- Chimera-users - RBVI Mailing Lists

question on monitoring hydrogen bonds
by knutsost 04 Feb '06

04 Feb '06

Hi: I am interested in monitoring the hydrogen bonds which form/break between specific residues over the course of a MD simulation in CHARMM. I am wondering if you have any way to record things like bond counts over time for the set of residues, or just to spit out a list of the bonds which form and break over the trajectory time course? I really appreciate any help you could give me with this! Thanks, Stacy Knutson Research Associate Wake Forest University

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Re: [Chimera-users] control the movie play speed
by Mingfeng Yang 31 Jan '06

31 Jan '06

Eric Pettersen wrote: > Hi Mingfeng, > It hadn't occurred to me that one might want more than a 1-second > delay per frame (which is what you get when the slider is all the way > over to the left). Maybe I can do something about that in the future. > You can define a script to avoid all that clicking. Use the Movie > dialog's Per-Frame->Define Script... menu entry to bring up a panel > that allows you to define a script to run at each frame. You can > define a script of Chimera commands or Python commands. For what you > describe, Chimera commands can do the job. In the "Script" field just > enter "copy file <FRAME>.png png". When the command is executed, > "<FRAME>" will be replaced with the current frame number. You might > want to check the "Use leading zeroes..." check button so that the > files sort into the correct order when you 'ls' them. Then just run > your trajectory (probably with the "Loop" button checked off). > Bravo! This command rocks. Thanks! I should forward this to the mailing list; someone else must want to know it. Mingfeng > --Eric > > On Jan 31, 2006, at 11:16 AM, Mingfeng Yang wrote: > >> Hi, Eric, >> >> I did get your email. I am sorry that I didn't get back to you in >> time. The position of the slider does control the playback rate, but >> even the slowest is not slow enough for my case. I want at least a >> second pause after each snapshot, so that people can see the >> conformational change clearly. Finally, I just export every snapshot >> as png image and make a gif movie by connecting all the snapshots. >> Though I have to spend more time on it, this way gave me better >> picture quality. >> >> Can I define a script which automatically export each frame in the MD >> trajectory as png image? It's really a pain to click "save as" again >> and again. >> >> Eric, you are such a nice person. Thank you very much! >> >> Mingfeng >> >> >> >> Eric Pettersen wrote: >>> Hi Mingfeng, >>> Did you get my mail where I attached the two MPEG-4 files? >>> >>> --Eric >>> >>> On Jan 27, 2006, at 2:01 PM, Mingfeng Yang wrote: >>> >>>> Eric Pettersen wrote: >>>>> Hi Mingfeng, >>>>> You can use the main interface's playback slider to change the >>>>> rate that frames are played back. With the slider to the far >>>>> right there is no delay between frames, with it to the far left >>>>> there is a one-second delay between frames. This interacts with >>>>> recording just like you would expect -- extra frames get recorded >>>>> during the delay which produces a movie with the same apparent >>>>> playback speed as with a non-recorded playback. >>>>> >>>> Hi, Eric, >>>> >>>> Thank you for your replay! But actually, the recorded playback is >>>> more faster than the non-recorded playback. I tried the slider at >>>> different position many times. BTW: I save the movie as mpeg >>>> format. As usual, gentoo linux, chimera buld 2186. >>>> >>>> Mingfeng >>>> >>> >>> >> > >

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Chimera memory management
by lutetium＠gmx.net 31 Jan '06

31 Jan '06

Hi, I am currently working on few datasets that exceeds the given memory limit for chimera. The log file indicates: MemoryError: can't allocate memory for array How can I increase the memory for chimera? Any suggestion regarding chimera´s memory management would be appreciated. Thanks a lot, Mike -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner

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problem in displaying pdb file
by venkataraman kabaleeswaran 30 Jan '06

30 Jan '06

I am having a problem in displaying the pdb file, chimera didnot display the whole molecule , around 100 residues is missing in the display, but other programs like pymol displaying without any problems. what is wrong? thanks vk Kabaleeswaran Venkataraman Arise, Awake and stop not until goal is Reached - Swami Vivekanand __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Fwd: control the movie play speed
by Eric Pettersen 27 Jan '06

27 Jan '06

Forgot to cc this to the list for the good of future generations. :-) --Eric Begin forwarded message: > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: January 27, 2006 1:42:37 PM PST > To: Mingfeng Yang <mfyang(a)gmail.com> > Subject: Re: [Chimera-users] control the movie play speed > > Hi Mingfeng, > You can use the main interface's playback slider to change the > rate that frames are played back. With the slider to the far right > there is no delay between frames, with it to the far left there is > a one-second delay between frames. This interacts with recording > just like you would expect -- extra frames get recorded during the > delay which produces a movie with the same apparent playback speed > as with a non-recorded playback. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > pett(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu > > On Jan 27, 2006, at 12:59 PM, Mingfeng Yang wrote: > >> Hi, >> >> I am using chimera to record the movie of a MD trajectory into a mpeg >> format vedio. How can I set the interval between neighboring >> snapshots? >> It seems the playback option in the MD movie dialog can't do >> that. Thanks! >> >> Mingfeng >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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control the movie play speed
by Mingfeng Yang 27 Jan '06

27 Jan '06

Hi, I am using chimera to record the movie of a MD trajectory into a mpeg format vedio. How can I set the interval between neighboring snapshots? It seems the playback option in the MD movie dialog can't do that. Thanks! Mingfeng

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Background transparency
by Alon Ben-David 27 Jan '06

27 Jan '06

Hi My name is Alon and I am a graduate student at the Technion, Israel institute of technology. My question is how can I create a transparent background to pictures I am generating with Chimera. I read at the site that not all hardware's permit a transparent background, but I don't know how can I check if my hardware do. Thank you in advance and best regards Alon

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command line for showing and hiding (same as clicking shown checkbox in model panel?) and volume viewer options in a cmd file?
by sabuj pattanayek 26 Jan '06

26 Jan '06

Hi, I'm trying to make a movie using a cmd file. I want to show and hide (same as clicking the checkbox for shown in the model panel) models from the cmd file since the system becomes too slow to do it manually while the movie is recording and timing frames is even more difficult. I also want to decrease and increase the isosurface threshold level in the volume viewer from the cmd file. Is it possible to do these without using the mouse while a movie is recording? Thanks, Sabuj Pattanayek

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Fwd: command line for showing and hiding (same as clicking shown checkbox in model panel?) and volume viewer options in a cmd file?
by Elaine Meng 25 Jan '06

25 Jan '06

> From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: January 25, 2006 10:42:40 AM PST > To: sabuj pattanayek <sabuj.pattanayek(a)vanderbilt.edu> > Subject: Re: [Chimera-users] command line for showing and hiding > (same as clicking shown checkbox in model panel?) and volume viewer > options in a cmd file? > > Hi Sabuj, > I failed to read Tom's mail first, oops. Just wanted to mention, > however, that I am pretty sure you want the command "modeldisplay" > and not "display": the latter turns all the atoms on, whereas > "modeldisplay" leaves the atom and ribbon display bits as they are > and is equivalent to the Show/Hide stuff in the Model Panel. > 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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Re: [Chimera-users] distance not shown
by Mingfeng Yang 25 Jan '06

25 Jan '06

Eric Pettersen wrote: > Hi Mingfeng, > ATI has come out with a new driver version for your card: > 8.21.7. Could you try that version and see if things start working? > Let me know. Thanks! > > --Eric > Hi, Eric, I just updated the driver to 8.21.7, and it can't work out. :( Meanwhile, I tried the radeon driver included in Xorg, and the distance can be displayed. So, yes, it's the driver's fault. Mingfeng > On Jan 11, 2006, at 6:09 AM, Mingfeng Yang wrote: > >> Hi, Eric, >> >> I am using ATI FireGL 8800 graphics card with driver fglrx-8.20.8. >> The 2D label does work. Labeling an atom or residue showed nothing. >> Change font size and style didn't solve the problem. >> I remember this feature works perfectly in the previous versions >> (probably before build 1.6???) on this same machine. >> >> Regards, >> Mingfeng >> >> >> Eric Pettersen wrote: >>> Hi Mingfeng, >>> You are the second person to report this behavior -- the other >>> person was also on Linux. Can you tell me what graphics cards you >>> have and what driver version? Do regular atom labels show up? Do >>> 2D labels work (Tools->Utilities->2D Labels)? Can you check your >>> Background preferences and make sure the default font size is > 0 >>> and try changing the font style to see if that makes any difference? >>> >>> --Eric >>> >>> Eric Pettersen >>> >>> UCSF Computer Graphics Lab >>> >>> pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu> >>> >>> http://www.cgl.ucsf.edu >>> >>> >>> >>> On Jan 10, 2006, at 2:56 PM, Mingfeng Yang wrote: >>> >>>> >>>> I am using Chimera build 1.2186 on Gentoo linux. Strangely, when >>>> the distance between two atoms is shown by the command "distance", >>>> the number is no longer displayed along the yellow dashed line. >>>> Did the developers removed this function? Or is it a bug? >>>> >>>> Regards, >>>> Mingfeng >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

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