- Chimera-users - RBVI Mailing Lists

crash on using Preset Publication 2
by Dieter Blaas 02 Aug '19

02 Aug '19

Hi, I have been using the Publication Preset 2 for making figures of a number of pdb structures without problems. However, I now have a pdb that shows up well in Chimera and does not have any obvious problems. However, when trying rendering it with the Preset Publication 2 (and only with this one) Chimera crashes with the error message below: *** stack smashing detected +++: /home/blaas/.local/UCSF-Chimera64-1.10.2/bin/python2.7 terminated Since I have prepared the other figures with this setting I'd like using it as well for the next figure but how? Thanks a lot, best regards, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. 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, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 1

Chimera Viewdock Bug
by Sacco, Michael 02 Aug '19

02 Aug '19

Hello all, I would like to report a bug. When using Chimera in dual monitor mode on windows OS and loading the viewdock module, Chimera becomes unresponsive. However, when the second monitor is unplugged, it functions normally. I have confirmed this on multiple computers. After force closing Chimera a pop-up appears with the message "Chimera exited abnormally; the exit code was: 1.". Thanks everyone! Michael

2 1

OBJ files are exported too small and won't open on other programs.
by Josh Moon 01 Aug '19

01 Aug '19

Hello! I am a relatively new and inexperienced user of Chimera. I am having a difficult time working with obj files. The Scenes I'm exporting as obj's end up having a very small file size (67 bytes in one case) and are being processed very quickly. The resulting file won't open successfully on any program that should understand an obj. Stl's are fine. Conversely, when I try to open an obj file into Chimera, it asks me to manually "Designate the File Type" as though it doesn't know what to do with it. Can someone please suggest what features I'm missing so that I can successfully export an OBJ? I'm also interested in how best to handle color information. Thank you! Josh ----------------------------------------- Josh Moon, Ph.D. (he/him/his) Educational Technology Specialist Kalamazoo College (269) 337-7415

2 1

inquire about molecular docking
by Mohamed Hegazy 31 Jul '19

31 Jul '19

Hey , My name is Mohamed Hegazy, beginner in molecular docking , recently I performed a molecular docking procedure using chimera and I found that the initial structure of the ligand differs from the minimized one , and the binding score for a ligand would change during my different runs. The binding score you obtain from my docking cannot be a constant number. Sent from Mail for Windows 10 Mohamed Said Hegazy --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

2 4

AreaSAS Issue
by Rucco,Dominic J 31 Jul '19

31 Jul '19

Hello, I'll start by saying your software has helped me visualize protein structure for quite some time and overall has been easy to use! I do have a question however: I was recently using the "render by attribute" feature to display areaSAS measurements but have run into an issue. I can no longer select this attribute from the dropdown menu. I noticed this when I attempted to render it on the protein mCherry (PDB 2H5Q). Even when I have gone back to other PDB entries I know have worked for areaSAS rendering, it doesn't appear as an option anymore. The only time I can get it to appear is when I load a session that already has the rendering performed on the protein. Any help would be appreciated, thank you, Dominic Dominic Rucco | Ph.D. Candidate George and Josephine Butler Polymer Research Laboratory Center for Macromolecular Science and Engineering Department of Chemistry University of Florida Leigh Hall 314 | PO Box 117200 | Gainesville, FL 32611-7200 drucco(a)ufl.edu<mailto:drucco@ufl.edu> | www.savin.chem.ufl.edu<http://savin.chem.ufl.edu/>

2 1

--nogui gets permission denied when fetching pdb id
by Ryan Harlich 30 Jul '19

30 Jul '19

Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

3 5

Minimization with sulfur atom
by sara20＠mail.ustc.edu.cn 30 Jul '19

30 Jul '19

Dear users I have complex structure with ligand having sulfur atom in it. I am trying to minimize it but it fails giving the following error: (LIG) /home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/antechamber: Fatal Error! (LIG) Cannot properly run "/home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/sqm -O -i sqm.in -o sqm.out". I assume it's because of sulfur atom in ligand because I tried running it with out sulfur and it worked fine. I checked MMKT Atom database for sulfur file and it's already there: name = 'sulphur' symbol = 'S' mass = [(31.97207070, 95.02), (32.97145843, 0.75), (33.96786665, 4.21), (35.9670806, 0.02)] color = 'yellow' vdW_radius = 0.18 b_coherent = 2.847*fm b_incoherent = 0.188*fm b_coherent_deut = 2.847*fm b_incoherent_deut = 0.188*fm Any help would be highly appreciated. Thanks Sara

2 1

Applying session parameters to another pdb file.
by David Sáez 29 Jul '19

29 Jul '19

Dear Chimera experts, I have saved a session of Chimera showing the perfect angle and size for the molecules of interest. Now I would like to apply the same parameters to visualize another (but similar, only differnet coordinates) pdb file. Is there a way to do that? Thanks in advance. David

2 2

Editing sequences within Chimera
by Joshua Plank 26 Jul '19

26 Jul '19

Hi, I am wondering if it is possible to edit the amino acid sequence somehow? I have a .pdb file of the protein I'm interested in, but would like to change two of the amino acids to something else. Is this possible? thanks, Josh -- *Joshua Plank* *PhD Student* *Department of Electrical and Computer Engineering* *University of California, Riverside* *email: jplan002(a)ucr.edu <jplan002(a)ucr.edu>* *phone: 505-977-9919*

3 4

Measuring the distance between residues and a surface
by Stanley, Julian A 25 Jul '19

25 Jul '19

Hello! I'm fairly new to Chimera, so if you're able to point me towards any resources that can help me answer questions like this one independently in the future, please do! Here's the question: I would like to measure the distance between the ends arginine and lysine residues and a surface, using Chimera's python modules. Typically, I would load my .pdb file, generate a surface, and then use the "measure distance" command and parse the output from the Reply Log. This approach works fine, except since "measure distance" prints to the reply log, I need to run my script in GUI mode. If possible, I'd prefer to run everything from the command line only. I thought that I might be able to do this with the distance() command, but I can't figure out how to pass a surface to that command. Does anyone have any tips/advice? In summary, what I usually do: ``` from chimera import runCommand as rc # load the file rc("open " + pdbFile) # Generate a surface rc("select protein") rc("split") rc("surface allComponents false") rc("~select") # Measure distance between arg and lys and the surface rc("select #0") rc("~select #0:@") rc("measure distance :arg@cd|:lys@ce selection multiple true show true") ``` And then I parse out the distances from the Reply Log. What I would prefer to do: It would be better to have the output to go to STDOUT when I run the script. I imagine that I'd use something like the `distance()` command, of the premade scripts (like here: http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/atomdist.py) but they are designed to measure the distance between atoms or residues, not between residues and a surface. Thanks for your help! Sincerely, Julian

3 2