February 2019 - Chimera-users - RBVI Mailing Lists

Seeking for help
by temban billyhp 27 Feb '19

27 Feb '19

SirI prepared the DNA molecule using the dock prep with its default options but when I lunched auto dock vina alongside with my ligand, I received a message that auto dock vina cannot prepare the receptor due to an error. How can I solve this problem. I will be greatful listening from you. Best wishes. Sent from Yahoo Mail on Android

2 1

Installation problem on Fedora 29
by Murpholino Peligro 26 Feb '19

26 Feb '19

[murphy@eva02 Downloads]$ ./chimera.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/murphy/Downloads' inflating: chimera_install_6JK7q6/installer inflating: chimera_install_6JK7q6/chimera.bin Enter install location: ~/.local/UCSF-Chimera64-1.13.1 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/murphy/.local/UCSF-Chimera64-1.13.1' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu and icon? yes Traceback (most recent call last): File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimeraInit.py", line 666, in init import chimera File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/__init__.py", line 2777, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/murphy/.local/UCSF-Chimera64-1.13.1/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_6JK7q6' Installation is done; press return. Help please.

2 1

how to hide just H-bonds between water molecules with themselves?
by masoud aliyar 22 Feb '19

22 Feb '19

Hello I want to find H-bonds between 3 residues and the ligand and the water molecules around the ligand in 3 angstrom, but I don’t want H-bonds between water molecules. I Just want h-bonds between residues together and residues with ligand and residues and ligand with water. I have used Per-Frame script system. But I have two problems. First, if I set selection mode on replace mode and write this script: ********************* ~display :SOL zonesel :279 3 :SOL select up display sel select :38:53:147:279 findhbond linewidth 3 color blue selRestrict :SOL:38:53:147:279 ********************* The result is fine and H-bonds that I want were display. But if I apply this script, the system searches every water residues for find H-bond and take a lot of time per frame. second, if I set selection mode on append and write this script: ********************* ~display :SOL zonesel :279 3 :SOL select up display sel select :38:53:147:279 findhbond linewidth 3 color blue selRestrict both ********************* The calculations are going faster, but also, show H-bonds between water molecules with themselves that I don’t want it. How can I hide H-bonds between water molecule with themselves but H-bonds between selected residues and ligand and water retain? Thank you, everyone,

2 1

Defining CMYK color scheme for color actions
by Boaz Shaanan 21 Feb '19

21 Feb '19

Hi, Some journals require usage of CMYK color scheme. I see that the CMYK option exists in the color editor but is it possible to define CMYK for all the color actions (actions --> color) without having to go through the color editor for each color? Or am I missing something altogether? Thanks for you advice, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

3 3

Measure angle and effect length
by Shishir Adhikari 21 Feb '19

21 Feb '19

Hi, What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? Thanks

2 2

ViewDock tool not showing PDBQT vina output file
by Walker, Kevin 21 Feb '19

21 Feb '19

The subject line summarizes the challenge. I can open all other file types of interest (pdb, pyc, py) for viewing. However, I am unable to open a pdbqt vinaout file within Chimera 1.13. The result: Chimera session freezes and can only be shut down through the Windows 10 task manager. Have uninstall and reinstalled Chimera, cycled computer off and back on, and updated graphic driver and rolled by graphic driver to previous version, all to no avail. Windows 10 64-bit Chimera 1.13 Graphics Card: AMD Radeon 480 Memory: 11 GB

3 3

Chimera PDB2PQR
by Sowmya Indrakumar 21 Feb '19

21 Feb '19

Dear Developers, I am try to use Chmiera for electrostatic calculations. I first make the PQR file using the PDB2PQR at different pH, however I do not see a change in the total charge, the REMARK section shows that total charge is 1 always. I'm using the default setting as shown in the attached screenshot. Please let me know what might be going wrong? I installed the new version twice. Thanks a lot for your help! Regards Sowmya [cid:cdf013bd-01d5-4d3d-9dd2-554c27674417]

3 2

Chimera
by Giovanny Rincon S 21 Feb '19

21 Feb '19

Hello, I am a graduate student in Balearic Islands, I am doing a protein study with Chimera, I wanted to ask if it is possible to change the background color to White. Thank you so Much

3 2

Broad selection with command
by masoud aliyar 21 Feb '19

21 Feb '19

I use "zonesel" command to select SOL residues around ligand. but this command did not select entire residue and just select atoms that are the given zone.how can I use command-line to broaden residue selection and select entire residue atoms?. I know I can use the keyboard to broaden selection, but I want to use the command-line

2 2

STL/OBJ 3D models exported by Chimera cannot be read in Office 2019
by Jaime Rodríguez-Guerra Pedregal 20 Feb '19

20 Feb '19

Hi, Chimera team! I have recently discovered that Office 2019 has support for 3D objects that can be rotated, animated, zoomed... So I was curious about the possibilities for our molecular presentations. I knew Chimera allows to export molecules to several 3D formats and crossed my fingers so there was at least one format supported by Office. - Good news: there are two! STL and OBJ are both exported by Chimera and supported by Office. - Bad news: while the files can be correctly "loaded" in Office, they are not displayed at all! "Image could not be shown". Is this something that must be addressed in Chimera or is Microsoft's fault? The error message is very succinct and does not provide more details. I have attached the files I created with Chimera just in case. Thank you very much! Jaime.

2 2