- Chimera-users - RBVI Mailing Lists

Bonds vs. Pseudobonds
by Dipl.-Ing. Thomas Mitterfellner 24 Mar '09

24 Mar '09

Hello again! I have a structure containing Germanium bonded to three oxygens and one methyl group. By default, all of the bonds between Germanium and its valences are considered as pseudobonds and hence drawn as such. In the manual, I read that Chimera uses an algorithm that considers atoms classically bonded if the distance is below the sum of their VDW radii (plus a margin of 0.4 A). However, no matter what I set the radius of the Ge atom to (setattr a radius xy Ge), I can't get Chimera to display a regular bond between Ge and its valences. Can you give me a hint how to set a rule when a normal bond is drawn, or how I can draw one manually? Thank you very much, Thomas

2 1

Using per-frame scripts with color by attribute/bfactor
by Andrew M. Simms 24 Mar '09

24 Mar '09

I am making some MD movies using the multiple-pdb file format. I am using coloring by attribute, in this case overriding the "bfactor" attribute for my own purposes. The nature of my analysis is such that the bfactor can change from frame to frame. I use this command in the per-frame script: rangecolor bfactor,a min white max green However, when I try to make a movie, it appears that the bfactor attribute changes are not reflected in the animation. If I look at generated structures individually they are fine. Is there something special I need to specify in per-frame script? Thanks! --Andrew

2 1

Split colors from Volume Viewer
by Damien Larivière 23 Mar '09

23 Mar '09

Dear Chimera team and users, When opening a map (EMD 1126 for example), the structure is displayed in grey. From the menu Volume and Surface colors, it is then possible to color the structure. I would like to export in the OBJ format the colored structure but this one still appears in grey when I display it in a modeler such as 3DSMax. And effectively, the MTL file created by the exporter only contains one color although the structure displayed in Chimera was multicolored. I look at a tutorial explaining that it is possible to Split map from the menu Volume/color zone. It seemed to me that it is a way to get a multicolored structure in the OBJ format. However, when I want to "split map", a message says "no atom selected". May you tell me how to get a multicolored structure (initially opened from a map) in the .obj format ? All the best Damien

2 1

amd64 installation
by Francesco Pietra 23 Mar '09

23 Mar '09

To deal with very large data files i tried to install chimera-1.3.2577-linux_x86_64.exe in /usr/local/chimera. Mainboard Tyan S2895 dual-opterons; OS Debian amd64 lenny; nvidia chipset 6600, nvidia-glx driver To simplify i made the chimera directory to belong to me as user. The installation from my home succeeded, though chimera did not launch. It appears in part for a moment as if there were no opengl support: francesco@tya64:/usr/local/chimera/bin$ ./chimera X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 (X_GetWindowAttributes) Resource id in failed request: 0xffffffff Serial number of failed request: 626 Current serial number in output stream: 627 I installed libmotif3. Same issue. Once the problem of running chimera is solved, I plan a reinstall in /usr/local/chimera root root. Should I run the installation from my home as superuser? thanks francesco pietra (I run successfully the 32 bit version of chimera on an old Athlon with libmotif3 support)

1 2

addna?
by julien(GWDG) 23 Mar '09

23 Mar '09

Dear all, I would like to know if there is a way in chimera to add nucleic acid to an existing RNA. Something like addna instead of addaa. many thanks Julien -- European Molecular Biology Laboratory Structural and Computational Biology Unit Meyerhofstraße 1 D-69117 Heidelberg Max-Planck-Institute for Biophysical Chemistry NMR based Structural Biology Am Fassberg 11 D-37077 Göttingen

2 1

Re: [Chimera-users] UCSF Chimera
by Elaine Meng 22 Mar '09

22 Mar '09

On Mar 22, 2009, at 8:36 AM, Tarit Mitra wrote: > Dear Dr. Meng, > I am trying to learn to use the Windows version of Chimera. I would > like to contact a Chimera user in UK. Is it possible to do so? Can > you please help? > With kind regards > Yours sincerely > Tarit Dear Tarit, You could try the e-mail list chimera-users(a)cgl.ucsf.edu (actually I cc'ed it on this message). However, you don't need a live person to help you learn how to use the program. The Chimera download includes several tutorials, some for beginners: choose "Help... Tutorials" from the Chimera menu to see the list. Our Web site has additional tutorials (not just the ones in the Help menu): <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html> Besides the tutorials, there is a complete user's manual (choose Help... User's Guide from the Chimera menu). Just start Chimera and try one of the beginner tutorials, or just experiment, and you will gradually learn! Best, Elaine

1 0

Changing properties by command line
by Dipl.-Ing. Thomas Mitterfellner 19 Mar '09

19 Mar '09

Hello again! I could not find out how to change radii of selected atom via the command line. I had hoped this would work via '@/radius=', which I read in the quick reference, but I turns out that I obviously misunderstood the usage of the hints given there. Is it also possible to change the color and linestyle of coordinative bonds in the command line? Related to this: can the status and color of the molecule silhouette be changed from the command line? Thank you very much! P.S.: Chimera really produces great pictures and I especially like the silhouette effect, which I, up to now, always had to (partially) draw myself with some image editor.

2 1

Chimera does not always recognise atom name in PDB ATOM records
by Christian Schudoma 19 Mar '09

19 Mar '09

Hello Chimera-Users and -Devs, I encountered the following problem when trying to visualise the following purine molecule (Actually, I tried to do something more complex(*) but the same problem can be reproduced with this more simple example). For clarification, the first lines contain the column numbers. 1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012345678 HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00 0.00 N HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00 0.00 C HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00 0.00 N HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00 0.00 C HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00 0.00 C HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00 0.00 C HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00 0.00 N HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00 0.00 C HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00 0.00 N When I load a pdb file containing these coordinates into Chimera, I get 9 non-connected dots (obviously representing the atoms) which can neither be coloured by hetero-atom, nor by element. Note that the atom names are located in the appropriate columns, i.e. between columns 13 and 16, more specifically in columns 15 and 16. I noticed that in other pdb structures 2-character atom names are located in columns 14 and 15 and when I put my atom names there, Chimera displays the purine ring system which then can be coloured by hetero-atom/element. Now it is nice that this workaround fixes my problem, however, according to the pdb file format specification (columns 13-16 are reserved for the atom name), atom names located in columns 15 and 16 are valid(*) and as such should be processible by visualisation tools etc. The behaviour occurs with the latest daily build as well as some older versions I found on my hard disk... (*) The purine is part of a larger cytokinin. I stumbled upon the described behaviour while using the AddHydrogen function on the whole molecule, which lead to the replacement of the purine with a hydrogen. (**) Unless there are some additional rules regarding the placement of atom names shorter than 4 characters, in which case I apologise for bugging you with this. Any comments on this? Best regards, Christian Schudoma -- Christian Schudoma, M.Sc. Bioinformatics Group System Integration Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 331 567-8624 email: schudoma(a)mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de

3 4

Re: [Chimera-users] Making movies
by Elaine Meng 19 Mar '09

19 Mar '09

> Hi Elaine, > BD simulations is brownian dynamics. Well my file is in a PDB > format, and basically consist of a single complex, with heteroatoms > living from one active site to the other. If you open the file as a > pdb file you will realized the heteroatoms HOH are static. But I > want them to be able to move from the active site of one enzyme to > the other in the complex. > > I was thinking that I can put the word Model, between the complex, > and each heteroatom HOH, so as to make the file seem to have many > pdb files. Hi Neville, Yeah, I eventually realized you meant Brownian dynamics! But what matters for Chimera is the format rather than how the trajectory was generated. To use "MD Movie" to play/record the trajectory, your PDB format options are: (a) put each frame in a separate PDB file The file names must include frame numbers, and files for all intermediate frames must also be present. The files must not contain END records. (b) put all the frames in one PDB file, but bracket each with MODEL and ENDMDL, as is done for NMR ensembles in the Protein Databank, e.g. 1g1p. The MODEL numbers are interpreted as frame numbers and should start with 1 or 0 and increment by 1. Either way, atom names, residue names/numbers need to be the same between frames. ** In general, each frame should have the same number of atoms. However, for "weird" cases where lots of atoms stay in the same position (which if I understand correctly is what you have), we have made a special provision: if the coordinates supplied for a frame represent only a subset of the atoms in the preceding frame, it will be inferred that the remaining atoms are present but have the same coordinates as in the preceding frame. Changes are cumulated in the forward direction and based on all frames, even when frames are skipped during playback. All of the atoms must be in the first frame, of course. In your case, I guess that would include the proteins plus the starting locations of the heteroatoms. You might need to renumber the HOHs to keep their identities across the frames... looks like what you sent gives each position a different residue number. This information as well as how to play the trajectory and record it as a movie are in the MD Movie manual page (choose Help... User's Guide, click Tools tab, click link "MD Movie"). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Question about adding a sequence to a previous structural alignment...
by Sergio Garay 18 Mar '09

18 Mar '09

Hi all I've prepared an structural alignment of my 3 protein templates using MatchMaker/Match-Align tools. The question is: when I add my target sequence to the profile obtained in the step before, Does this procedure change my previous structural alignment?, or It just aligns the added sequence to my profile. The parameters that I used to add my target sequence are: Blosum-62, gap open, and gap extension penalties: 12 and 1 respectively. The second problem I have, its not related to chimera, but may be one of you can answer it. My target only has 29 % of identical residues with my templates, so Should I use a less stringent parameters to make my alignment? Any help would be appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

2 1