April 2018 - Chimera-users - RBVI Mailing Lists

Error in Windows saving a session
by Joel Mackay 22 Apr '18

22 Apr '18

Hi all Have other people seen (and solved!) this error before (below)? I'm having it crop up pretty much all the time now when I try to save a session (on my Win7 machine - running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay(a)sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/

3 7

run chimera remotely over nice dcv
by Mihajlo Vanevic 20 Apr '18

20 Apr '18

Dear Chimera users and developers, We are trying to run Chimera remotely on our cluster via Nice DCV visualization software: https://www.nice-software.com/products/dcv This package provides GPU acceleration for OpenGL and DirectX applications. It indeed works for most of apps, however with Chimera we get the following startup error X Error of failed request: GLXBadContext Major opcode of failed request: 152 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 73 Current serial number in output stream: 73 Our cluster visualization node has nvidia GeForce GTX 1080 Ti cards and nvidia drivers 384.81 Chimera works if we use software mesa rendering, but it would be great if we can make it work remotely with hardware rendering. With kind regards, Mihajlo Vanevic Cryo-EM group, Utrecht University

2 1

Adding quadrant lines to atoms
by Trevor Harris 20 Apr '18

20 Apr '18

Hi, Is there a way to add quadrant lines to atoms similar to how Houkview does it in CylView, pictured below. If not, could you add this feature as an option? All the best, Trevor Harris

3 4

Superimpose map with fitted atoms
by Luca Pellegrini 20 Apr '18

20 Apr '18

Hi, I’d like to superimpose a cryoEM map with fitted atoms onto a second cryoEM map. I do this using ‘fit in map’, but only the map moves, the fitted structure does not. Is there a way to update the coordinates of the fitted structure according to the map superposition? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

2 1

Saving multiple identical PDB in a single file with unique chain ID
by Ahmad Abdelzaher 20 Apr '18

20 Apr '18

Hello, I'm building a tubulin lattice. I want to save the structure as a single model, however, the chain ID for each monomer should be different from the other ones. If I copy/combine my alpha-beta tubulin monomer, I get another structure with A and B chains. What I want is different chain letters. How can I do it? Regards.

2 5

Making chimera selections on the fly
by Bala subramanian 19 Apr '18

19 Apr '18

Dear chimera lovers, Good day. I wrote a small script (pasted below) to monitor the dipole vector of water molecules during MD. The script was adopted based available example. rc('close #1-500') m = chimera.openModels.list()[0] wat = m.residues[2449] com = Point([a.coord() for a in wat.atoms], [a.element.mass for a in wat.atoms]) # dipl = Vector() No working, Use numpy instead dipl = np.array( [0.0,0.0,0.0] ) for atm in wat.atoms: #dipl += atm.charge * atm.coord() dipl += atm.charge * np.array( atm.coord().data() ) vend = np.array(com) + 5 * dipl of = open('current.bild','w') of.write('.color green\n') of.write('.cone %f %f %f %f %f %f 0.5 \n' % (com.x,com.y,com.z,vend[0],vend[1],vend[2])) of.close() rc('open current.bild') Query 1) The following syntax given in a example doesnt work. What is the chimera point object indeed, an array or list ?. How to do math operations on point object. dipl += atm.charge * a.coord() Error: TypeError: unsupported operand type(s) for *: 'float' and '_chimera.Point' Query 2) In my example, I choose a specific water molecule by residue index. I am looking for some way to select the water (or get list of water residues) that satisfy a selection on the fly, lets say that water within 3 A from a prot. residue. In short, how to handle selections inside python script in chimera framework. I tried to play with chimera.selections but I didnt succeed. Any example could be of help. Query 3) Invoke data calculated out of chimera inside a perframe script. If I have say 100 frames. I can do the dipole vector calculation outside chimera and write separate “.bild” files, 1.bild, 2.bild, …..n.bild. Then inside the perframe script, I can invoke a particular .bild fine corresponding to the frame no. Please help me with an syntax example if this is possible. Thanks in advance, Bala -- C. Balasubramanian

2 1

Re: [Chimera-users] multiple structures to minimize
by Elaine Meng 19 Apr '18

19 Apr '18

> On Apr 19, 2018, at 5:21 AM, Lu Yang <luy(a)princeton.edu> wrote: > > Hi Elaine, > I’m a Chimera-user and have a question of structure minimization. I have multiple structures to minimize for ligand docking simulation. I wonder if I can open them all in chimera, and select all of them for structure minimization? Will they affect each other? Because otherwise I’ll have to go through open -> minimize -> wait -> save one by one. > Best, > Ling > ----------------------------------------------------------------------- > Lu (Ling) Yang > Ph.D candidate | Andolfatto Lab > Ecology & Evolutionary Biology | Princeton University > www.luyangevolution.com > Hi Ling, It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’d here) to ensure getting an answer. As it says in the “minimize structure” help page, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize…> "All chosen models are treated as a single system” which is not what you want. It sounds like it would be better to write a script using Chimera’s “minimize” command. First try this on one ligand structure by entering the command directly, to figure out what command options to use. After you figure out the correct Chimera command, you can write a Python script to loop through multiple ligands, opening (“open” command), minimizing, and saving (“write” command) them one by one. See documentation for individual commands and their options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> … and for writing a Python script to loop through multiple structures: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Residue selection for simulation/energy-minimization
by Kim, In-Kwon (kimiw) 19 Apr '18

19 Apr '18

Dear, I am trying to publish our structure and modeling done by CHIMERA. My questions are 1. What is the default option for distance for selecting residues around ligand (e.g., XX A around ligand). 2. Any time scale for simulation? Here is my method description. Any suggestion, related citation, and help would be appreciated. “~. Residues within XX A of the ligand was selected for simulation. The model was then subjected to energy minimization using the AMBER ff14SB protein force field in the Chimera package (34).” Thanks, In-Kwon In-Kwon Kim, Ph.D. Assistant Professor Department of Chemistry University of Cincinnati

2 2

BIOMT symmetry matrices
by Healey, Joe 19 Apr '18

19 Apr '18

Hi Chimera Team, I'm familiar with the sym command within chimera, specifying particular degrees of rotational symmetry for instance. As the biological unit feature tends to work quite nicely for this for a number of the proteins that I'm working on, I was wondering if there is a simple way to apply the BIOMT matrix for one protein to another? The proteins I want to apply them to are homology models of the equivalent proteins, so their biological unit information should be meaningful. If its possible to do this in chimera that would be great, but if you have any alternative suggestions (perhaps its possible to copy the BIOMT lines from one PDB text file to another? Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

3 6

SwissSidechain plugin for Chimera
by Madeline Rollins 17 Apr '18

17 Apr '18

To whom it may concern, I am trying to mutate a residue of my protein of interest to one of the non-natural sidechains (phosphoserine) in the SwissSidechain database. I downloaded the SwissSidechain plugin onto my computer a few months ago and it worked fine, but it recently disappeared and I have been trying to re-download it. I have downloaded the zip file from the SwissSidechain website, extracted all of the files inside (both the dependent and independent Rotamer folders) and have added the directory containing the location in the tools category. However, the SwissSidechain module still doesn't appear under the Tools > Structure Editing menu. When I try to use the command "swapna SEP #0:95.A" (for example), I get an error message that reads "No connectivity template for residue 'SEP'." Do you have any advice on how to solve this issue? Thank you, Madeline Rollins

2 4