- Chimera-users - RBVI Mailing Lists

Pioglitazone Tautomers
by Nancy 10 Jan '11

10 Jan '11

Hi All, I am performing molecular docking and molecular dynamics simulations of the thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous different tautomeric states; I have attached a figure depicting several of them. Which tautomer would be dominant at the physiological pH of ~7.0? Also, are there any software programs that can predict which tautomer would be correct? Thanks in advance, Nancy

2 1

Morphing surface
by Sumitro Harjanto 05 Jan '11

05 Jan '11

Hi elaine, Thanks for the prompt responses on earlier queries. I have one more question: Is it possible to morph between 2 surfaces? Basically, I would like to show the effect in the surface contour due to a residue change. Thanks, 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 2

Amber trajectory rmsd
by George Tzotzos 05 Jan '11

05 Jan '11

I'd be grateful if you informed if there's a way one can plot protein backbone rmsd fluctuations of trajectories. I checked file:///Applications/Chimera.app/Contents/Resources/share/chimera/helpdir/ContributedSoftware/movie/movie.html#rmsd I may have missed the salient points. Many thanks in advance George

2 1

Togl patches?
by Clifford Yapp 05 Jan '11

05 Jan '11

Hi! I recently learned that Chimera has produced some patches to the Togl widget that allow it to work with Cocoa based Tk: http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/foreign/Togl Are these updates available under Togl's current license or are they restricted by the Chimera license? Thanks, CY

3 2

Enabling multithreading in chimera
by Akshaykumar Ganguly 05 Jan '11

05 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 05 Jan '11

05 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 05 Jan '11

05 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 03 Jan '11

03 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 03 Jan '11

03 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

Re: [Chimera-users] center of rotation
by Elaine Meng 30 Dec '10

30 Dec '10

Hi Bill, If command "cofr sel" is too long, you could (a) use the command "alias" to alias it to a shorter command, e.g. alias ^blah cofr sel which would then allow you to use the command "blah" or if you don't use the Command Line, (b) define your own keyboard shortcut <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accel…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accel…> However, the latter requires some Python, on which I cannot advise. Elaine 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! > > On Dec 30, 2010, at 11:18 AM, Eric Pettersen wrote: > >> Alternatively, you can control-click on the atom to select it and then >> choose Actions->Set Pivot in the menus to make it the center of >> rotation. >> >> On Dec 30, 2010, at 9:51 AM, Elaine Meng wrote: >> >>> Hi Bill, >>> You can use the command "cofr" with specified atoms (including "sel" >>> as the specification if the atom or atoms are selected). >>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html> >>> >>> There are several different rotation modes, and you can switch among >>> them using either "cofr" or the Rotation tool (under Tools... >>> Movement in the menu). >>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation >>>> >>> On Dec 29, 2010, at 3:55 PM, Bill Montfort wrote: >>> >>>> I'm returning to chimera after many years away and am quite >>>> impressed with the program, save for one issue: rotating about the >>>> screen center. My favorite way of viewing structures is for the >>>> rotation to be about a center of my choosing, as is common in many >>>> graphics programs (e.g. COOT). I would prefer to pick an atom on >>>> the screen and have this become the rotation center. Is there a >>>> simple way to accomplish this in chimera? A small point perhaps, >>>> but one that is frustrating for me....... >>>> >>>> Bill Montfort

1 1

center of rotation
by Bill Montfort 30 Dec '10

30 Dec '10

I'm returning to chimera after many years away and am quite impressed with the program, save for one issue: rotating about the screen center. My favorite way of viewing structures is for the rotation to be about a center of my choosing, as is common in many graphics programs (e.g. COOT). I would prefer to pick an atom on the screen and have this become the rotation center. Is there a simple way to accomplish this in chimera? A small point perhaps, but one that is frustrating for me....... Bill Montfort

3 3

Quiero ser tu amigo en Quepasa.com
by Sergio Garay 27 Dec '10

27 Dec '10

1 0

average structure of superimposed models
by Sumitro Harjanto 23 Dec '10

23 Dec '10

Hi Elaine, I have superimposed a few highly similar models of the same protein family. They are >80% identical in sequences. I would like to find an 'average' structure as a representative model of these proteins. Can I achieve this through Chimera..? Cheers, Sum 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 2

[chimera-users]about "color key"
by C.J. 22 Dec '10

22 Dec '10

Dear all, I seek for help that how to change the unit of "color key" to angstrom. As the default value displaied in "color key" is just number, I wonder what it means. Any reply will be greatly appreciated. -- Regards! C.J.

2 10

CASTp .poc
by S. Shunmugasundararaj 22 Dec '10

22 Dec '10

Hi Everybody, I loaded the CASTp *.poc file in Chimera and saved as a *.py file. When I open the .py file later, I do not see the .poc details. Is it hidden somewhere or how do I get that details? I do not see the "instance" item in the Tools menu. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html page does not seem to have the details about that. Thanks Raj

2 1

File conversion: strange behaviour
by George Tzotzos 22 Dec '10

22 Dec '10

Hi everybody, I'm attaching a pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres. Any explanation for this behaviour? Many thanks and best regards George

3 2

File conversion: strange behaviour
by George Tzotzos 22 Dec '10

22 Dec '10

Hi everybody, I'm attaching a pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres. Any explanation for this behaviour? Many thanks and best regards George

1 0

Re: [Chimera-users] [chimera-dev] Coloring
by Elaine Meng 21 Dec '10

21 Dec '10

Hi Hajeung, To color all carbons green the command would simply be color green,a C whereas "byatom" means to use the built-in element coloring scheme, not a specific color <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#byelement> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> and @ means atom name, not element, so "@C" would only get the atoms named C (not CA,CB, etc.). General user questions should probably go to chimera-users(a)cgl.ucsf.edu (chimera-dev is for development/programming questions). 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 On Dec 19, 2010, at 5:36 AM, Hajeung Park wrote: > Hello, I want to color “C” to a certain color. The manual is not very clear bout it. > My understanding is > > Color green byatom ,a @C > > But it give me error. > > Thanks.

2 1

Curves+ graphics of DNA
by Richard LAVERY 21 Dec '10

21 Dec '10

I am trying to visualize the graphic output from the Curves+ of a DNA duplex, which consists of two smooth backbone traces linked by vectors indicating the measured widths of the minor and major grooves. In the test case shown, adding two atoms defining one such vector and a single CONECT line linking them together (see attached PDB file) leads to three new bond vectors in the representation shown below. Am I making a mistake, or is this a problem with Chimera? Richard LAVERY richard.lavery(a)ibcp.fr http://web.mac.com/laveryr/Homepage Institut de Biologie et Chimie des Protéines 7 passage du Vercors, Lyon 69367, France Tel: +33 (0)4 72 72 26 37, Cell 06 62 76 84 47

3 2

changing HIS to HIP
by Francesco Pietra 16 Dec '10

16 Dec '10

Hello: I need to change several histidine residues (both HIS and HIE, although both called HIS) to HIP. I tried manually. In case of monoprotonation at NE2: modify structure element N bonds 3 geom trigonal connect to preex atoms color by element change modified residue's name to HIP set atom names to ND1 or retain current atom names In both cases the proton attached to ND1 takes the name "H1" instead of the expected HD1. Is that error in the above procedure or chimera bug? (chimera alpha version 1.5 (build 30702) on GNU/LINUX 32bit) Addendum: is there any other method of accomplishing the task with chimera? It is rather troublesome to go through all monoprotonated histidines of this large homomer (in different chains HIS of the same number have been differently protonated by reduce). A problem with reduce (if not my misuse of reduce) is that all histidines become monoprotonated, while the experimental pH is such that all should be diprotonated. I must add that I am bound to reduce because the program that I use subsequently goes through reduce. thanks for help francesco pietra

2 1