June 2015 - Chimera-users - RBVI Mailing Lists

ImportError: no module named chimera
by ryanch＠mail.ecust.edu.cn 15 Jun '15

15 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

1 0

restoring sessions with python & triggers
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

Normally a save session by a python extension is invoked by a trigger SAVE_SESSION. For restoring a session, several related chimera APIs are available that are typically not used. 1) post model restore: SimpleSession.registerAfterModelsCB(afterModelsRestoredCB, arg) 2) BEGIN_RESTORE_SESSION and END_RESTORE_SESSION triggers. I need to reset extension gui values based on midas positions. I presume a normal restore in the session file does not guarantee that these midas positions will be loaded at that time, so I need to delay the gui updates until the restore process has ended or possibly when the models are loaded loaded. What is the distinction between END_RESTORE_SESSION and registerAfterModelsCB? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

setting viewing pref using python
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

the viewing dialog sets the Camera:Stereo parameters:units to inches, and Side View:Side to right. using python how can I reset them to mm & top? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

Re: [Chimera-users] Request for axes measurements
by Elaine Meng 14 Jun '15

14 Jun '15

Hi, You’re welcome, but I don’t have any further details than what is already given in the manual: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> It’s recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of me directly, in case others may be able to provide better answers! Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 31, 2015, at 6:26 PM, Jayaraman T <jram(a)pusan.ac.kr> wrote: > > Hi Elaine Meng, > Yes i could figure now the axes as well as angle measurements between them and thanks for your timely help. > > I would be happy if you could tell me the principle on which these axes are calculated. I have noticed that it's from Eigen vector values that are calculated for the coordinates of the set of atoms. > > I'm really interested on the backend for this calculation particularly, might help a bit progressing more for my research. > > Thanks again.

2 6

on MD movie and morph conformation by chimera
by Smith Liu 12 Jun '15

12 Jun '15

Dear All, Will you please introduce to me on how to combine chimera MD movie function and morph conformation function to make conformation change movie files to insert into PPT files? Smith

2 1

mol2 for NH3
by MPI 11 Jun '15

11 Jun '15

Dear Users, I try to prepare a mol2 from pdb for ammonia (NH3) and ammonium (NH4+), respectively. I used two commands: addh and addcharge with am1 method. eg, addh addcharge all method am1 It turns out that Chimera gave two similar mol2 files for NH4+ but NOT for NH3. I wonder what command and parameters are needed to produce a correct mol2 for NH3. Here are the input pdb files for NH3 and NH4, respectively. # NH3 HETATM 2860 N NH3 A 402 53.512 -12.964 -36.364 0.88 45.66 N # NH4 HETATM 2858 N NH4 A 404 56.362 -12.467 -27.097 1.00 30.80 N Thanks, Dewey

2 5

Problems detecting a left-handed helix
by Felipe Vasquez 11 Jun '15

11 Jun '15

Hi, I am trying to visualize several of the secondary structure details on a protein of interest, and I recently had notice (by several research papers) about the existence of a left-handed helix on it. However, I could not detect the helix using UCSF Chimera (it is simply considered as a loop). Why could this happen and how could be resolved? I have tried to modify the ksdssp cut-off parameter, but it was unsuccessful, so I think now that maybe the specific nature of the helix (left-handed polyproline-like type II) could be a bit tricky for the program. What would you suggest? Thanks in advance for your help an patience. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

2 3

Determination of angles formed by distances and ring axes
by Felipe Vasquez 10 Jun '15

10 Jun '15

Hi, I have problems trying to calculate the angle between two lines: one is really built as the distance between a residue atom from a protein and the centroid of a benzene ring (from a ligand), and the other is the line corresponding to the axis of the benzene ring. How could I accomplish this objective? I have read similar issues by chimera-users on the web, but I could not find enough information to complete the calculation (I could only estimate the first distance). In case of problems to clearly comprehend this particular task, please refer to the page 3, Fig 1, panel C in the attached research paper (phi angle). PD: Is it normal that the centroid of a benzene ring is above the ring itself? Because in the process of build the first distance, I don't know whether I have to calculate the distance between the centroid and the residue atom (which I found to be shorter), or instead calculate the distance between the center itself of the plane and the residue atom (which would be a bit longer). Thanks in advance for your time and assistance in this matter. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

2 1

file size of a trajectory
by MPI 10 Jun '15

10 Jun '15

Dear Users, I use the lastest version of Chimera to read trajectory (.xtc) files output from Gromacs ver 4.6.5. When a .xtc file size larger than 2GB in most cases and 1GB in some cases, Chimera gets choked and crashed. When a .xtc file size < 1GB, Chimera works very well. I wonder if this is a limitation for reading Gromacs trajectory files. Is there a solution ? Thank you. Dewey

3 4

tetrahedral symmetry
by Morris, Kyle 10 Jun '15

10 Jun '15

Dear Chimera Developers, I have a volume reconstructed from Relion 1.3 imposing tetrahedral symmetry. Curiously, I am not able to find the symmetry group using: $ measure symmetry #0 Chimera returns C3, even with adjusting the parameters it uses to identify the symmetry group. The model is aligned as following the Xmipp convention for T symmetry (http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry#T) which is the same as what Chimera calls T,z3? Any advice on getting the measure command to work in this convention would be greatly appreciated. Thanks! Best wishes, Kyle Morris University of Warwick, UK

2 1

Chimera-users June 2015