April 2009 - Chimera-users - RBVI Mailing Lists

[Chimera-Users] help with IDLE
by cdlau＠ucsd.edu 20 Apr '09

20 Apr '09

Dear Sir/Miss, I am using the IDLE extensively and I have noticed I cannot paste text or <arrow up> to run previous commands. I was wondering if anyone knew how to change these features or if it is possible. I explored the options>configure IDLE, but haven't found any preference changes that change these problems I am having. Thanks for your help in advance. Best Regards, Christopher

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Straighten a helix
by Francesco Pietra 19 Apr '09

19 Apr '09

I would like to straighten a helix in a complex composition of helices, i.e., at least some of them may vdw interact with each other if moved. Therefore, I plan to let molecular dynamics (MD) changing dihedral angles at the pivot amino acid. I wonder whether chimera might aid through "adjust torsion" or other tool. If not else to provide alternative conformations for input to MD and see if the adjustments converge. Bending of the helix occurs along 5 amino acids, the central one probably the pivot. Thanks francesco pietra

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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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Chimera-users April 2009