April 2008 - Chimera-users - RBVI Mailing Lists

Chimera - Surface Residue Identification
by Thiruvarangan Ramaraj 07 Apr '08

07 Apr '08

Hello, I am new to Chimera, I am trying to identify the residues that lie on the surface of a antigen complex that are within certain distance from the antibody. Any help would be greatly appreciated. Thank You --------------------------------- You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.

2 1

chimera explodes
by liane saiz 05 Apr '08

05 Apr '08

Hello everybody: I had some problems with chimera. I installed version 2470 but it explodes when I try to select anything with the following error: Segmentation fault (core dumped) I tried also version 1.2422 and I got the same error. All other features of chimera seems to work properly. In both cases the installation process seems normal. I'm running chimera in linux (ubuntu gutsy) with a 2.6.22-14-generic kernel. In other computer in the lab with the same linux distribution and kernel, all features in chimera 1.2470 work fine (including the select menu). Thanks in advance for any help. Liane

2 2

Chimera crashes
by Ben Keshet 04 Apr '08

04 Apr '08

Hi, I have been using Chimera on my desktop successfully - great program. However, when I run Chimera on my laptop, Chimera tends to crash, usually when the screen saver starts. the message I have is: chimera failed abnormally; the exit code was :3. I am not sure how to open the debug mode (I tried to right-click ==> properties and change the target by adding '--debug' but I am getting an error message that the name is not valid. my machine is Dell Vostro 1500 with XP with a GeForce 8400M GS video card. Any suggestion are welcome. Thanks, Ben

3 4

surface color command
by Michael DiMattia 04 Apr '08

04 Apr '08

Hello, Is there a command for "surface color"? The menu window that lets you color a molecule radially. I'm wondering if there is a command-version of this task so that I can put it into a script. I looked up "surface color" in the Chimera help files but I don't see a command. Thanks! Mike

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 60, Issue 4
by Boyle, Joseph J 03 Apr '08

03 Apr '08

Hello, Is it possible to use Chimera to dock a small ligand into a binding pocket pdb - and if so how is the ligand imported into the protein pdb file ? Yours Sincerely, Joseph Boyle ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu on behalf of chimera-users-request(a)cgl.ucsf.edu Sent: Thu 03/04/2008 8:41 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 60, Issue 4 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. Re: Smooth Trajectory in MD Movie Tool (Eric Pettersen) 2. Re: Smooth Trajectory in MD Movie Tool (Yan Liang) 3. chimera manual (bala) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Apr 2008 16:37:42 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Smooth Trajectory in MD Movie Tool To: Yan Liang <liangyan(a)cems.umn.edu> Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> Message-ID: <7524F1C4-94F1-487C-A67F-FA6A5B4778DB(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Yan, You _could_ write a script to do the averaging, but you would pretty much have to be an expert on how Chimera handles trajectory data to be able to write it in any reasonable amount of time. Since I am such an expert, I've written the script for you and attached it to this message. To do the averaging, simply have your trajectory open and then open the script (either with the File...Open menu or with the "open" command). Note that the script rewrites the coordinates of the trajectory. The only way to restore the trajectory to the "unaveraged" state is by reopening the original files. The main parameter in the script you might want to change is the "window" variable, which controls how many adjacent frames contribute to the averaging. The value in the script right now is 2, which means that the two frames to each side of a frame contribute to the average (with further-away frames contributing less). --Eric ? On Apr 2, 2008, at 2:36 PM, Yan Liang wrote: > Thank you very much Eric. I have tried "Hold selection steady" > function, and it helps a lot to reduce the overall movement of the > large molecule. But as for the residuals, they are still very shaky. > > I am thinking about writing a script to average the movement of > each atom, but I have no experience in Chimera scripting. Do you > think it is possible to write such scripts in Chimera? Thanks. > > Sincerely, > > Yan Liang > Graduate Student > Department of Chemical Engineering and Materials Science > University of Minnesota > > > > On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote: >> Hi Yan, >> Chimera doesn't yet support smoothing per se. What you can do is >> use "Hold selection steady" in MD Movie's Actions menu to hold one >> or more atoms (possibly all atoms) as steady as possible across >> the trajectory -- which will mostly eliminate the translational >> component of the "shakiness". This "holding steady" is most >> useful for small-molecule trajectories and replica-exchange >> trajectories. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/> >> >> >> On Apr 2, 2008, at 10:44 AM, Yan Liang wrote: >>> Hi >>> >>> I am using Chimera to make a MD movie. The problem is the movie >>> is too >>> shaky. Is it possible to smooth the trajectory by writing a Per- >>> Frame >>> script in MD Movie tool? >>> >>> Thanks, >>> >>> Yan Liang >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

2 1

chimera manual
by bala 03 Apr '08

03 Apr '08

Hello all, I want to have the pdf version of chimera manual/user guide. I am not finding it anywhere ?. Where can i find it. The only pdf i see is the chimera quick reference guide. Thanks, Bala

2 1

Re: [Chimera-users] Smooth Trajectory in MD Movie Tool
by Eric Pettersen 02 Apr '08

02 Apr '08

Hi Yan, You _could_ write a script to do the averaging, but you would pretty much have to be an expert on how Chimera handles trajectory data to be able to write it in any reasonable amount of time. Since I am such an expert, I've written the script for you and attached it to this message. To do the averaging, simply have your trajectory open and then open the script (either with the File...Open menu or with the "open" command). Note that the script rewrites the coordinates of the trajectory. The only way to restore the trajectory to the "unaveraged" state is by reopening the original files. The main parameter in the script you might want to change is the "window" variable, which controls how many adjacent frames contribute to the averaging. The value in the script right now is 2, which means that the two frames to each side of a frame contribute to the average (with further-away frames contributing less). --Eric On Apr 2, 2008, at 2:36 PM, Yan Liang wrote: > Thank you very much Eric. I have tried "Hold selection steady" > function, and it helps a lot to reduce the overall movement of the > large molecule. But as for the residuals, they are still very shaky. > > I am thinking about writing a script to average the movement of > each atom, but I have no experience in Chimera scripting. Do you > think it is possible to write such scripts in Chimera? Thanks. > > Sincerely, > > Yan Liang > Graduate Student > Department of Chemical Engineering and Materials Science > University of Minnesota > > > > On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote: >> Hi Yan, >> Chimera doesn't yet support smoothing per se. What you can do is >> use "Hold selection steady" in MD Movie's Actions menu to hold one >> or more atoms (possibly all atoms) as steady as possible across >> the trajectory -- which will mostly eliminate the translational >> component of the "shakiness". This "holding steady" is most >> useful for small-molecule trajectories and replica-exchange >> trajectories. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> On Apr 2, 2008, at 10:44 AM, Yan Liang wrote: >>> Hi >>> >>> I am using Chimera to make a MD movie. The problem is the movie >>> is too >>> shaky. Is it possible to smooth the trajectory by writing a Per- >>> Frame >>> script in MD Movie tool? >>> >>> Thanks, >>> >>> Yan Liang >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

2 1

Smooth Trajectory in MD Movie Tool
by Yan Liang 02 Apr '08

02 Apr '08

Hi I am using Chimera to make a MD movie. The problem is the movie is too shaky. Is it possible to smooth the trajectory by writing a Per-Frame script in MD Movie tool? Thanks, Yan Liang

2 1

chimera
by somnath Dutta 02 Apr '08

02 Apr '08

2 1

chimera segmentation fault
by Selami ERCAN 01 Apr '08

01 Apr '08

hi. i'm using chimera-1.2470-linux_x86_64.exe on suse 10.3. in addition to this my graphic card is nvidia geforce 8600m gt 512 mb and also i have installed mesa and xorg softwares. and here is problem: using 1EP4.pdb from rcsb.org causes problem.whenever i select structure-->main, then action-->surface-->show it crashes. and it gives the report shown below. Copyright M.F. Sanner (March 2000) Compilation flags WARNING: class_arete2: warning hole in a reentrant face 17081 WARNING: class_arete2: warning hole in a reentrant face 22603 WARNING: classe_aretes1: No cycle in face 25771 (nba=-4) WARNING: classe_aretes1: No cycle in face 25772 (nba=-1) WARNING: classe_aretes1: No cycle in face 25774 (nba=-1) WARNING: classe_aretes1: No cycle in face 25776 (nba=-3) WARNING: classe_aretes1: No cycle in face 25779 (nba=-1) WARNING: classe_aretes1: No cycle in face 25781 (nba=-1) WARNING: classe_aretes1: No cycle in face 25783 (nba=-1) WARNING: classe_aretes1: No cycle in face 25785 (nba=-1) WARNING: classe_aretes1: No cycle in face 25787 (nba=-1) WARNING: classe_aretes1: No cycle in face 25789 (nba=-1) RESTART FROM SES: 1 radius of atom 2855 goes from 1.760000 to 1.860000 radius of atom 2857 goes from 1.640000 to 1.740000 radius of atom 2858 goes from 1.760000 to 1.860000 radius of atom 2871 goes from 1.880000 to 1.980000 radius of atom 6942 goes from 1.880000 to 1.980000 radius of atom 6945 goes from 1.760000 to 1.860000 radius of atom 6946 goes from 1.760000 to 1.860000 radius of atom 6947 goes from 1.760000 to 1.860000 radius of atom 6948 goes from 1.760000 to 1.860000 radius of atom 6987 goes from 1.460000 to 1.560000 radius of atom 6988 goes from 1.760000 to 1.860000 Partial mode Segmentation fault

3 2

Chimera-users April 2008