- Chimera-users - RBVI Mailing Lists

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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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 24 Jan '06

24 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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Question
by Jin Chai 23 Jan '06

23 Jan '06

Dear Sr/Ms, I wonder if chimera molecular modeling system can be used beyond molecular level. we try to use chimera to create 3D images on mouse colon crossection images(dataset) we collected from SKYSCAN Micro-CT 1076 . Do you think it will work? Looking forward to your opinion. Thanks in advance, Jin --------------------------------- Yahoo! Photos Showcase holiday pictures in hardcover Photo Books. You design it and well bind it!

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CIF file format?
by Jason Sharpe 17 Jan '06

17 Jan '06

Hi, how do I open mmCIF (.cif) files in Chimera. This is the standard format of structure files supplied by the Cambridge Structural Database. thanks, Jason Sharpe University of Toronto

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Saving a multiscale model in VRML
by R. Andrew Byrd 17 Jan '06

17 Jan '06

Greetings, Our publications group has a new device that they call a 3D printer. It can make solid models from a data file. They have made models from pdb files as ball-and-stick, and I saw one surface rendered model. They tell me that the input is in VRML. So, I am wondering how to make a VRML file from a session in Chimera where Multiscale Model tool is used to make a surface rendering of a complex model...several proteins. My model is not as complex as the virus examples for multiscale models, but the ability to make different resolution surfaces is a powerful aid. I would like to try and 'print' a 3D model of this surface rendered complex. Any help in out to output the VRML file for the printer?> Thanks Andy -- R. Andrew Byrd, Chief Structural Biophysics Laboratory National Cancer Institute V 301-846-1407 F 301-846-6231 -------------------------------------------------

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Slow framerates (on a nice laptop)
by Charlie Moad 17 Jan '06

17 Jan '06

So in general I get really good performance with chimera, but for some reason I get really bad frame rates with more recent releases on windows with my laptop. It has a really nice card, GeForce 6200TC Go. It is even on a pcix16 bus. I am guessing that since it is a newer chipset, chimera is using shaders of some kind? The molecule looks visually smoother/better than when in linux. In any case, it seems something is getting enabled that really bogs it down, and I would like to be able to disable it. Sony Vaio FS500 Chimera 1.2184 Thanks, Charlie

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distance not shown
by Mingfeng Yang 10 Jan '06

10 Jan '06

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

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yet another binary plugin question
by Charlie Moad 06 Jan '06

06 Jan '06

So I have been able to create a working binary plugin for windows/linux 1.2184 and osx.4 1.2186. My problem now is osx.3 1.2184. I can compile the plugin, but it crashes chimera with a TCLfree call to a null pointer. I used the chimera-1.2183-linux-headers.tar.gz download. The 1.2186-osx headers didn't work either. 1.2186 won't launch for 10.3 either. The python module is matplotlib. It uses Numeric, freetype, tcl/tk, and libpng. I provide the only missing dep, libpng, and compile against the rest which are provided in chimera. Any help on what approach I should be using? Thanks, Charlie

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Help or feature request
by Mingfeng Yang 22 Dec '05

22 Dec '05

It's a very common problem to calculate the twist angle between to beta-strands or two alpha-helix. So I am wondering if Chimera can fit a group of atoms into a straight line, and give the angle of two fitted line. If chimera does do this, hopefully somebody can tell me how to do this. If not, it would be worthwhile to add this function in. Thank you very much! Happy holiday! Mingfeng

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Save image from Chimera
by Juhan Kim/CIRES 22 Dec '05

22 Dec '05

Hello, Does anybody know how to save the image from the chimera? I'm using PC version of Chimera and whenever I'm trying to save the image using the menu file>save image, I always fail to save the image and only get the following "reply log" ----reply log----- Opening "file.pdb" Done opening "file.pdb" Unable to save image: (0, 'Error') Unable to save image: encoder error -2 when writing image file Unable to save image: encoder error -2 when writing image file Unable to save image: (0, 'Error') If anybody knows how to solve this please let me know. Thank you. Juhan UCB, Boulder

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how to not include CONECT, RIBBON, HELIX, SHEET keywords in a pdb when saving from the pdb file dialog
by Sabuj Pattanayek 19 Dec '05

19 Dec '05

Hi, I was wondering how it might be possible to not include the CONECT, RIBBON, HELIX, or SHEET keywords in a pdb when saving from the save pdb file dialog? It can be done using "pdbrun nouser cat | grep -v HELIX | grep -v SHEET" ...etc but I can't save the pdb model relative to another model on the screen using that command. Thanks, Sabuj Pattanayek

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Fit Models
by Bernard Heymann 14 Dec '05

14 Dec '05

I'm interested in using the "Fit Models in Maps" feature in Chimera. However, the version I installed (release 1.2184) under Mac OSX 10.4 does not have this in the Tools/Volume Data menu as described in the documentation. Can anyone tell me if this is intentional or can I get this feature? Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892 Tel. 301-451-8241, Fax. 301-480-7629

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new version available
by Eric Pettersen 14 Dec '05

14 Dec '05

Hi all, We've put out a new version (1.2180) which we believe fixes the problems that some people were having on XP platforms. We're hoping that those of you that were having problems will try out the new version at your earliest convenience and let us know how it works. Thanks! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 12 Dec '05

12 Dec '05

Greetings, I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

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Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 08 Dec '05

08 Dec '05

I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

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