- Chimera-users - RBVI Mailing Lists

Hbond analysis in trajectories
by George Tzotzos 21 Dec '11

21 Dec '11

I'm trying to analyse Hbond formation during a 2ns AMBER trajectory involving receptor ligand complex. The trajectory loads as expected. I've selected the ligand and I checked the boxes "Only find H-bonds with at lease one end selected" and "Write information to file" . The output hbond.info contains information of a single frame. My question is whether there's a way by means of which information of ALL frames can be printed out. Many thanks and best regards George

3 2

minimization error
by divya neelagiri 20 Dec '11

20 Dec '11

Hello, I got this error when I was trying to minimize a structure. please tell me what went wrong. Executing testchim.py...Opening test1_chimera.mol2...1 model opened Traceback (most recent call last): File "/data/pgm/chimera/chimera_1.2422/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1253, in open File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython File "testchim.py", line 10, in ? rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") File "CHIMERA/share/chimera/__init__.py", line 1912, in runCommand File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand File "CHIMERA/share/MMMD/ChimeraExtension.py", line 29, in cmdMMMD File "CHIMERA/share/Midas/midas_text.py", line 281, in doExtensionFunc File "CHIMERA/share/Midas/midas_text.py", line 1885, in _getRealKw MidasError: Keyword 'nsteps' doesn't match any known keywords Error while processing testchim.py: MidasError: Keyword 'nsteps' doesn't match any known keywords (see reply log for Python traceback info) This is my program. I tried to execute it from command line using chimera --nogui testchim.py import os import chimera from chimera import runCommand as rc from chimera import replyobj os.chdir("/data2/di/database_build/outputs/outputs_mol2_sdf") fn = "test1_chimera.mol2" rc("open " + fn) rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") rc("write format mol2 0 min/" + fn) rc("close all") rc("stop now")

3 4

Rotating a model by exactly 90 degrees
by Konrad Hinsen 20 Dec '11

20 Dec '11

Hi everyone, I need to rotate a model by exactly 90 degrees around the Y axis. Mouse precision is not enough. I spent some time searching the command list for something appropriate, but without success. Is there really no way to do this? Thanks in advance, Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research AT khinsen DOT fastmail DOT net http://dirac.cnrs-orleans.fr/~hinsen/ ---------------------------------------------------------------------

3 3

Surface not including all molecules?
by Gustaf Olsson 20 Dec '11

20 Dec '11

Hello I'm trying to create a "cavity" model for visualization, I've done it before (a long time ago) and it worked great. But this time I'm having some problems. When trying with all molecules, I got some error regarding the calculation, so I split the model up into pieces and now it almost works. The problem I'm having is when I try creating a surface of one of the molecular species, I only get three "blobs" and not one big surface for all molecules. Any suggestions are most welcome. Don't know if it works, but I'll attach the PDB file for the molecules not being displayed as a surface properly.

4 8

Chimera 1.53 64bit and 12-16-2011 alpha both segmentation fault
by Starr Hazard 16 Dec '11

16 Dec '11

Folks, I have a chimera 1.41 running on an oldercluster head node with RHEL 4 something so its been a while since I did this procedure.... I have a newer cluster based on RHEL 6.1. When I try to launch either 1.5.3 or the alpha daily build I see the initial chimera banner but then only a text message reporting segmentation fault. Should these chimera's crash due to the fact that they are RHEL 5 compatible or is it something in my X11 setup? Will there be a log file anywhere that would provide clues? Where would that file be located? Thanks Starr

2 1

Posing Small Molecules
by Yoshus Kumka 15 Dec '11

15 Dec '11

Hello, I was wondering if there is a way to place in a molecule into a DNA and then minimize that structure either with chimera or in combination with other programs using chimera. For example, on page "1928" of the paper I attached they discuss posing a small molecule in between bases of the DNA. Here's the paragraph and the underlined sentences are of interest to me. If you are wondering why I don't use DeepView for this, my answer is that it is very unstable and crashes more often then producing useful results. Thanks for your help in advance. In a second stage, the crystallographic receptors were replaced by canonical B-DNA with similar sequences, generated with X3DNA.49 Since structural changes in the macromolecule are not allowed during docking, one canoni- cal oligomer was previously modified to include an “inter- calation gap”. In this way, Swiss PDB Viewer was used to pose an ellipticine molecule between two base pairs of canonical DNA, parallel to the base rings. After that, the complex was minimized by the steepest descent method, using the GROMACS package with the GROMOS 53A6 force field. The result was a modified B-DNA in which the base pairs flanking ellipticine were separated by 6.50 Å. Ellipticine was removed from the complex, and the modified B-DNA (see Figure 6B/F) was used as a target for docking with ellipticine. The sequences of the X3DNA generated oligomers are d(CGCAATTGCG)2 (without gap) and d(CG- GCATGCCG)2 (with gap, indicated in bold) .

2 1

problem with match function (superposition)
by Ken Shimo 14 Dec '11

14 Dec '11

Hello, I'm working with evolutionary algorithms applied to protein-protein docking. I'd like to calculate de RMSD between the native complex and the complex achieved with my docking model. For that I was trying to make the superposition of the complexes using the match function through the Chimera command line. I called the function as: match #0 #1 and got the following message: Atoms in each selection must be in the same model I'd like to know what am I doing wrong, or if there is anyway other way to obtain the RMSD and the superposed complexes. I'm using the complex code PDB 1CHO. Thanks for any help, -- Helder Ken Shimo BSc in Biomedical Informatics (University of São Paulo - Brazil) MSc candidate in Bioinformatics (University of São Paulo - Brazil) -- "When I get sad, I stop being sad and be awesome instead." (Neil Patrick Harris as Barney Stinson)

2 1

Error in using Chimera
by Poornima Josyula 14 Dec '11

14 Dec '11

Hi, I installed Chimera 1.5.3 in my system today. I have a Windows 7 64-bit machine with a processor that is, Intel i7-2600, CPU@ 3.40 GHz. After I open the image, I get the following error. I copied this from the debug window of Chimera. * initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit* I would be glad if anyone can help me fix this issue. Thank you. -- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula(a)gmail.com

2 1

Regarding estimation of volume in 2D
by Poornima Josyula 14 Dec '11

14 Dec '11

Respected Sir/Madam, My name is Poornima and I am a Ph.D. student from India. My area of research is Biofluid Mechanics. I am modeling bubble transport in bifurcating microchannels. I am performing 2D simulations for the above problem using a commercial Computational Fluid Dynamics (CFD) software called ANSYS Fluent. ImageJ is currently used for the purpose of post processing. But, I haven't entirely been successful in estimating the volume accurately. Please find attached a snapshot of the simulation. In that snapshot, my region of interest (ROI) is the red colored area whose volume I have to find out. Is there a way Chimera can help me estimate this volume? Please let me know your suggestions. Thank you for your time and patience in reading my mail, despite your busy schedule. Kindly excuse me for any inconvenience caused. Look forward to receive a positive response at the earliest. Have a good day. -- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula(a)gmail.com

3 3

how to change the atom type in chimera
by Hina 13 Dec '11

13 Dec '11

Dear All, Can you kindly let me know how to change or edit atom typing in chimera and how to visualize the ligands in the form that double bond single bonds aromatic centers are clearly seen.

2 1