- Chimera-users - RBVI Mailing Lists

DMS installation
by Steven Finckbeiner 06 Feb '06

06 Feb '06

The Dockprep and WriteMol2 files worked like a charm. Could anyone give me any pointers on installing DMS? I have spent the better part of a day following the instructions on the web site and I can't get the damn thing to work. I've gotten this far: 2187 atoms usr/local/lib/dms/radii: no such file or directory Thanks again! "Sometimes, life hits you in the head with a brick." Steve Jobs ---------------------------------------------------------------- Steve Finckbeiner 132 Grace Cancer Drug Center Roswell Park Cancer Institute Elm and Carlton Streets Buffalo, NY 14263-0001 (716)845-5818 --------------------------------- Brings words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail.

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Re: [Chimera-users] Dockprep and WriteMol2
by Eric Pettersen 04 Feb '06

04 Feb '06

Hi Steve, Your Googling hit our development documentation, which includes features not in the latest production release and in some cases features that aren't in any release yet. Dock Prep is one of those. We are preparing a release candidate that we anticipate being on the web early next week that will include Dock Prep -- though I can't absolutely guarantee that there won't be an unforeseen hangup that delays it a few days. If you want to use Dock Prep ASAP, I could send you the relevant Python files to drop into your 1.2186 distribution -- let me know. As you noticed, the WriteMol2 module got mistakenly left out of the 1.2186 snapshot, so I would be sending you the files for that as well. The files I'd send you would include one small feature that won't be making it into the release candidate: structures with alternate atom locations will have them pruned to the locations with highest occupancy. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 4, 2006, at 4:13 PM, Steven Finckbeiner wrote: > I have Chimera beta version 1 build 2186. I think it's the latest > beta available. I'm trying to clean up some structures to run in > Dock. When I do a google search, the following page comes up: > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ > dockprep.html > > I can't find Dockprep under the Surface/Binding Analysis menu. Is > this something that will come out in future versions but the web page > is already built? Or is it in later versions? If so which? My > particular situation makes it hard to get to SYBYL to assign charges > and define rigid and anchor sets. I was thrilled to see that > something like Dockprep has at least been concieved of. > > Also, when I try to save as mol2, I ! get the following error: > > "Import Error: No module named WriteMol2." > > I apologize ahead of time if this marks me as a hopeless novice. Any > help would be much appreciated. > > Steve > > > "Sometimes, life hits you in the head with a brick." > Steve Jobs > > ---------------------------------------------------------------- > Steve Finckbeiner > 132 Grace Cancer Drug Center > Roswell Park Cancer Institute > Elm and Carlton Streets > Buffalo, NY 14263-0001 > (716)845-5818 > > Yahoo! Mail - Helps protect you from nasty > viruses._______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Dockprep and WriteMol2
by Steven Finckbeiner 04 Feb '06

04 Feb '06

I have Chimera beta version 1 build 2186. I think it's the latest beta available. I'm trying to clean up some structures to run in Dock. When I do a google search, the following page comes up: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.… I can't find Dockprep under the Surface/Binding Analysis menu. Is this something that will come out in future versions but the web page is already built? Or is it in later versions? If so which? My particular situation makes it hard to get to SYBYL to assign charges and define rigid and anchor sets. I was thrilled to see that something like Dockprep has at least been concieved of. Also, when I try to save as mol2, I get the following error: "Import Error: No module named WriteMol2." I apologize ahead of time if this marks me as a hopeless novice. Any help would be much appreciated. Steve "Sometimes, life hits you in the head with a brick." Steve Jobs ---------------------------------------------------------------- Steve Finckbeiner 132 Grace Cancer Drug Center Roswell Park Cancer Institute Elm and Carlton Streets Buffalo, NY 14263-0001 (716)845-5818 --------------------------------- Yahoo! Mail - Helps protect you from nasty viruses.

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question on monitoring hydrogen bonds
by knutsost 03 Feb '06

03 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 26 Jan '06

26 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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