- Chimera-users - RBVI Mailing Lists

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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