1.980000 radius of atom 6 goes from 1.880000 to 1.980000 radius of atom 1569 goes from 1.420000 to 1.520000 Partial mode /software/chimera_headless/bin/mscalc 1.400000 10.000000 0 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags RESTART FROM TRI: 1 radius of atom 5 goes from 1.880000 to 1.980000 radius of atom 6 goes from 1.880000 to 1.980000 radius of atom 1569 goes from 1.420000 to 1.520000 Partial mode Calculation of some surface components failed. A single component of the surface was calculated correctly - the failure occurred for disconnected additional components such as inside bubbles. If the desired surface is already shown, there is no need for concern. However, if it is not shown, see below for possible fixes. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 10 1 connected surface components Total solvent excluded surface area = 10036.7 Total solvent accessible surface area = 11266.5 Surface 6c7m.pdb, category main has 1 components Rendering high resolution image... Segmentation fault

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Activation buttons (namely "All")
by Eric Pettersen 01 Aug '18

01 Aug '18

Hi all, The activation buttons below the command line have an “All” button that works much the same way as the “activate all” button in the Model Panel works: if you check it on, then all models are activated for motion; if you check it off then the previous activation states are restored. It has been suggested that the behavior could instead be that when checked off all models would be deactivated (making it easier in some cases to go from moving all models to moving just one). I’m trying to find out if any users make strong use of the current behavior of that button and wouldn’t want it changed. Conversely, I wouldn’t mind hearing people who would really like to see the behavior switched. Regardless of the outcome of the discussion, the behavior of the corresponding Model Panel button would remain the same for a couple of reasons: 1) when clicked, the text of the button changes to “restore activities” so there’s less chance of confusion, and 2) there’s a separate “deactivate” button. I will interpret lack of feedback as “sure, go ahead”. :-) —Eric Eric Pettersen UCSF Computer Graphics Lab

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fixed: error saving scene with independent rotation
by Elaine Meng 31 Jul '18

31 Jul '18

Hi Yanhe, The bug you reported a few days ago has been fixed! I just confirmed that with the current daily build of Chimera, you can now save scenes with independent rotation and use them in the Animation tool and in scripts. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Is there any tool to write some calculated attribute into a header format?
by Sergio Garay 31 Jul '18

31 Jul '18

Hi All! I would like to know: Is there any way or tool to write some calculated attribute into a header format? I want to see the same color values obtained for some a calculated attribute projected onto a sequence. I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute. Thank you in advance. -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Fwd: Inquiry for new/re-registration license key_Arifuzzaman Sarder
by Elaine Meng 31 Jul '18

31 Jul '18

> From: Sarder Arifuzzaman <arifpharmju(a)gmail.com> > Subject: Inquiry for new/re-registration license key_Arifuzzaman Sarder > Date: July 31, 2018 at 9:08:53 AM PDT > To: chimera-announce-owner(a)cgl.ucsf.edu > > Hi > Greetings. > This is Arifuzzamman Sarder. I am an earlier user of chimera software tool. Recently I installed the updated version (v1.13). However, I could not draw any chemical structure by inputting canonical smiles or any other chemical ID in this tool. Even it can not capture any chemical structure from PDB, unlikely it is giving us only protein structure. Could you please let me know how can I revive this tool, so that I can use it for molecular docking and chemical structure as well. > Thank you very much in advance. I am looking forward for your response please. > Sincerely > Arifuzzaman, Sarder > PhD research fellow > Chung-Ang University > Mobile: 010-2654-2606 > E-mail: arifpharmju(a)gmail.com <mailto:arifpharmju@gmail.com> > Web: https://sarderarifuzzaman.wixsite.com/arif <https://sarderarifuzzaman.wixsite.com/arif> HI Arifuzzamman Sarder, (forwarding to the proper address for asking Chimera questions: chimera-users(a)cgl.ucsf.edu ) There is no reason it should not work as before. Chimera does not use a license key. For example, in Chimera 1.13, command: open pubchem:12123 (- or -) open smiles:C1CCNC1 …shows a small molecule in sticks, and command: open 2gbp … shows PDB entry 2GBP; protein ribbons with ligand (glucose) as sticks and nearby sidechains as sticks. If you mean that your Chimera 1.13 is not showing small molecules, or not showing sticks, I only have two ideas: (A) graphics/rendering problem of your computer or (B) New Molecules preferences was set to show only ribbons. To check (B), show Preferences from the Favorites menu, then change to category: New Molecules and check that the settings are what you want, and then click Save. The behavior I described is for the default, “smart initial display” true. If you had it false, and also had “show atoms” false, it would not show atoms when you open a structure. If you feel it is a bug, you can use menu: Help… Report a Bug and describe in detail what you did and what the problem is. However, if it is a graphics problem of your computer, it is not something we can fix. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Extracting asymmetric unit
by Tom Goddard 31 Jul '18

31 Jul '18

Hi Martin, Fit an atomic model of the asymmetric unit then use volume zone (Volume Viewer menu entry Feature / Zone) then save the map (Volume Viewer / File / Same Map As…). See the maskZone option description in the volume save command for details https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> Tom > On Jul 31, 2018, at 7:00 AM, Martin Moncrieffe <mcm35(a)cam.ac.uk> wrote: > > Hi Tom, > > A quick question. I have a helical reconstruction (EM) and would like to extract the density for the asymmetric unit from the map. How does one do this? > > Best. > > __martin > >

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Surface vertex density
by Tom Goddard 31 Jul '18

31 Jul '18

For a density map you can control the number of surface triangles and vertices by choosing the subsampling “step” size in the Volume Viewer dialog. Step 2 will use every other grid point along x,y,z axes and result in a coarser mesh. For molecular surfaces computed from atoms, change the vertex density as described here http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html> Tom > On Jul 31, 2018, at 5:53 AM, ⁨עמיחי הולצר⁩ wrote: > > And another question - there is "Surface and Mesh options" under the "Features" tab, so one can control the smoothing of the surface, thickness, etc. How can I control the number of nodes of the surface? I mean, I want the mesh not to be so dense. Is it possible? > > Thanks again! > > 2018-07-31 13:38 GMT+03:00 עמיחי הולצר : > When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)? > I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh? > > Thanks, > Amichai > > 2018-07-30 19:37 GMT+03:00 Tom Goddard : > Hi Amichai, > > Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> > > Tom > > >> On Jul 29, 2018, at 3:06 AM, ⁨עמיחי הולצר⁩wrote: >> >> Hi Chimera support, >> >> I have 2 questions: >> >> 1. How does Chimera calculate the mesh from the density map? >> >> 2. How can I save the mesh as a file? >> >> Thanks a lot, >> Amichai Holzer >> Huji >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> > >

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Re: [Chimera-users] [chimera-dev] Save density map as a mesh
by Tom Goddard 31 Jul '18

31 Jul '18

If you want to save atoms, bonds and surfaces and load them into Chimera later, then save a session, menu File / Save Session As…. Tom > On Jul 31, 2018, at 3:38 AM, ⁨עמיחי הולצר⁩ <⁨amiholz(a)gmail.xn--com-yx0a> wrote: > > When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)? > I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh? > > Thanks, > Amichai > > 2018-07-30 19:37 GMT+03:00 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>: > Hi Amichai, > > Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> > > Tom > > >> On Jul 29, 2018, at 3:06 AM, ⁨עמיחי הולצר⁩ <⁨amiholz(a)gmail.com <mailto:amiholz@gmail.com>⁩> wrote: >> >> Hi Chimera support, >> >> I have 2 questions: >> >> 1. How does Chimera calculate the mesh from the density map? >> >> 2. How can I save the mesh as a file? >> >> Thanks a lot, >> Amichai Holzer >> Huji >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> > >

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display floating XYZ axes
by Pranav Shah 26 Jul '18

26 Jul '18

Dear Chimera Users and Devs, Is there a possibility to display the XYZ axes *a la* coot in chimera, so that one can keep a track of the direction of the views in the window? Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Harvard Medical School 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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(no subject)
by Yanhe Zhao 26 Jul '18

26 Jul '18

Hi, This is Yanhe. I want to make movies of side-by side rotaing structures, I set "center of rotation method" to "independent", when I try to save the scenes, chimera give error report as attached file shown. what should I do now? I really appreciate it if you can do me the favor. Best, Yanhe

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Removing structure segment and connecting the edges with dashed line
by Ahmad Khalifa 26 Jul '18

26 Jul '18

Hello, Selecting a segment of a structure and deleting it does remove that segment, but the ends are not connected. How to do the same and make the edges connected with a dashed line? Best regards.

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Problem with minimizing structure
by Renee Arias 26 Jul '18

26 Jul '18

Hello all, I am having a problem with the minimizing structure function in Chimera. I am just trying to change a single residue on a very small protein (88 residues), but I keep getting the error: No MMTK name for atom "H1" in standard residue "GLN". Previous message boards seem to just point to bug fixes in Chimera, but I am running the newest version available for Windows 10. I would appreciate any help! Thanks so much, Renee

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Click-and-drag selection still not working for chimera in Mac OSX....any plans for improvement
by Carmen Bayly 26 Jul '18

26 Jul '18

Hello Chimera users, I'm working with Chimera on an OSX 10.12.2 (intel core processor). I noticed that the click-and-drag selection function doesn't work, and saw a bug report from 2015 explaining it was because of the intel processor. However, it's 2018 now - does anyone know any fixes besides the wire display style? Thanks, Carmen

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action of labels
by Yanhe Zhao 25 Jul '18

25 Jul '18

To whom may concern, This is Yanhe Zhao, from ut southwestern medical center. After I add the 2D labels, i know how to move them, but could I rotate them? I really appreciate if someone can do me the favor. Best, Yanhe

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Aligning structure based on a specific secondary structure
by Ahmad Khalifa 25 Jul '18

25 Jul '18

Hello, All the options I see in Matchmaker is based on aligning whole chains. Is it possible to align structures based on a specific secondary structure, like a specific alpha helix for example? How to do so? Thanks in advance.

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How to place two identical proteins "near" each other
by Marla DeKlotz 24 Jul '18

24 Jul '18

I am trying to prepare a pdb to use in Rosetta docking. I need to place two copies of the same protein "near" each other, in roughly the alignment they should have after they dock together. Chimera seems to always overlay the two copies and I can't figure out a way to separate them and move/rotate each one independently. I don't want a tile view, I need them to have a real relationship in space so Rosetta knows where to "aim" its docking protocol. Thanks, Marla

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Including halogen atoms in findHBond tool?
by Nawel Mele 23 Jul '18

23 Jul '18

Dear Chimera users, I am looking for hydrogen bonds between a receptor and an ensemble of docked ligands with different structures including halogen atoms. I would like to know if there is a way to include halogen atoms in the hydrogen bond (findHBond) facility ? Best regards, Nawel -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK)

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Question about disulfide bonds and energy minimization
by Steven Douglas Aird 23 Jul '18

23 Jul '18

Dear Elaine, For the first time in about three years, I need to do a little more modeling. We sequenced an NADase and I used Galaxy to create a model using a known CD38 structure as a template (attached). Chimera displayed everything, but the disulfide bonds, of course. So I entered the specifications for those manually into the PDB file (attached). Two of the disulfides displayed properly, but four appear as thin dashed lines. At least one, at the C-terminus is clearly way too long. I tried to do an energy minimization, but while Chimera executed the steps, nothing in the structure moved. It used to be that one could watch the structure flex as it assumed the most energetically favorable conformation, but not this time, yet some of the disulfide bond lengths are clearly wrong. I also tried to use the set length command, in the forms: set length 2.05 / Set Length [2.05] but Chimera does not like either of these commands. If the manual included examples of the command format for each command, that would be really useful, because it is not clear where the syntax problem lies. As always, thanks for your help! Sincerely yours, Steve Steven D. Aird Technical Editor Faculty Affairs Office Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

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Morph Conformations tool doesn't produce a model with ribbons + *atoms*.
by Alex Nazlidis 22 Jul '18

22 Jul '18

Hello, I am trying to use morph conformation tool to produce a morph in a ribbon + atoms representation. While my 2 models are represented exactly as I want, when I create the morph the atoms diasappear and I'm left with the ribbon representation. Is there a way to create what I want? Regards, Alex

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Truncating fitted structures using a map mask
by Ahmad Khalifa 20 Jul '18

20 Jul '18

Hello, I have a tubulin lattice (sheet) fitted into a microtubule map. I want to generate a structure that has only one dimer, surrounded by only fragments from the other dimers on the top, bottom and sides. Is there a way to do that in chimera? Regards.

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Problems with V1.13
by Stefan Kunert 20 Jul '18

20 Jul '18

2 1