- Chimera-users - RBVI Mailing Lists

Manually assigning secondary structure to residues
by Oren Shalev 16 Aug '07

16 Aug '07

Dear Chimera team and users, I'm modeling chains with gaps using in-house software. When opening in Chimera a model in which a secondary structure element is broken or flanked by the start/end of a gap, the secondary structure of the residue adjacent to the gap is assigned to be 'coil'. I guess this is expected, since one needs to know both Phi and Psi angles to determine the secondary structure of a given residue, yet I always have knowledge that the residue adjacent to the gap does indeed belong to a secondary structure element. My question is this: is there a way to assign the secondary structure of a given residue to either 'helix' or 'strand'? I'm interested in this for imaging purposes, so potential negative consequences on other aspects of Chimera's operation (perhaps on analysis tools?) don't matter to me. Thank you, Oren

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sym command in Chimera
by Z. Nevin Gerek 15 Aug '07

15 Aug '07

Dear Chimera team, I am trying to use sym command to generate symmetry related copy of a protein. I followed this link: http://www.cgl.ucsf.edu/chimera/experimental/symmetrycopies/ symcopies.html The version I am using is 1.2422. When I write sym, I get this error: "unrecognized command: "sym" Then I found this link http://www.cgl.ucsf.edu/pipermail/chimera- users/2005-September/000464.html and put necessary files to Chimera.app/Contents/Resources/share folder. Then I restart Chimera, I get same error. Is there another way to use sym command in Chimera? Thanks for your help, Z. Nevin Gerek, Ph.D. Postdoctoral Fellow ----------------------------------------------------- The Center for Biological Physics Arizona State University PO Box 871504 Tempe, AZ 85287-1504 Phone: (480) 727-8897 nevin.gerek(a)asu.edu On Aug 11, 2007, at 12:00 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. transposing a pdb structure ("copy & paste") (Ben Keshet) > 2. Re: transposing a pdb structure ("copy & paste") (Elaine Meng) > 3. Re: transposing a pdb structure ("copy & paste") (Eric > Pettersen) > 4. Re: chimera on AMD workstation (Vinay Kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 10 Aug 2007 15:53:33 -0400 > From: "Ben Keshet" <keshet1(a)umbc.edu> > Subject: [Chimera-users] transposing a pdb structure ("copy & paste") > To: <chimera-users(a)cgl.ucsf.edu> > Message-ID: <000001c7db88$238da8b0$29ad5582@umbc80a173302c> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera fans and team, > > I have a pdb file of a fragment of an amyloid fibril constructed of > 8 layers > (8 parallel strands of beta sheet). I would like to overcome the end > effects when modeling it, so I would like extend the existing > structure by > duplicating it at its end. > > Does Chimera has a tool do the following: duplicate existing pdb > molecule > coordinates, position the duplicated molecule at a desired > location, and > then align it reasonably with respect to the original molecule? > > Thank you very much for your time and help. > > Ben > > > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Aug 2007 16:04:20 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] transposing a pdb structure ("copy & > paste") > To: "Ben Keshet" <keshet1(a)umbc.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <8f3e5fad823ed51cc9da3fa7677864cc(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Dear Ben, > Chimera doesn't have the ability to figure out for you the proper > position of one copy relative to another. You could open multiple > copies, perform manual positioning, and then write out all the > coordinates, but I imagine it might be difficult to get the right > position of one copy relative to another, even manually/interactively. > > To manually position a structure relative to another, you could > interactively rotate/translate and/or use the "move" (translation) and > "turn" (rotation) commands. You can freeze/unfreeze a copy using the > Active checkbox in the Model Panel (in the Favorites menu by default), > the command "select," or the little checkboxes under the Command Line > (also under Favorites). > > If you did manage to position copy 2 relative to copy 1 to your > liking, > you could write the transformation matrices out (see "matrixget" > command). From those you could calculate the transformation of 2 > relative to 1 and also generate appropriate matrices that would then > position 3, 4, ... correctly (see "matrixset" command). I admit I > don't know how to do those calculations. Anyone? > > Yet another snag depends on how you will be using these coordinates. > Does it require all the PDB files to be merged into one? If so, can > they be in a multi-MODEL form, or in a single model? Chimera can > output separate PDB files or a single multi-MODEL PDB file. If you > need all the coordinates to be in one model, however, you would > have to > edit the PDB output from Chimera so there are not atoms with duplicate > atom numbers and chain IDs. However, it all depends on what the > *next* > program you will be using requires and expects. If you will just be > using Chimera, however, no further editing would be required (in fact, > you could just save a session rather than writing out coordinates). > > Maybe someone else will have a smarter and less discouraging set of > suggestions! Best, > Elaine > > On Aug 10, 2007, at 12:53 PM, Ben Keshet wrote: > >> Dear Chimera fans and team, >> >> I have a pdb file of a fragment of an amyloid fibril constructed of 8 >> layers >> (8 parallel strands of beta sheet). I would like to overcome the end >> effects when modeling it, so I would like extend the existing >> structure by >> duplicating it at its end. >> >> Does Chimera has a tool do the following: duplicate existing pdb >> molecule >> coordinates, position the duplicated molecule at a desired location, >> and >> then align it reasonably with respect to the original molecule? >> >> Thank you very much for your time and help. >> >> Ben > > > > ------------------------------ > > Message: 3 > Date: Fri, 10 Aug 2007 16:53:36 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] transposing a pdb structure ("copy & > paste") > To: Ben Keshet <keshet1(a)umbc.edu> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <E5C1411A-58C1-49A8-8899-24816E53E043(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Aug 10, 2007, at 4:04 PM, Elaine Meng wrote: > >> To manually position a structure relative to another, you could >> interactively rotate/translate and/or use the "move" (translation) >> and >> "turn" (rotation) commands. You can freeze/unfreeze a copy using the >> Active checkbox in the Model Panel (in the Favorites menu by >> default), >> the command "select," or the little checkboxes under the Command Line >> (also under Favorites). >> >> If you did manage to position copy 2 relative to copy 1 to your >> liking, >> you could write the transformation matrices out (see "matrixget" >> command). From those you could calculate the transformation of 2 >> relative to 1 and also generate appropriate matrices that would then >> position 3, 4, ... correctly (see "matrixset" command). I admit I >> don't know how to do those calculations. Anyone? > > It's a little tricky. Basically, you want to get copy 1's matrix to > be the identity matrix while keeping copy 2 in the same relative > position. Here's one way to do it (and maybe someone can suggest > something better): > > 1) open yet another copy (copy 3) as a reference > 2) use "matrixset" to set copy 3's matrix to be the identity matrix > 3) use the "match" command with the 'active' keyword to match copy 1 > onto the reference (copy 3) while also moving copy 2 appropriately > 4) use "matrixget" to get copy 2's new transformation matrix > > I would imagine that copy 2's matrix is essentially all translation > components (i.e. the upper 3x3 is all zeroes or near-zeroes) so all > you need to do to place additional copies to multiply the translation > components by 2, 3, etc. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > pett(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu > > >

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Request
by Rajendra P. OJHA 14 Aug '07

14 Aug '07

Dear Sir, After installation on a AMD opetron machine(64 bit) it gives the following error message Pease rectify the problem and oblige. Thanks Ojha ************************** Message ********************** ./chimera-1.2422-linux_x86_64.exe UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/rpo/CHIMERA' inflating: chimera_install_KUOeVj/installer inflating: chimera_install_KUOeVj/chimera.exe ./installer: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by ./ installer) result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_KUOeVj' Installation is done; press return. ____________________________________________________________________________________ Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool. http://autos.yahoo.com/carfinder/

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stereo display
by Rutledge, Robert (NIH/NCI) [V] 14 Aug '07

14 Aug '07

I am trying to get stereo working with Chimera. I use the --stereo switch when I start up the program. This results in the following error: "unable to find hardware stereo support (Togl: couldn't choose stereo pixel format)". The graphics card connected to the CRT monitor is NVIDIA 7900GS. I run Chimera under Windows XP media center edition. I have a cheap pair of shutter glasses (edimensional), which work properly when tested by the test application on the graphics card. Do I need another graphics card or glasses, or is something else the problem? Robert Rutledge

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modeling non-standard amino acids
by Dan Wendt 14 Aug '07

14 Aug '07

Hello, My name is Daniel Wendt and I work for Biomarin Pharmaceuticals in Novato, Ca. I'm trying to use Chimera's modeling software to predict structural changes that are imparted on my 22 amino acid peptide by the insertion of two non-standard changes to the peptide bond. In one case, I am adding a methyl group to the backbone amide bond. In another case, I'm removing a carbonyl from the backbone amide bond. This peptide then needs to be cyclized by the formation of a intra-disulfide bond. I do have x-ray crystal structure data of my cyclized peptide bound to one of its receptors. Do you know how one goes about doing this? Do you have any references that might help? Thank you in advance! Daniel Wendt Senior Scientist BioMarin Pharmaceutical Novato, Ca 94949 (415) 506-6131 This message is intended only for the confidential use of the intended recipient(s). If you have received this communication in error, please notify the sender by reply e-mail, and delete the original message and any attachments. Any unauthorized disclosure, copying, or distribution of this message (including the attachments), or the taking of any action based on it, is strictly prohibited.

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mrc maps
by Gorelik, Tatiana 13 Aug '07

13 Aug '07

Dear Chimera-team, Can I load several .mrc maps at a time and rotate them one against another? Thanks, Tatiana ************************************ Tatiana Gorelik, PhD, Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Welderweg 11 55099 Mainz Germany Tel.: 0049 6131 39 22347 Fax: 0049 6131 39 23768 e-mail:gorelik@uni-mainz.de ************************************

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macintosh/stereographics/boot camp
by Dougherty, Matthew T. 11 Aug '07

11 Aug '07

There are some difficulties deep in the apple graphics driver implementation that prevent X11 and openInventor and openGL stereographics. I can report that mac-bootcamp-windows running with a quadro fx 4500 (card supplied by apple, other cards have the wrong firmware); does correctly do stereographics under XP windows correctly with no noted problems. ========================================================================= Matthew Dougherty *** 713-433-3849 National Center for Macromolecular Imaging ========================================================================= =========================================================================

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chimera on AMD workstation
by Vinay Kumar 10 Aug '07

10 Aug '07

Hello all, recently we bought a AMD workstation. I tried to install chimera_linux x86_64 on it. But it did not install. went through installation instructions. still did not work. i would like you to give me some suggestions and some variations that i could try to install chimera. Thank you Elaine, for your post on spheres. shall inform when my adventures have a result. regards, Vinay

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Teaching with Chimera
by Fabian Glaser 09 Aug '07

09 Aug '07

Dear Chimera team, I'd like to use both chimera and chimera tutorials for a new "Structural Bioinformatics practical course" I am preparing here at the Technion in Israel. I will of course acknowledge appropriately. Is there any legal limitation for using chimera for this purpose? Thanks for creating such a fantastic tool Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: fglaser(a)tx.technion.ac.il Tel: +972-4-829-3701 Cell: +972-52-2357731

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writing translation/rotation
by Thomas C. Marlovits 08 Aug '07

08 Aug '07

Hi, am looking for an analysis tool in Chimera that would write out - let's say a matrix for translation/rotation of a pdb-file in respect to another one. Usage: would like to align chain A and chain B present in a pdb-file and want to know which translation/rotation matrix has to be applied in order to convert the non-aligned pdb-coordinates of chain B to the 'new" aligned pdb-coordinates. Thanx for your help, -Thomas ------------------------------------------------------------------------ ------- Thomas C. Marlovits, PhD, M.A.S. IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

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how to select spheres for docking?
by Vinay Kumar 06 Aug '07

06 Aug '07

Hello all, I have a few queries to ask. hoping you all will reply. i use DOCK6.0, the dms program under DOCK, can create and execute a total of 9999 spheres. I would want to know, how do i selectively select spheres using chimera? Is it possible to select certain residues and generate the molecular surface for it? and use it for docking?? My previous problem with chimera got resolved. Thank you Greg. I had to change the OS from RHL9.0 to fedora core. with regards, Vinay ps- please ignore if off-topic. i have posted the same query on dock mailing list. still awaiting a reply there.

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Re: [Chimera-users] odd glare when volume rendering
by Tom Goddard 03 Aug '07

03 Aug '07

Hi Jeff, Aha! Now I see Chimera is working as expected and I can reproduce the glare on my computer. If you have depth cueing set to "No color", which is the default, *and* you use a light background color, then Chimera interprets "no color" as white. With a dark background color, I use black, "no color" for depth cueing is interpreted as black. So all I had to do was set by background color to a light shade to see the glare. So this is bad behavior. The white depth cue color does not work with volume rendering -- it is way too powerful -- all the far planes in the data become slightly white, and this ends up making a very white brick. Oddly, I have already fixed the problem, accidently! My current development version of Chimera (not on the web) has a new blending mode for volumes. I made the change to address a serious problem you raised earlier that the brightness in volume rendering changes a lot when you change step size. The new mode fixes that and will be the default in the next snapshot. Coincidentally the new blending mode also makes white fog work as expected without an overly powerful effect. I have also added better handling of large EM tomography maps -- file loads report progress and can be canceled, default initial display can show a single z plane, the z plane slider is built into volume viewer, hdf5 format map files can be written which contain subsampled versions of the map allowing rapid display of the data at any scale. I'm testing all this on an 2048^3 map. A snapshot should be out in a month or so, though if you really want bleeding edge stuff I could probably give you an earlier version for mac os. Tom William Jeffrey Triffo wrote: > hello, > > I am getting an odd glare when I use solid rendering in VolumeViewer - > it is orientation dependent, which makes me think it has to do with > lighting? I am using build 2416; is it possible to forward a screenshot > to the list? > > thanks, > >

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odd glare when volume rendering
by William Jeffrey Triffo 02 Aug '07

02 Aug '07

hello, I am getting an odd glare when I use solid rendering in VolumeViewer - it is orientation dependent, which makes me think it has to do with lighting? I am using build 2416; is it possible to forward a screenshot to the list? thanks, -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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Problem with Gasteiger charges of a formally charged ligand
by cdeligka＠purdue.edu 02 Aug '07

02 Aug '07

Dear all, I tried to calculate the Gasteiger charges of peroxynitrite anion using Chimera (I tried the version that was recently released as well as some previous ones). This is my PDB file: HEADER HETATM 1 O 2 2 1.225 0.000 1.819 HETATM 2 N 2 2 0.138 0.000 1.281 HETATM 3 O 2 2 0.138 0.000 -0.086 HETATM 4 O 2 2 1.359 0.000 -0.746 The formal charge of this molecule is -1. For some reason Chimera generates the Gasteiger charges for the molecule but these charges correspond to a formal charge of zero and not -1. If I try the other method AM1-BCC the charges that are calculated do correspond to a formal charge of -1. In my calculations I do need the Gasteiger charges and so I cannot use the ones that are calculated by AM1-BCC. If you have any suggestions please let me know. Are you aware of any other software that might be able to do this calculation? Thank you all, Christos

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Moving individual markers
by J. Evan Sadler 02 Aug '07

02 Aug '07

Is it possible to move single markers from the command line, instead of using the mouse under the Volume Path Tracer tool? If so, it would greatly simplify certain model constructions. Evan Sadler

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Chimera on Linux
by Beale, John 30 Jul '07

30 Jul '07

I have been using Chimera on a Linux-equipped laptop for a long time. All that I had to do to get the software working was to download the appropriate version of Chimera and click on the executable. I am trying to install Chimera on a new Linux workstation. I downloaded the program for Linux, but when I try to run the executable I get a message that says that the software downloaded is for MS-DOS and not Linux, and I am unable to install Chimera. Has anyone run into this problem, and is there a fix for it? John Beale

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CSB 2007 Molecular Visualization tutorial
by Conrad Huang 30 Jul '07

30 Jul '07

Scooter Morris and Conrad Huang will be giving an introductory molecular visualization tutorial using Chimera on August 13 at CSB 2007 (the Conference on Computational Systems Bioinformatics) in San Diego. Interested folks can visit http://www.lifesciencessociety.org/CSB2007/index07.html for more information on CSB 2007. The tutorial abstract is attached below. An Introduction to Molecular Visualization Tutorial at the Computational Systems Bioinformatics (CSB) conference (AM2) University of California, San Diego August 13, 2007 Abstract Projects such as Structural Genomics are providing increasing numbers of experimental protein and protein-complex structures. Furthermore, increasing numbers of theoretical models are being predicted from primary sequence. Biologists have an increasing need to understand and communicate the structures, functions and relationships between these protein and protein-complex structures. As a result, molecular visualization is becoming an important tool for the presentation and communication of the results of biological experiments and research. This tutorial will provide a basic foundation for the understanding of molecular structures through use of visualization tools. Attendees will learn the basics of molecular visualization and will be provided an overview of available tools and techniques for visualization, analysis and modeling of protein structure. To make these concepts more concrete, attendees will be shown the academic program UCSF Chimera in more detail, and receive instruction in its features and use. The field of structural biology is still changing, and new techniques are continually being developed. Attendees will be shown how they can add new analysis techniques and their own data to the visualization. Outline: 1. Introduction to Molecular Visualization 2. Available Tools 3. Using UCSF Chimera 4. Scenarios of use 5. Extending Chimera

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Fwd: CCL: hydroxide for dock
by Elaine Meng 25 Jul '07

25 Jul '07

Begin forwarded message: > From: "Yubo Fan yubofan|-|mail.chem.tamu.edu" <owner- > chemistry(a)ccl.net> > Date: July 25, 2007 7:50:36 AM PDT > Subject: CCL: hydroxide for dock > Reply-To: "CCL Subscribers" <chemistry(a)ccl.net> > > Hi, everyone, > I'm preparing structures with Chimera for docking with Dock6. There > is a Zn-coordinating hydroxide that I want to keep in the > structure. When I prepare dock files, Chimera always treat it as a > water. Is there any way to define it as a hydroxide in Chimera? > Thanks, > Yubo > ============================================================ > Dr. Yubo Fan Email: yubofan_+_mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-5237 > Texas A&M University > College Station, TX 77843 > ============================================================ Dear Yubo, I could answer more precisely if I could see the file, but without seeing it, I recommend: (a) looking at the residue name of the hydroxide in the text of the file. Is it WAT or HOH? If so, you could edit it to a different name, say XOH or HOM. (b) then, run Dock Prep in Chimera including hydrogen addition and all the steps before that (but don't assign charges or write the Mol2 file). (c) check the structure; if hydrogen is added where you didn't want it, simply delete it. For example, Ctrl-click to select an atom and use "Actions... Atoms/Bonds... delete" in the menu to delete it. The protonation states are intended to be reasonable at physiological pH, but if a group is expected to have a perturbed pKa (for example, in an active site or near an ion), it is a good idea to check it and manually add/delete hydrogens as needed. ( more details in http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html ) (d) run Dock Prep again with only the steps AFTER hydrogen addition (charge assignment and Mol2 file output) turned on. If it asks for the net charge of XOH (or whatever you named it), indicate -1. (e) that procedure will use Antechamber to calculate the partial charges on the hydroxide O and H. If, however, you already know the charges you want to use for these atoms, you can edit the charge values in the output Mol2 file. In that case you wouldn't even have to go through all these steps, but could simply also delete the extra hydrogen from the Mol2 file, if you can figure out which line it is! I just realized this last point, so it wasn't in my original reply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Windows Vista
by Jason M Walraven 23 Jul '07

23 Jul '07

I just installed the latest version of Chimera on my Windows Vista operating system (home basic). Everything seems to work perfectly, except that the colors appear to be messed up. The colors appear darker than on my previous computer (with Windows XP). Has anyone else had this problem? All colors in all other programs are normal on my computer except for in Chimera. I assume it is a compatibility issue, but I don't know enough about it to say that for sure. jw

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Re: [Chimera-users] Reading a data set from a text file
by Thomas Goddard 17 Jul '07

17 Jul '07

Hi Kyaw, I see what you've done and see that you have a set of (x,y,z) coordinates. But I'm not sure what you want or what these coordinates represent. To make a surface out of a set of points you need to know which points are next to each other. In Chimera you need a set of points, and a set of triangles, each triangle defined by 3 integer indices into the set of points that give the triangle vertices. If you can define the set of triangles I can tell you how to make the surface. Tom Kyaw Zeyar Myint wrote: > Hello Tom, > I apologize for not being able to respond to you earlier. The > set of view vectors that I want to make surface out of it are in (x, y, > z) coordinates. > > So far, I've done a quick and 'rough' way of using these vectors for > display. What I did in chimera was that I wrote a mini plugin which > makes a .bild > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> file with a > set of cylinders, given a set of vectors. > Each cylinder is centered at origin (0,0,0) and drawn according > to the vector (which is from my set of view vectors). So if the V(x,y,z) > has (0.0523, 0.0000, 0.9986), then the cylinder is drawn by: > /.cylinder 0 0 0 0.0523 0.0000 0.9986 0.03 / in .bild file. > Then .bild file is fed into chimera and then a set of cylinders > is displayed. In a sense, each cylinder represents each view vector in > the set. But this is just a quick solution. > If you can share some ideas of how to better do this, please let > me know. I'd really appreciate your help. > > Thanks a lot! > Kyaw > (P.S: I've attached .bild file which you can display in chimera and see > what inside using a text editor.) > > ------------------------------------------------------------------------ > > > On Jun 29, 2007, at 1:03 PM, Tom Goddard wrote: > >> Hi Kyaw, >> >> I'm not sure I understand what type of data you want to display in >> Chimera. Is it a list of density values, or is it a list of x, y, and >> z coordinates? If it is density values in text rather than binary, >> you could reformat it into XPLOR format >> >> http://www.scripps.edu/rc/softwaredocs/msi/xplor981/formats.html >> >> which can be read into Chimera. >> >> Tom >

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presets criteria
by Roberta King 17 Jul '07

17 Jul '07

Hello, I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within "Interactive 1:setup ribbons" preset for determining which residue side chains are depicted as sticks in the binding pocket? This is a useful shortcut, but I would like to understand the specific criteria. Thank you very much, Roberta ******************************** Roberta S. King, Ph.D. Associate Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island http://www.uri.edu/pharmacy/faculty/king

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 16 Jul '07

16 Jul '07

Hi Pasquale, You can definitely open multiple PDB files and move them independently. By default everything will move together, which might even be what you want. However, if you don't want them to move together, you can freeze any structure in place ("deactivate" it), move the other(s), and then "activate" the first structure again if you want it to be movable. There are several ways to control activation/deactivation; probably the easiest is to open the Model Panel (Favorites... Model Panel). Then just uncheck/check the box in the Active column to freeze/ unfreeze a model. We use the word model to mean the contents of a structure file (PDB, Mol2, etc.), so if you read in two separate PDB files, there would be two models listed in the Model Panel. Alternative ways of controlling activation/deactivation are with the little checkboxes under the Command Line and using the command "select". You would still be able to minimize multiple models as a single system by choosing all of them in the "Minimize Structure" dialog. Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 16, 2007, at 7:59 AM, Pasquale Iacono wrote: > well in order to make the dimer i used two separate pdb files and > imported them both into the same gaussian gjf file. then i imported > that file as a mol2 file into chimera, so unless i can manipulate > separate pdb files in chimera then that would be great but i cannot > figure out how to move separate pieces of my dimer. > > On 7/15/07, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Pasquale, > I had one long-shot possibility for getting the correct atom and > residue names - did you start with a PDB file before the guassian > calculations? If so, that file may have had the correct atom and > residue names. If that starting file had all the same atoms > (including hydrogens) and the order of the atoms is exactly the same > in that gaussian output, you could simply replace (probably with a > script) the coordinates in each line of the starting PDB file with > those from the gaussian output. That would only work if the order is > exactly the same, however. > > Otherwise it would be extremely tedious to figure out which > coordinates go with which atom/res/number. > Best, > Elaine

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ValueError: More than 2 coplanar positions specified!
by Mike Gretes 13 Jul '07

13 Jul '07

Hello, When trying to calculate hydrogen bonding between two molecules, I get the error: "ValueError: More than 2 coplanar positions specified!" I have successfully calculated h-bonding between two other similar molecules, so I'm not sure what the problem is (I have no alternate conformations or anything weird in the PDB files I don't think... is there anything that usually triggers this error?) thanks! mike ___________________ Michael Gretes PhD Candidate (Structural Biology) Senior Graduate Trainee, Michael Smith Foundation for Health Research NCJ Strynadka Laboratory Dept. of Biochemistry, University of British Columbia Life Sciences Center, 2350 Health Sciences Mall Vancouver, BC Canada V6T 1Z3 phone 604 822 7729 fax 604 822 5227 ____________________

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Forward of moderated message
by mailman-bounces＠cgl.ucsf.edu 13 Jul '07

13 Jul '07

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 11 Jul '07

11 Jul '07

Hi Pasquale, As Eric figured out, your mol2 file does not contain substructure information. For the structure to be read by Chimera as a series of residues, there would need to be residue information in each line in the @<TRIPOS>ATOM section and then a corresponding @<TRIPOS>SUBSTRUCTURE section at the bottom. You would have to edit that information into your file. Otherwise, the structure appears as one big residue. Mol2 format description: http://www.tripos.com/mol2/mol2_format8.html ATOM section - need substructure ID and name (residue number and name) for each atom http://www.tripos.com/mol2/mol2_format33.html#1370 SUBSTRUCTURE section - more information on those substructures (residues) To get an example mol2 file, open a PDB file of a protein in Chimera, add hydrogens if you want those in your example, and then write it out as Mol2 (File... Save Mol2...) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 6, 2007, at 10:57 AM, Eric Pettersen wrote: > Hi Pasquale, > If your structure all got put into a single residue named UNK, > that typically means that your file was missing the @SUBSTRUCTURE > section (http://www.tripos.com/mol2/mol2_format33.html#1370) > There is an entry in our bug database (#3518) for better handling > of files with missing @SUBSTRUCTURE sections. I will add your name > to that report so you'll know when it gets fixed. For now, you > will have to edit your file and add an @SUBSTRUCTURE section "by > hand". > > --Eric >> >> On Jul 6, 2007, at 8:54 AM, Pasquale Iacono wrote: >> >>> Hey Elaine, >>> My structure is currently being labeled as one big residue >>> (UNK) and when I minimize it it says it does not recognize the >>> residue, so it seems like the calculation program is using >>> residue parameters and not those for specific atoms. Also, my >>> structure contains a Zn(II) metal center and I was wondering if >>> the parm files would detect it as such if it actually used the >>> atom types. I attached my mol2 file so you can check it out. Thanks >>> -Pasquale Iacono

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