- Chimera-users - RBVI Mailing Lists

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."

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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

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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

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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

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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."

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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

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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

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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."

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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

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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.

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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

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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

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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

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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

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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

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

27 Dec '10

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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."

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[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.

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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

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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

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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

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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.

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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

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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

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selection line-width
by Daniel Gurnon 15 Dec '10

15 Dec '10

Hi everyone, Two requests that would help with interactive demonstrations to large audiences: In preferences/background, the selection mode can be "fill" or "outline". Is it possible to add a line-width option for outline? I want to increase the thickness of a selection outline to make it easier for my students to see when I'm projecting an image, but I don't want to use the fill option and lose residue color information. I suspect that's an easy fix, but this one might be more difficult: Transparent surfaces are very informative when combined with underlying ribbons or stick representations of atoms. But if a residue is visible beneath a transparent surface, selecting it (via the command line) does not show the selection outline. Is it possible to make that work? Thanks, Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] [Chimera-announce] Chimera 1.5 release
by Elaine Meng 15 Dec '10

15 Dec '10

Hi Surendra, Yes, if you are doing map-in-map fitting, it calculates the correlation values, in 1.5 and also in earlier versions. You have the choice of calculating the correlation about zero or about the mean. If you are doing atoms-in-map fitting, it does not give correlation values UNLESS you turn on the "Use map simulated from atoms" option, and in that case you also need to enter a resolution value for the simulated map. If you click the Help button on the dialog it will show the manual page with more detailed explanations, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht…> 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 15, 2010, at 9:33 AM, Negi, Surendra S. wrote: > Hi Elaine, > In EM fit, Is it possible to calculate the Correlation? I am using current version 1.5 of UCSF chimera. > Thank you. > Surendra > ps: the snapshot is available at : http://img221.imageshack.us/img221/2492/screenshotpt.png

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Maximum surface areas for each amino acid
by Boaz Shaanan 15 Dec '10

15 Dec '10

Hi Elaine, The values in the table you mentioned seem to correspond to side-chain accessibility only, if I compare them to those for Gly-X-Gly peptide as in the classical paper by Miller et al. (1987), 196, 641-656. Their table can also be found in the book by Creighton: Proteins, 2nd edition, p. 142. Best regards, Boaz ----- Original Message ----- From: chimera-users-request(a)cgl.ucsf.edu Date: Tuesday, December 14, 2010 21:11 Subject: Chimera-users Digest, Vol 92, Issue 11 To: chimera-users(a)cgl.ucsf.edu > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Maximum surface areas for each amino acid (Tom > Goddard) 2. Center of segmentation regions (Tom Goddard) > 3. Chimera Error (Kshatresh Dutta Dubey) > 4. Re: Chimera Error (Elaine Meng) > 5. Re: Maximum surface areas for each amino acid > (Elaine Meng) > 6. 3D-Stereo. (ayassin(a)wadsworth.org) > 7. merging 3D volumes (Marlovits,Thomas) > 8. Re: merging 3D volumes (Elaine Meng) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Mon, 13 Dec 2010 18:08:11 -0800 > From: Tom Goddard <goddard(a)sonic.net> > Subject: [Chimera-users] Maximum surface areas for each amino acid > To: iropson(a)psu.edu > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4D06D18B.7040806(a)sonic.net> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Ira, > > I don't know of any table of maximal solvent > accessible surface areas > for each residue type when bounded by glycines. Maybe > someone on the > Chimera mailing list will know. > > A Chimera Python script could run through the PDB > and accumulate > per-residue surface area statistics. One trouble with that > would be > that surface calculation fails in Chimera in some percentage of > cases > (~5%) due to numerical problems. > > Tom > > > Hi Tom, > > > > Love the software. Do you have a table for calculating the > maximum > > available surface area for amino acids eg.(Gly-Xxx-Gly) so > that I can > > get a relative percentage exposed surface area from the > calculations? > > Do you know how to find one in the literature? Has anyone > written a > > program that describes the possible surface exposure for a > residue in > > a particular secondary structure and/or a particular sequence? > This > > maximal value would certainly be different depending on the > local > > sequence and structure. For example, a residue in the middle > of a > > helix would have to be shielded from the solvent by the i+4 > and i-4 > > residues, and the size of those residues would matter. > > > > Thanks, > > Ira > > > > > > On 12/10/10 2:41 PM, Tom Goddard wrote: > >> Hi Sumitro, > >> > >> I made a Chimera video tutorial showing how to > determine which > >> residues are on the surface. > >> > >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html > >> > >> Tom > >

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delete named selection
by S. Shunmugasundararaj 14 Dec '10

14 Dec '10

Hi, How do I delete the "Named selection" from the chimera file? I could not get the info from the archive or by searching the web. Thanks in advance Raj

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3D-Stereo.
by ayassin＠wadsworth.org 14 Dec '10

14 Dec '10

Hello, Will the sequential stereo work with the Nvidia 3D vision kit available with the Toshiba 3DV series laptops? if not, What would be the best option for sequential stereo? Thank You. Aymen Yassin. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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merging 3D volumes
by Marlovits,Thomas 14 Dec '10

14 Dec '10

Hi, I was wondering, whether a 3D map can be placed into a box with a user defined number or x/y/z planes ? Ideally, I would like to place several 3D maps into boxes of the same dimensions and would like then to merge all maps into one 3D map file. Is this possible ? Tx for your fast answer, Best, -Thomas Thomas C Marlovits Research Group Leader marlovits(a)imp.ac.at

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Chimera Error
by Kshatresh Dutta Dubey 14 Dec '10

14 Dec '10

Dear All, When i am trying to assign partial charge on a molecule, it is giving error something like this- AttributeError: '_chimera.Atom' object has no attribute 'gaffType' File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", line 289, in writeMol2 atomType = atom.gaffType I am using chimera 1.5 on linux 64-bit Kindly help to resolve this problem Thanks in advance kshatresh

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Maximum surface areas for each amino acid
by Tom Goddard 14 Dec '10

14 Dec '10

Hi Ira, I don't know of any table of maximal solvent accessible surface areas for each residue type when bounded by glycines. Maybe someone on the Chimera mailing list will know. A Chimera Python script could run through the PDB and accumulate per-residue surface area statistics. One trouble with that would be that surface calculation fails in Chimera in some percentage of cases (~5%) due to numerical problems. Tom > Hi Tom, > > Love the software. Do you have a table for calculating the maximum > available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can > get a relative percentage exposed surface area from the calculations? > Do you know how to find one in the literature? Has anyone written a > program that describes the possible surface exposure for a residue in > a particular secondary structure and/or a particular sequence? This > maximal value would certainly be different depending on the local > sequence and structure. For example, a residue in the middle of a > helix would have to be shielded from the solvent by the i+4 and i-4 > residues, and the size of those residues would matter. > > Thanks, > Ira > > > On 12/10/10 2:41 PM, Tom Goddard wrote: >> Hi Sumitro, >> >> I made a Chimera video tutorial showing how to determine which >> residues are on the surface. >> >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html >> >> Tom

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Center of segmentation regions
by Tom Goddard 13 Dec '10

13 Dec '10

Hi Tyler, The Chimera Segger segmentation tool currently doesn't report the geometric center of segmentation regions or the principal axes. I've attached a Python script that will do that. Select the regions in Chimera then open the script (File / Open). The results will appear in the reply log (menu Favorites / Reply Log). The results are in physical coordinates (taking account of volume grid spacing), not grid index units. Tom > Dr. Meng, > > I am using Segger in Chimera and displaying the principal axes for > some of my segmentations. I am wondering if there is a way to find > the XYZ coordinates of the origin of the principal axes for each of my > segments. Is there a way to put the coordinates for these axes in a > text file? > > Thank you, > > Tyler Steele >

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Inatallation Location
by Stephen P. Molnar 13 Dec '10

13 Dec '10

Chimera 1.5 (32-bit) on OpenSuSE 64-bit v11.2 I have just installed 1.5 on my syustem.. The installer insists on an installation in /home/computation/.local in spite of my attempts to install in a location of my choice. This is rather annoying as I prefer to install software on a hard drive that will not be overwritten when I upgrade the OS. Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivarate http://www.FoundationForChemistry.com

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Chimera Error
by יוכבד 13 Dec '10

13 Dec '10

---------- Forwarded message ---------- From: יוכבד <ybaime(a)gmail.com> Date: Mon, Dec 13, 2010 at 11:44 AM Subject: Chimera Error To: chimera-users(a)cgl.ucsf.edu Hi I'm trying to open a density map file using chimera and for some reason the file won't open. The opening is followed by an error message regarding the file size being too small for the grid size. The same error appears also in the old version (1.4.1) and also in the newest version. How can I solve this problem? How can I change the grid size? The same file opens successfully on a friends computer with the 1.4.1 version and so I assume the file is not corrupted. Attached is an image of the error message. I'd appreciate your response. Thank you Yocheved Baime Bar-Ilan univ.

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Calculating Solvent Accessible Surface of individual residue in a model
by Sumitro Harjanto 10 Dec '10

10 Dec '10

Hi Meng, I would like to find out if I can use Chimera to calculate the solvent accessible surface(SAS) of each residue in a model..? I would like to find out, basically, if I show the surface of the molecule, which are the residues buried (SAS = 0) and which are the ones contributing to the surface contour (SAS > 0). 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."

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Measuring the volume enclosed by a complex
by Anindito Sen 10 Dec '10

10 Dec '10

Dear All This question may have been answered before but will be helpful if you can let me know - How can I measure the volume enclosed by a protein complex. Thanks Andy Dr. Anindito Sen (Ph.D) School of Biological Sciences University of Auckland 3A Symonds Street Room 420 Auckland City. New Zealand. Tel: +64 -9- 373-7599 ext: 87593

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Recommended HW for Chimera 3D
by Marek Basler 07 Dec '10

07 Dec '10

Hi, what would be recommended HW and OS for trouble free 3D using glasses with new 120Hz LCDs? Linux or Win? What is the best graphics card? I don't care about money but nothing crazy either. Any suggestions? Thanks a lot! Marek

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Re: [Chimera-users] Query regarding Fit in Map
by Tom Goddard 07 Dec '10

07 Dec '10

Hi Arun, So you just want to measure the correlation for a selected atoms in a map, no fit optimization. This can be done without Python. Make a simulated map with the Chimera "molmap" command, and report the correlation with "measure correlation". molmap sel 12.5 modelId #5 measure correlation #5 #0 Here the map is #0, selected atoms are referred to using "sel" and a simulated map for those atoms is created as model #5. Results with be in Chimera reply log (menu Favorites / Reply Log). I don't think you want to turn off the "use only data above contour level". If you do it will measure the correlation of the entire box of simulated data including all the zeros far from the atom, which probably will not match the non-zeros in your map. If you really want that use option "aboveThreshold false" with the measure correlation command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat… Tom > Hi Tom, > > Thank you very much for your kind reply. It is quite helpful to know. > I am able to run the script and fit a map on to a map. But the problem > at had is slightly different. I have got the fits done already with > Flex-EM and I am actually trying to measure (ideally automate it with > the Chimera script) the correlation for the currently selected atoms > in the given map using the 'Update' option available in the Fit in Map > dialog. I would also like to specify the following option in the script. > > Real-time correlation / average update (turn off within the script) > Use map simulated from atoms, resolution = value > use only date above contour level from the first map (turn off within > the script) > optimize correlation > correlation calculates about mean data value (turn off within the script) > rotation (turn off within the script) > shitf (turn off within the script) > Move whole molecule (turn off within the script) > > I am not sure how to put all this options in a script and calculate > the correlation for the currently selected atoms with the Update > option. I would greatly appreciate if you could provide me with some > more insight on how to change the code specifically. Thanking you. > > with kind regards, > Arun Prasad > > > Tom Goddard wrote: >> Hi Arun, >> >> Yes you can use Fit in Map in a script. I've attached an example >> Python script. This script comes from the Chimera Python scripts web >> page but that web site is down right now. It is necessary to use >> Python rather than a simpler Chimera command script because there is >> no Chimera command to use Fit in Map. There probably should be, but >> since Fit in Map only does a local optimization you need some way to >> initially position the molecule or map you are fitting. That is the >> hard part and so there hasn't been much demand for the fitting command. >> >> The Python code for the Fit in Map dialog is included in all >> Chimera distributions in the directory >> >> chimera/share/FitMap >> >> You could look at the __init__.py and gui.py to learn what the >> available functions are. The gui.py (graphical user interface) file >> shows how those functions are called by the dialog. >> >> Tom >> >>> Hi all, >>> >>> I would like to know whether its possible to automate the operations >>> available with 'Fit in Map' tool and its options within a script. >>> Actually I would like to calculate the correlation for certain segments >>> of the atomic structure and it would be help if I could do it with a >>> script rather that the GUI. Any suggestion is greatly appreciated. >>> >>> Thank you, >>> Arun Prasad >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> >

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problem in showing disulfide bonds
by Pardeep kumar 06 Dec '10

06 Dec '10

Hi, I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....

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"Surface calculation failed, mscalc returned code 5"
by Sumitro Harjanto 06 Dec '10

06 Dec '10

Hi Meng, I've run into this problem a few times when I wanted to calculate and show the surface of a pdb model. I got the following on my reply log: C:\Chimera\bin\mscalc.exe 1.400000 2.000000 1 Calculation of some surface components failed. Falling back to single-component calculation. C:\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 Sometimes I managed to go around it by resaving the pdb file in Chimera, or removing some irrelevant chains. but other times it just doesn't work. Any suggestions? One particular file that gives me the problem is 1IGT from PDB. I've tried removing all the heteroatoms and water molec, for I only need the chains A, B, C and D. but still the problem persists. 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."

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Query regarding Fit in Map
by Arun Prasad Pandurangan 03 Dec '10

03 Dec '10

Hi all, I would like to know whether its possible to automate the operations available with 'Fit in Map' tool and its options within a script. Actually I would like to calculate the correlation for certain segments of the atomic structure and it would be help if I could do it with a script rather that the GUI. Any suggestion is greatly appreciated. Thank you, Arun Prasad

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need examples of Chimera crash on Mac OS X 10.6.5
by Greg Couch 03 Dec '10

03 Dec '10

There have been occasional reports of Chimera crashing in the graphics driver on Mac OS X 10.6.5. However, the reports have not included enough information to allow us to reproduce the problem and debug it. If you observe this crash, please report it to Apple (a dialog to do this will appear when the crash happens). The next time you start Chimera after the crash, another dialog will appear with the option to send us a bug report too. Please go ahead and do that, including a description of what you were doing before the crash, and your email address in case we need to request further details. Thank you, Greg

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how to product a color scale bar
by C.J. 03 Dec '10

03 Dec '10

Dear all, I am writing to ask how to product a scale bar to indicating different radius with different color when I visualizing a spheric structure with Chimera. Thanks. Regards! C.J.

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unable to show disulfide bonds
by Mahlawat, Pardeep 02 Dec '10

02 Dec '10

Hi, I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....

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display angle label
by Gesa Volkers 02 Dec '10

02 Dec '10

Dear all, I measured an angle (or better torsion) between four atoms. How can I display the angle with a label? I only found how to diplay measured distances with a label, but not angles/torsions. Thanks in advance, Gesa -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Re: [Chimera-users] Exporting .stl
by Greg Couch 01 Dec '10

01 Dec '10

Forgot to reply to list as well. -------- Original Message -------- Subject: Re: [Chimera-users] Exporting .stl Date: Tue, 30 Nov 2010 13:33:23 -0800 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: Dennis Kolva <dk429(a)cornell.edu> On 11/25/2010 06:29 PM, Dennis Kolva wrote: > I have been using Chimera to export .stl files of proteins and RNA for 3D printing. The surface models print OK, but sticks or ribbons choke the printer. I looked close at the output meshes, and they have many extra surfaces which should be removed to make "legal" .stl format. > > Is that portion of the code open source? I'd like to take a closer look and see if it's possible to fix. It would be much easier to rectify the bad surfaces upon creation, rather than trying to remove them by post-processing. > > Thanks, > > Dennis Kolva > Cornell U. Presumably , you don't have a Z-Corp printer and their ZPrint software, otherwise you would output VRML from chimera and have ZPrint do the proper conversion to STL. So yes, the source code is available at http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/apps/x3d2/stl, and we would welcome improvements. I believe that the problem is that chimera does not output manifold geometry and that the X3D to STL converter would need to perform CSG operations on all of the geometry, especially the spheres and cylinders, to eliminate interpenetrating surfaces. Another issue to consider is what to do about ribbons and cylinders that are too thin for the printer you're using. Feel free to contact me directly with questions about the code or use the chimera developers mailing list, chimera-dev(a)cgl.ucsf.edu, Greg

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pythonw.exe error
by Hunmin JUNG 01 Dec '10

01 Dec '10

Hi, Whenever I open the chimera after the installation, it gives me an error 'pythonw.exe has stopped working'. It didn't matter the version of the chimera. Please what I need to do to resolve the problem. Thanks, Hunmin (Mike) Jung Department of Chemistry Texas A&M University (979)862-7639

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Closest Waters
by Beale, John 30 Nov '10

30 Nov '10

I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to? Thanks! John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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Merging mrc map
by Massimiliano MALETTA 30 Nov '10

30 Nov '10

Hello I would like to know if merging two maps is possible in Chimera. I have two *mrc map files and I would like to figure out how to get a third file containing the two maps, just summed. I tried the option morph volume, but in fact it is always down weighting one of them respect to the other. Thank you for the help. ----------------------------- Post-doc IGBMC/ FRANCE MALETTA Massimiliano Equipe/Service: KLAHOLZ TEL : +33 (0) 3 88 65 57 53 FAX : +33 (0) 3 88 65 32 01

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