- Chimera-users - RBVI Mailing Lists

Enabling multithreading in chimera
by Akshaykumar Ganguly 06 Jan '11

06 Jan '11

Dear Sir / Madam, I use chimera 1.5 regularly for protein studies on a Quad core machine with Nvidia graphics running Ubuntu. However, the application does not support multi-threading and hence, runs quite slow. Is it possible to enable multi-threading in the existing release or will such a version of chimera be released in the near future? Regards, Akshay Kumar Ganguly Research Fellow, Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India

2 1

retrieving assigned color and ribbon thickness
by Sumitro Harjanto 06 Jan '11

06 Jan '11

Hi Elaine, I'm wondering if it is possible to retrieve the numerical (RGB) values of the color & ribbon width that I have previously assigned to certain residue(s). I often try out a certain color and save it in a session, but when I come back to the session and try to apply the color to the other residues I realized I forgot what's the RGB value I've assigned and have to resort to visual inspection (which is not very accurate). The same problem I have experienced with the ribbon thickness. Is there a way for me to keep a record of / retrieve these values? Thanks! Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

3 3

bond rotation
by Elaine Meng 06 Jan '11

06 Jan '11

On Jun 25, 2010, at 10:20 AM, Watson, Lisa wrote: > Hi Elaine, > I have changed several nucleotide bases in the DNA structure I am working with so that I can model in cytosine methylation. Is there a way that I can rotate the changed bases so that they are aligned to base-pair properly? > Thanks for your help! > -Lisa Hi Lisa, Sure, you can interactively rotate bonds. If you Ctrl-doubleclick a bond it should show a little menu where one of the choices is to rotate that bond. After you activate the rotation, the "adjust torsions" dialog will appear, which includes various ways to rotate the bond. You can have several rotatable bonds at the same time. Here is more about Adjust Torsions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> Also, the tutorial "Structure Comparison and Analysis" includes measuring distances, finding H-bonds and clashes, and rotating bonds: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

4 6

Silhouette edges around dashed wire-style bonds
by Dipl.-Ing. Thomas Mitterfellner 05 Jan '11

05 Jan '11

Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas

4 3

Adjusting the quality of surface while preserving other settings
by Sumitro Harjanto 04 Jan '11

04 Jan '11

Hi Elaine, Is there a way to adjust the quality of the surface. I often use the preset publication setting to make the surface smoother before rendering images. But after activating publication quality, the speed will slow down, and I will experience lag (especially with large models) when I try to move/turn the models around. I wondering if I can toggle between 'interactive' and 'publication' quality for the surface only without affecting the background /ribbon settings..? thanks! Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

2 1

index out of range
by Francesco Pietra 04 Jan '11

04 Jan '11

Hello: Two not new questions. (1) I am trying to read prmtop/mdcrd files from Amber MD with chimera alpha version 1.5 (build 30702) 2010-06-10 23:51:24 GMT, getting "index out of range" (the files are correct, they open with VMD) MDTools 1.2 Exp (2005-08-20) by James Phillips. Trajectory.DCD.MDToolsMarch97.md.help() for more info. - HomoCoord 1.3 Exp (2005-08-20) - Constants 1.1 Exp (2004-05-17) - AtomGroup 1.4 Exp (2007-02-07) - local 1.1 Exp (2004-05-17) Unknown OSTYPE ??? set. Viewing and plotting are disabled. - Trans 1.2 Exp (2005-08-20) - DCD 1.10 Exp (2007-02-07) - Data 1.2 Exp (2005-08-20) Traceback (most recent call last): File "/usr/local/chimera/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera/share/chimera/baseDialog.py", line 342, in command getattr(s, buttonFuncName(txt))() File "/usr/local/chimera/share/chimera/baseDialog.py", line 560, in OK self.Apply() File "/usr/local/chimera/share/Trajectory/EnsembleLoader.py", line 92, in Apply self.callback) File "/usr/local/chimera/share/Trajectory/DCD/__init__.py", line 72, in loadEnsemble addTrajKw=self.addTrajKw) File "/usr/local/chimera/share/Trajectory/DCD/__init__.py", line 85, in loadEnsemble ensemble = DCD(psf, dcd, startFrame, endFrame) File "/usr/local/chimera/share/Trajectory/DCD/DCD.py", line 24, in __init__ mdtMol = md.Molecule(psf=psfPath) File "/usr/local/chimera/share/Trajectory/DCD/MDToolsMarch97/md_AtomGroup.py", line 356, in __init__ nrecs = int(psfrec[0]) IndexError: list index out of range IndexError: list index out of range File "/usr/local/chimera/share/Trajectory/DCD/MDToolsMarch97/md_AtomGroup.py", line 356, in __init__ nrecs = int(psfrec[0]) See reply log for Python traceback. ************************************************ (2) Although I suppose I used in the past ATOM ATTRIBUTES to display chloride anion at its standard radius in preparing figures for publication, I just get it now as a tiny dot as set by MODELLER. That with proteins without or with non-polar hydrogens. For example TER 6750 LYS A 426 ATOM 6751 Cl- Cl- A 427 -31.021 4.748 41.205 1.00 6.32 Cl TER 6752 Cl- A 427 ATOM 6753 N LEU B 1 -13.959 20.979 -35.226 1.00 63.95 N I can't remember how to specify the chloride radius in command sel :427@Cl- ************************************************ Thanks for pointing me to the correct procedure francesco pietra

2 2

query
by SURESH KUMAR 04 Jan '11

04 Jan '11

hello sir, I need to find electron density of protein, i am planning to use UCSF Chimera software for that... so please help me how to find protein electron density using UCSF Chimera thank you A.Suresh Kumar, M.Tech Biomedical Engineering, Amrita School of Engineering, Ettimadai, Coimbatore.

2 2

Re: [Chimera-users] center of rotation
by Eric Pettersen 03 Jan '11

03 Jan '11

On Dec 30, 2010, at 11:02 AM, Bill Montfort wrote: > Thanks! This works well. If there were a quicker means for > activating Set Pivot, this would be even better (e.g. keyboard or > mouse combination). Cheers! Okay, for added convenience I've put a "Set Pivot" item in the atom context menu, which you can access by control-double-clicking an atom. This is only available in the 1.6 daily build and only as of tonight's upcoming build (so 1.6 builds dated Jan 3 or later). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Mirror image proteins
by Stephen B.H. Kent 03 Jan '11

03 Jan '11

How can I invert the configuration of a pdb file to create the mirror image model of the protein molecule? Thanks, Steve Kent Stephen Kent Professor of Chemistry Professor of Biochemistry & Molecular Biology Institute for Biophysical Dynamics Mail: Gordon Center for Integrative Science, Room W204 University of Chicago 929 East 57th Street Chicago, IL 60637, USA Tel: +1 773 702 4912 Email: skent(a)uchicago.edu

3 3

Thiazolidinedione Tautomers
by Nancy 03 Jan '11

03 Jan '11

Hi All, I am performing molecular docking and molecular dynamics simulations of thiazolidinediones (TZDs) binding to the ligand binding domain of the PPAR-gamma receptor protein. The thiazolidinedione ring can exist in numerous different tautomeric states (see attached figure); is there any particular tautomer(s) that would be dominant, and thus most appropriate for docking and molecular dynamics simulations, at pH 7.4? I have read the article "Metformin and glitazones: does similarity in biomolecular mechanism originate from tautomerism in these drugs?" J. Phys. Org. Chem. 2008, 21 30–33, as a reference, but it does make it clear as to which tautomer is most appropriate for simulating binding to a receptor protein at pH 7.4. Thanks in advance, Nancy

2 1