- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] reflection of docking poses with chimera
by Elaine Meng 18 Apr '09

18 Apr '09

On Apr 18, 2009, at 9:43 AM, Antonios Kolocouris wrote: > Hi Elaine, > I have obtained the results of the docking claculations of some > compounds > with a symmetric - by 180 degrees - receptor. To obtain a > consistent set of > structures for further 3D QSAR I need to know how I can reflect a > docking pose by 180 degrees > vertically and horizontally with Chimera. > My kind regards, > Antonios > ---------------------------------------------------------------------- > --------------------- > Antonios Kolocouris, Assistant Professor of Medicinal Chemsitry > Department of Pharmacy, Univ. of Athens, Greece > Hi Antonios, The main issue is figuring out the proper transformation to superimpose one binding site on the other. It will not exactly be a reflection (you will still have the same enantiomers) but a rotation. You would need a recent daily build for what I describe. If you are certain only rotations about the exact horizontal and vertical axis are needed, and you know what the center of rotation should be, use the "turn" command with specified axis and center of rotation to move the ligand model(s). The horizontal axis is x, the vertical axis is y. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> The rest of this message addresses the more general case where the axis of symmetry and thus the proper transformation is not known: -- To find out the transformation, (A) put the two parts containing the two binding sites in different models. This could be done by manually text-editing your PDB file to create two files that can then be read into Chimera. Or, if they are already two different chains, you can use the "split" command to divide the already open model into separate models. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> (B) superimpose the two binding sites. It could be done with matchmaker, or match, or manually. Which is best depends on the situation. These methods are discussed and there are links to their manual pages here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (C) find out the relative transformation of the two models using the "measure" command, for example to report the transformation of model #0.2 relative to #0.1: measure rotation #0.1 #0.2 the transformation is sent to the Reply Log (under Favorites menu), both as a matrix and as an axis of rotation and point on the axis, as described in the manual page: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html> -- To apply the transformation to the ligands, I would first use the command "reset" (without arguments) to put everything back into their untransformed positions and then either (A) use the "turn" command with specified axis and center of rotation to move the ligand model(s) - or - (B) save the matrix from the Reply Log to a file and then apply it with the "matrixset" command I'm not sure if the "reset" is necessary (some of these transformation issues confuse me), but that's what I would try first. I recommend sending questions to chimera-users(a)cgl.ucsf.edu rather than to me directly, to be certain they will not fall through the cracks. 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

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Re: [Chimera-users] Superimpose
by Elaine Meng 17 Apr '09

17 Apr '09

Hi Cedric, The "match" command fits whatever atoms you specify: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> I should mention that MatchMaker (or "matchmaker" command) generally does pretty well even with low sequence identity because it also uses secondary structure assignments: the score favors aligning helix with helix, strand with strand. However, if you need it, "match" can be used in any situation, including molecules other than proteins and nucleic acids. The tradeoff is that it is more work for the user, since you have to tell it which atoms to use. Discussion of the different ways to superimpose structures in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this helps, Elaine On Apr 17, 2009, at 8:26 AM, Cédric Govaerts wrote: > Hi Elaine, > > So of course I have a new question: > > Matchmaker will take to proteins, align the sequences and then > align the > structures. > > But what I need to do is to align the structure according to the > pairs of > atoms I have selected. > > For example this could be particularly useful for : > > 1/ Superimpose two structures that are different but have a few common > catalytic residues. They would be two different for Match maker to > find the > correct alignment, however, the user (that's me) would know which > residues > should be used. > > 2/ I tried to superimpose two isoforms of the same proteins using > ions or > ligand as superimposing element. I wanted to see what was the > conformational > change *relative* to the bound metals. > > I believe that creating an alignment for MultiAlign would not work for > either. > > Is there a way I can superimpose two structures after explicitely > choosing > the pairs (minimum) and the Chimera would make a lest-square > regression > based on those ? > > Thanks again > > Cedric >

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making slow movie
by Bala subramanian 16 Apr '09

16 Apr '09

Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded. 1) How can i record a movie with low playback speed. 2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated. 3) Kindly suggest me some better setting to record a movie with high clarity based on your experience. Thanks, Bala

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correction: selecting by element
by Elaine Meng 16 Apr '09

16 Apr '09

Begin forwarded message: >> >> You can use all the end entries in the Select... Chemistry menu also >> in the command line. These symbols are in the element submenu. In >> cases where there is ambiguity, for example H appears both under >> element and under IDATM type, you can disambiguate like >> >> select element.H >> >> It will work to use element.Mg and element.Ca ... it's just more >> typing. > > Hum that does not seem to work oddly. "Select element.Ca" gives me a > "mangled atom specifier" (that why I asked you in the first place). > Same thing for Mg btw (I originally though there was some ambiguity > between > Calcium and carbon-alpha naming). Whoops, my bad. Actually Mg and Ca are not at the top level of "Select... Chemistry... element" but in further submenus. You could use "Md-Ni.Mg" and "Be-Cl.Ca" but I don't think there is a need to use anything longer than Mg and Ca. Ca will not conflict with atom name because the command-line syntax requires @ to indicate atom name. "@ca" are atoms named CA, "@c" are atoms named C, "Ca" are calcium ions/atoms, "C" are carbon atoms. The capitalization is not important for atom names, but it IS important for the things that are also menu entries and should match what is shown in the menu. The potential for ambiguity with element symbols is with the entries under "Select... Chemistry... IDATM type" but in fact H is the only one I can think of that appears in both places. Best, Elaine

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Re: [Chimera-users] making slow movie
by Bala subramanian 16 Apr '09

16 Apr '09

Hi Benoit, Thank you. Actually i was recording the movie with the Record movie option in the MD movie tool where this setting is not there. I will try with movie recorded. Thanks, Bala On Thu, Apr 16, 2009 at 1:26 PM, Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk>wrote: > Hi Bala, > regarding your first point: you can set the number of frames per second in > the movie recorder window. Alternatively, if you encode your movie with a > command line, you can set the number of frames per second with the option > framerate > > Ben > > Bala subramanian wrote: > >> Friends, >> >> I am using MD movie with chimera to see the motion of a single pdb >> containing 25 models. I kept the play back speed at low value, then recorded >> the movie. But the movie comes very fast. I guess there is no related >> functionality between playback speed and the speed with which the movie is >> recorded. >> >> 1) How can i record a movie with low playback speed. >> 2) Is it possible to split the chimera screen in to two halfes or as >> quadrants (like in sybyl) and then load the molecules wherever we want. >> Now why i need it ?. >> I have two pdb files (each consisiting of 25 models). If i can split the >> chimera screen, i would like to load pdb1 left and pdb2 in rigth side using >> MD movie, then record the movie. Any better idea than this to achieve the >> same would be highly appreciated. >> >> 3) Kindly suggest me some better setting to record a movie with high >> clarity based on your experience. >> >> Thanks, >> Bala >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > > -- > Benoīt Zuber > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH > United Kingdom > +44 1223 402209 > bzuber(a)mrc-lmb.cam.ac.uk > >

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How to save fitted map as MRC file.
by 横山武司 15 Apr '09

15 Apr '09

Dear chimera developer I want to save fitted map after using "Tools/Volume Data/Fit in Map" as MRC file. How can I do this? Is there the same kind of function when we save fitted PDB file related to Map. Thank you in advance, Takeshi ------------------------------------------------------------------------------------------------------------------------- Takeshi yokoyama Ph.D. Postdoctoral scientist Wadsworth Center New York State Department of Health USA yokoyama(a)wadsworth.org -------------------------------------------------------------------------------------------------------------------------- _________________________________________________________________ 世の中、仕事は一つじゃない! 自分にピッタリの仕事してますか? http://career.jp.msn.com/article2/genba/default.htm

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Fwd: Copy and Pasting sequences
by Eric Pettersen 15 Apr '09

15 Apr '09

Begin forwarded message: > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: April 14, 2009 2:36:02 PM PDT > To: hsosa(a)aecom.yu.edu > Subject: Re: [Chimera-users] Copy and Pasting sequences > > Oooh, you're right -- that's missing. There's a whole passel of > improvements I need to do for the sequence viewer and now that > you've pointed it out that's certainly one of them. There'll be > some kind of replacement functionality by the next release. In the > interim, a possible workaround is to save the sequence to a file > (using the viewer's File-Save As) and copy from that. Probably the > simplest format (and therefore the easiest to copy from) is FASTA. > > --Eric > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Apr 14, 2009, at 1:22 PM, hsosa(a)aecom.yu.edu wrote: > >> Hi >> >> I noticed that in the latest version of Chimera (1.4) the sequence >> display tool (Model Panel > sequence) is different (nicer looking) >> than >> in previous versions. However, before I was able to copy the >> sequence as >> text and paste it into a text editor (using CTR-C & CTRL-V in >> Windows) >> but that is no longer the case. Is there an easy way to get this >> functionality back. >> >> Thanks >> >> Hernando >> >> >> -- >> ----------------------------------- >> Hernando Sosa >> Dept. of Physiology and Biophysics >> Albert Einstein College of Medicine >> 1300 Morris Park Av. >> Bronx NY 10461 >> phone (718) 430-3456 >> FAX (718) 430-8819 >> email hsosa(a)aecom.yu.edu >> ----------------------------------- >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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coloring with partial charges
by Bala subramanian 15 Apr '09

15 Apr '09

Friends, How to do electrostatic coloring based on partial charges. I have a pdb generated from amber, i would like to assign amber charges and color the surface using assigned charges. Bala

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graphics problems, BIOMT, selecting by element, etc.
by Elaine Meng 15 Apr '09

15 Apr '09

On Apr 15, 2009, at 5:30 AM, Cédric Govaerts wrote: > Hi Elaine, Hi Cedric! I will put responses below, after your individual questions... > > I'm not posting my question to the mailing list because most of it > might be > due to my machine. > I've been encountering some problems running chimeras and I suspect a > graphic card issue(s). > Mostly it's the display that goes bananas, lows the machine ending > (sometimes) in a chimera crash. It's OK -- even if due to the machine, other people have these problems too and might want to see the discussion. > > Here are some of the issues : > > 1/ When I zoom in/out using my mouse wheel sometimes all the > displayed atoms > change from wire to CPK representation. I must explicitely change it > back to > wire to go back. > Normal ? > > 2/ When changing the display I have sometimes some very odd graphic > behavior, including part of the window turing colored or black. I > attach a > couple of screenshots. This started just after typing a display > command. For > a while everything became very slow until I tried to save the image > using > chimera itself which seemed to reset the graphics back to normal. > As you can see on the screenshots, some Photoshop tool windows (PS3 > was > running in the backgournd) appear on the image (although not visible > on > chimera itself) which leads me to think that it's a graphics card > issue or a > graphic card+Photoshop issue. These definitely sound like graphics driver issues. Definitely not normal behavior! Things to try are to update your graphics driver as possible, and/or use the Debug Graphics Driver dialog to selectively disable OpenGL features. One way to show this dialog is to go to Preferences (under Favorites), General category, set "debug OpenGL on startup" to true, quit, and restart Chimera. Documentation of the debug dialog and discussion of graphics driver problems: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html > <http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html> > > 1/ Can I easily build a biomolecule from the PDB file ? > I tried with > i) MultiScale Models but could only get low res surfaces > ii) Unit Cell but got the copies from the SMTRY records of the PDB > file, could not specify the BIOMT > I believe the "sym" command should work but I dunno how to make it > read the > BIOMT matrix in the PDB file. > For building using BIOMT: If you use Multiscale Models, you can force loading of the atomic coordinates for all copies by selecting All chains in the multiscale dialog and then changing the Style to anything other than surfaces. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… > You can also use the "sym" command. If your structure with BIOMT records is model 0, for example, command "sym 0 0": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> > 2/ Is there a way I can select specifically all Mg atoms ? Or - > trickier- all > calcium (Ca) atoms ? commands: select Mg select Ca You can use all the end entries in the Select... Chemistry menu also in the command line. These symbols are in the element submenu. In cases where there is ambiguity, for example H appears both under element and under IDATM type, you can disambiguate like select element.H It will work to use element.Mg and element.Ca ... it's just more typing. > > 3/ When I select with the mouse, I only select one atom at a time. > What > would be the easiest/fastet way to display the residue that the > currently > atom belongs to ? > A/ Can I do it with the command line (does the command line > recognize the manually selected atoms?) ? > B/ I can use the menus and do Actions->Atoms->Backbone->Full and > then Actions->Atoms->Sidechain->Show, but that's a bit cumbersome to > do each > time I wanna see a residue it seems.. If you have some atom or bond in a residue selected, just hit the keyboard up arrow to broaden the selection to the whole residue. That is the same as using the command: select up <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html> You can specify the current selection regardless of how it was created (with mouse, Select menu, etc.) in commands with the word "sel" "selected" or "picked". <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > For example, pick one atom, hit up arrow, use command "display sel" to display the whole residue. Actually if you use "rlabel sel" (show residue label for any selected atoms) you don't even need the up arrow part. > > That's it for now.. brr, thanks ! > > C > You're welcome! 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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interhelical angle
by Shuanghong Huo 14 Apr '09

14 Apr '09

Dear Chimera Developers, My group needs to calculate the inter-helical angle for a large trajectory. We know Chimera can calculate the inter-helical angle for a conformation. We are wondering what the easiest way to use Chimera to process the whole trajectory. It is amber trajectory. Thanks, Sharon Huo, Ph.D. Associate Prof. of Chemistry & Biochemistry Clark University

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