October 2012 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] multialign
by Tom Goddard 17 Oct '12

17 Oct '12

Hi Ed, I don't know if more than one chain can be associated with a sequence in Multalign Viewer. The documentation says " A structure (even if it has multiple chains) cannot be associated with more than one sequence, but a single sequence can be associated with more than one structure." http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu… That doesn't really say whether multiple chains of a single structure can associate with a sequence, only that multiple structures (different PDB models) can associate with the same sequence. So I tried it as I'm sure you did and I was not able to make it associate more than one chain (I used groel 1grl) with the same sequence in a multiple alignment. When I load the structure it associates chain A but not any of the other chains. Then if I use MultAlign Viewer menu Structure / Associations... to associate chain B with the same sequence then it seems to lose the association of chain A. At least when I select residues on the sequence, only chain B on the structure has residues selected. I'm forwarding this to the Chimera list since Elaine Meng or Eric Pettersen will have a better answer. Tom > Hi, > I am wondering if this is a bug or limitation in Chimera, or if I am > missing something. I have a molecular model of F-actin, with many > identical chains. Using the Multialign Viewer, it appears that I can > only do a 1 to 1 mapping of a single chain to a single sequence. How > can I map 10 identical chains to one sequence? > Regards, > Ed > -- > > <imap://goddard@imap.sonic.net:993/fetch%3EUID%3E.INBOX%3E23891?header=quotebody&part=1.2.3&filename=signature.html> > > Edward H. Egelman, Ph.D. > > Professor > > Dept. of Biochemistry and Molecular Genetics > University of Virginia >

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(no subject)
by Ondřej Holas 17 Oct '12

17 Oct '12

Greetings, I have encountered this problem with energy minimization of pyrazinamidase molecule. This molecule contains within its structure iron atom which Chimera does not support. Therefore I cannot find the way to overcome this problem. Is there any way to add iron to supported elements or any other way to solve this? Best regards -- Ondrej Holas Ph.D. Department of Pharmaceutical Chemistry and Drug Control Faculty of Pharmacy Heyrovského 1203 500 05 Hradec Kralove Czech Republic

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Need Information
by wisdom＠sanbi.ac.za 16 Oct '12

16 Oct '12

Hi, I am Wisdom, an MSc Bioinformatics student of the University of the Western Cape, South Africa. I wish to understand the meaning of the colouring of the individual amino acids in the sequence window of multiple sequence alignment as per the attached. I one see that all the Rs indicated by the black arrow are all red while the blue arrow has black Rs and orange Gs in the same column. There are other similar coloring all over the alignment. What does each (green, black, blue, orange, purple,red ) colour represent? Thanks Wisdom

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density maps & sub-region selection.
by Hernando J Sosa 16 Oct '12

16 Oct '12

Hi, I am trying to select subregions in two density maps using the subregion selection option in the volume viewer. When selecting the same subregion different sub-volumes in the two maps are selected (there is a displacement between the ROIs along the Z axis) even though the two maps are aligned to each other (or appear to be aligned in the display window). Both maps are in the MRC format and both have a voxel size of 2A/pix. ? Ideally what I want to do is to select equivalent regions of the two maps and then save them as new density maps. How can I best do this? Thanks Hernando. UCSF Chimera version alpha 1.7 (build 36659) on Windows 7 64b

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Trajectories, movies and multi-scale models
by Evan Kantrowitz 15 Oct '12

15 Oct '12

Hi I have a series of pdb files corresponding to a quaternary conformational change involving 12 chains. I can read these pdb files into Chimera via the MD movie, and I can view the conformational change. What I would like to do is to convert the movie into one using multiscale models with one surface for each chain. If I go into multiscale I can convert the initial pdb to multiscale, but it does not carry over to the other pdb files corresponding to the conformational change. Any suggestions would be appreciated. Evan Kantrowitz ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow Chestnut Hill, MA 02467 -------------------------------------------------------------------

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Re: [Chimera-users] Any option for terminating minimization without losing prior iterations?
by Elaine Meng 12 Oct '12

12 Oct '12

On Oct 11, 2012, at 5:42 PM, Thomas W. Sturgill wrote: > Dear Elaine, > Is there a way to interrupt minimization run without losing everything? > Is this running on the laptop or at a computer at UCSF? > Any link to list of your prior answers to questions on the minimization? > Thank you, > Tom Sturgill Hi Thomas, There is no "restart" if you interrupt the minimization, but you will still have the coordinates of the last update (you don't lose everything). The calculation runs on your own computer. You can see the minimization help by clicking the Help button on the GUI, or using command "help minimize". <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.…> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me personally -- the chimera-users messages can be searched (for example, for "minimization"): <http://www.cgl.ucsf.edu/chimera/docs/feedback.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Depicting buried surfaces
by Tom Goddard 12 Oct '12

12 Oct '12

> Hi Tom, > I have a non-EM density question! > Is there a way to display the buried surface between two PDB chains in Chimera? Something like what GRASP does: > http://www.csb.yale.edu/poststructure/grasp/grasp2.html > > I know I can measure the area with: > "measure buriedArea :.A :.B" > but is there a way to display the buried surfaces? > Thanks! > -gabe > > Hi Gabe, The measure buriedArea command sets a value for each atom giving the area buried (square Angstroms). So you can use measure buriedArea :.A :.B surfcat a :.A surfcat b :.B color pink :.A color lightblue :.B surface @/buriedSESArea>1 The surfcat command just defines chains A and B as two different objects for surfacing and the surface command show the surface patches associated with all atoms having buried solvent excluded surface area greater than 1 square Angstrom. It shows the entire patch of area for those atoms, not just the part that is buried. So it is pretty ugly and a bigger surface then just the buried part. For a much prettier picture but a slightly different measurement you might try instead split #0 surface measure contactArea #0.1 #0.2 2 slab 0.5 The split puts chains A and B in two models #0.1 and #0.2. The "surface" makes surfaces on each. And the "measure contactArea..." finds all points on one surface within 2 Angstroms of any point on the other surface and displays a pretty looking slab depicting the surface (attached picture). This is a different definition of buried area but might do. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#… Tom

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Sybyl - Amber atom type dictionary
by Nikolay Igorovich Rodionov 12 Oct '12

12 Oct '12

Hi all, I was wondering if there is a text editor readable dictionary file that shows Sybyl atom types and their complementary Amber/GAFF atom types names inside the Chimera program contents folder. Thanks, Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

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Re: [Chimera-users] APBS interface in Chimera
by Elaine Meng 11 Oct '12

11 Oct '12

Hi Boaz, It is brand new, so you have not at all been negligent! I only documented it a few days ago. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> Currently it does not have the option to use a locally installed APBS -- it uses an APBS web service provided by the National Biomedical Computation Resource. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 8, 2012, at 9:24 AM, Boaz Shaanan wrote: > Hi, > Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams! > > Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something? > > Cheers, > Boaz

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How to change the font for residue label
by Jean Didier Pie Marechal 11 Oct '12

11 Oct '12

Hi, I would like labels to appear bigger like with a bold font. How is that possible? Best JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Octubre 10, 2012 9:00 pm Assumpte: Chimera-users Digest, Vol 114, Issue 11 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Coloring nucleic acid ladder with opacity. Possible bug? > (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 10 Oct 2012 10:04:13 -0700 > From: Tom Goddard <goddard(a)sonic.net> > To: Rebecca Swett <rswett(a)chem.wayne.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > opacity. Possible bug? > Message-ID: <5075AA8D.5050304(a)sonic.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Rebecca, > > I put in a fix so that nucleotide ladder transparency looks right > in > tonight's daily builds. The fix applies to all Chimera VRML models > when > single-layer transparency is used. If multi-layer transparency is > used > then the opacity times the red,green,blue values of all transparent > layers are added together without regard to which layers are in > front of > which other layers, and that will still produce overly bright and > incorrect transparency. That is hard to fix. The single-layer > transparency mode is the default in Chimera 1.6 and later. > > Tom > > -------- Original Message -------- > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > opacity. > Possible bug? > From: Tom Goddard > To: Rebecca Swett > Date: 10/9/12 6:11 PM > > Hi Rebecca, > > > > Transparency does not work well with Chimera's nucleotide > > representations (slabs, ladder). Here's a technical explanation > that > > may help you understand why you see what you see. The > transparent > > nucleotide ladder is shown by multiplying the red, green, blue > color > > components (range 0 to 1) by the opacity (= 1 - transparency) and > > those color values are simply added to the image. Even in > > single-layer transparency mode both the back and the front of the > > cylinders are being added which makes the colors twice as bright > as > > they should be and can make it appear entirely white if rgb > values all > > end up greater than 1. > > > > This is a defective way to show something transparent. > Nucleotides > > are drawn as "VRML" models and all such Chimera models have this > > deficiency. Normal surfaces and molecules in Chimera do not have > this > > problem with transparency. It may be possible to fix the VRML > > transparency so it respects the "single-layer transparency" > option and > > that would make it much better since front and back side colors > would > > not get added creating an overly bright (sometimes white) > appearance.> > > Tom > > > > > > -------- Original Message -------- > > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > > opacity. Possible bug? > > From: Greg Couch > > To: Rebecca Swett > > Date: 10/9/12 5:31 PM > >> It's not a feature. :-) For me, transparency for ladder rungs > kinda > >> works -- the rungs are transparent, but not enough. And I only > see > >> opaque white when the ladder rungs are facing the key light. You > >> could mitigate the opaque white by moving the model or the key > >> light. If you are seeing different results or if you're > interested > >> in being notified after the bug is fixed, please file a bug report. > >> > >> FYI, in the Chimera daily build (available tomorrow), I've > eliminated > >> the extra cylinder caps that are exposed when you make the > ladder > >> transparent, so you can get a slightly better picture. > >> > >> HTH, > >> > >> Greg > >> > >> On 10/07/2012 07:01 PM, Rebecca Swett wrote: > >>> Hey all, quick question on coloring here. I'm handling a > structure > >>> that has nucleic acids and protein. I'd like to represent the > >>> nucleic acids with the ladder representation and then have them > at a > >>> lower opacity to bring focus to the protein structure. When I > try > >>> coloring the ladder with opacity, the ribbons color just fine, > but > >>> the rungs go opaque white. Is this a bug, or has anyone gotten > this > >>> to work? I just updated to 1.6.2. Thanks for any help. > >>> ~Rebecca > >>> > >>> Rebecca Swett > >>> Wayne State University > >>> 357 Chemistry > >>> Detroit, MI 48201 > >>> > >>> Lab Phone 313-577-0552 > >>> Cell Phone 906-235-0768 > >> > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 114, Issue 11 > ********************************************** >

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Chimera-users October 2012