October 2014 - Chimera-users - RBVI Mailing Lists

Question about unit of electron density
by Matthias Fellner 13 Oct '14

13 Oct '14

Dear Elaine Thank you for the long response and sorry for my late one as I just finished a publication where I used Chimera for the first time and also cited it. You answered everything I wanted to know. So I wanted to wait for my thanks to see if I can ask another question right away: What unit do I report for the "level" of a shown electron density map. I assume it is σ (lower case letter sigma) for example 1.2σ? I just could not find the unit in the tutorial or a search through your board, so I wanted to double-check. Thank you Matthias Fellner ________________________________________ From: Elaine Meng [meng(a)cgl.ucsf.edu] Sent: 04 October 2014 06:50 To: Matthias Fellner Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Question about RMSD calculation of MatchMaker Hi Matthias! As shown in your image of the dialog, you’re using the “Iterate by pruning…” option that removes farther-apart pairs from the fit. That’s why you could get different numbers of pairs used to calculate the RMSD even if all chains contain the same numbers of residues. Iteration is described in the MatchMaker docs: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> If you turn off the “iterate” option, it will not try to improve the fit by pruning and will instead use all the pairs (CA-CA atom pairs of residues aligned in the sequence alignment). If the structures include the same residues for each chain, the pairwise chain-chain RMSDs will all be calculated from the same number of CA-CA atom pairs. The dialog image also shows you are fitting A-B, A-C, A-D. For completeness you may also want to try B-C, B-D, C-D. Another issue is that MatchMaker or its command equivalents (mmaker, matchmaker) only use one atom per residue, CA, and only considers aligned biopolymer chains (peptides, nucleic acids). If that’s what you want, no worries. However, you could use the “match” command instead and specify any sets of atoms for RMSD calculations, such as all backbone, with or without iteration. However, it’s harder to use since you have to specify the atoms in the command line yourself, unlike MatchMaker that figures out which atoms to pair automatically. You could include waters, but it would be tedious/difficult to specify each water residue by name, in the corresponding orders, for the two structures to be matched. Also the waters would have to be in the respective models. Matchmaker vs. match is discussed in the following link: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> “match” command manpage, examples: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> command-line atom specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> another “match” example in a tutorial, see the Matching section in: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html> If you are interested in the variation over the length of the chain as opposed to getting a single number, a nice way to show that is to first superimpose the chains, then associate them all with a single copy of the sequence. Then over the sequence you can display an RMSD histogram showing the alpha-carbon (or other atoms, depending on which RMSD you choose) structural variability at each position in the sequence. To do that: (1) superimpose chains however you like (Matchmaker or match) (2) show sequence of any one of them, presumably they are basically the same (menu: Favorites… Sequence, choose one) (3) in the sequence window, use Structure… Associations to associate all copies of the structure with the single sequence (4) in the sequence window, use the Headers menu to show the RMSD of interest (and hide other headers you don’t want to see) You can even show these RMSD values with colors or worm thickness on one of the copies, as described in more detail here: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009710.html> I hope this helps, 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 1, 2014, at 9:38 PM, Matthias Fellner <mfellner(a)chemistry.otago.ac.nz> wrote: > Good day > > I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I will use a citation for sure when I publish using your software. > A current analysis of mine involves a crystal structure that has 4 chains in the asymmetric unit. They chains are very similar when aligned and I would like to have a statistic to show this. > > I assume the RMSD is the way to go. So I saved each chain as its own pdb, loaded them in Chimera and used your MatchMaker to align chain B,C and D to chain A (randomly chosen because of notation of chains). > > The chains have an identical amino acid sequence (~200 residues), I just build 1-5 residues more or less at each end of the chain but otherwise they should all be the same. Now the reply log gives out the RMSD and the number is under 1Å as I expected and I can quote that. But my question would be why did it use a different numbers of atom pairs for the different chains (191 or 188 or 193) and which atom pairs are those. I assume it picks one atom from the main chain of each residue and the different number comes from the difference residue number at the end of the chains. > > I searched through your help files and with google through your board but could not find the answer to what atoms are paired and if you can change the pair for example to include all atoms of the mainchain or even all atoms all together. > > Sorry for the long question but I wanted to give all the details, attached also the (default) options I had for the MatchMaker and the reply log. > > In addition a small question which I guess wont be possible – is there any way to also align water molecules adjacent to the chains although all water molecules are saved in chain S together? > > Thank you > Matthias > > > <image001.png> > > Matchmaker chainA.pdb, chain A (#0) with chainD.pdb, chain D (#3), sequence alignment score = 999.7 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 191 atom pairs is 0.506 angstroms > > > Matchmaker chainA.pdb, chain A (#0) with chainC.pdb, chain C (#2), sequence alignment score = 999.1 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 188 atom pairs is 0.551 angstroms > > > Matchmaker chainA.pdb, chain A (#0) with chainB.pdb, chain B (#1), sequence alignment score = 987.2 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 193 atom pairs is 0.336 angstroms > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Measuring volume inside virus caspid
by Tom Goddard 13 Oct '14

13 Oct '14

Hi Reggie, I measure the volume inside the capsid of bacteriophage P22 from Electron Microscopy Databank entry 1220 as about 77,000 cubic nanometers. Here’s how I calculated it in Chimera. The idea is to fit a surface that is something between an icosahedron and a sphere to the inside of the capsid then measure the volume within that surface. The Chimera Icosahedron Surface tool (menu Tools / Higher-Order Structure) can make this surface. But the problem is that the EMD 1220 density map is not in a standard icosahedral orientation. The closest orientation is 2-fold symmetry axis along x, 3-fold symmetry axis along z (called 2n3r in Chimera). That orientation looks to be about 5 degrees out of alignment with the virus. So I set the radius to 320 (about the size of the capsid), sphere factor to 0.5 to approximate the spherical shape of the virus, and subdivision factor to 100. Then I created a density map that is ones inside this surface and zeros outside with the command “mask ones #1” (the icosahedron surface is model #1, as shown in the Model Panel dialog, Favorites menu). Then I fit this icosahedron map to EMD 1220 to get the correct alignment using the Fit in Map tool (menu Tools / Volume Data / Fit in Map, fit #2 in #0). I judge the fit is good by seeing that the virus capsid proteins stick out uniformly from the surface of the fit mask map. Then I align the original icosahedron surface to the fit mask using “matrixcopy #1 #2”. Then I adjust the icosahedron surface radius and sphere factor (285 and 0.54) to visually match the inner boundary of the EMD 1220 capsid. To see that I clip the EMD 1220 map in half using Per-Model Clipping (menu Tools / Depiction). Then I measure the enclosed volume of that aligned icosahedron surface using the Measure Volume and Area tool (menu Tools / Volume Data), and I get 77 million cubic Angstroms, or 77,000 cubic nanometers. See attached picture with aligned icosahedron surface shown transparent and brown. Tom On Oct 13, 2014, at 10:40 AM, Reginald McNulty wrote: > Hi Tom, > Can you tell me the tricks of how to calculate the volume of just the interior for EMD-1220? > Reggie > > On Oct 9, 2014, at 5:58 PM, Tom Goddard wrote: > >> Hi Reggie, >> >> What are you trying to calculate? Chimera can calculate the volume inside your density map surface if that is what you want. If it is just a capsid map then it won’t include the hollow interior. There are tricks to include the interior. If you really care about icosahedron volumes Chimera gives the exact value by summing polyhedral volumes. The Chimera icosahedron radius is the distance from the center to a vertex. The measure volume command reports the enclosed volume of the icosahedron with its flat faces as 58.7e6 for radius 285. As you note a sphere of radius 285 has volume 95e6. >> >> Tom >> >> >> On Oct 9, 2014, at 5:34 PM, Reginald McNulty wrote: >> >>> Dear Tom, >>> >>> Eager to hear your thoughts on what’s below. >>> >>> I’ve done the math by hand for how to calculate the volume of an icosahedron. One of them (exsphere) gives the exact answer shown in Chimera with 'measure volume'. I’ll give a brief definition below and then show all calculations. The volume (V) of an icosahedron depends on the length of the edge (distance between five folds). My understanding is that there are different ways of drawing the radius (R) to calculate the length of an edge (a). Assuming an exsphere radius of 285 angstroms, I can calculate a volume of 58709669.80741614 cubic angstroms (or 59 million cubic angstroms) which is exactly the answer shown in chimera. However, I suspect the midsphere radius of 285 angstroms, yielding a volume of 95379640.39879936 cubic angstroms (or 95 million cubic angstroms) is a closer approximation, as this answer is very close to that obtained assuming V=4/3*(pi)*r^3 (97 million cubic angstroms). >>> >>> Definitions: >>> Inscribed sphere: http://en.wikipedia.org/wiki/Inscribed_sphere >>> Midsphere: http://en.wikipedia.org/wiki/Midsphere >>> exsphere: http://en.wikipedia.org/wiki/Exsphere_(polyhedra) >>> >>> Useful online calculator: http://calcverter.blogspot.com/2014/08/icosahedron-edge-area-volume-exspher… >>> >>> Assuming a radius of 285 angstroms, here are the calculations for volume 3 different ways: >>> >>> Method A >>> R(m)- Midsphere radius= 285 Å >>> >>> R(m)=a / 4 * ( 1 + √5 ) >>> --------------------------------------- >>> multiply both sides by 4 >>> --------------------------------------- >>> 285(4)= a(1+√5) >>> = a(3.23606797749979) >>> ---------------------------------------- >>> a=285(4)/3.23606797749979 >>> ---------------------------------------- >>> a=352.27937358744003 >>> ---------------------------------------- >>> Now that we have the icosahedral edge length (a), we can calculate the volume of the virus with: >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> >>> = 5/12 * 43718136.95711854 *(3 + √5) >>> = 5/12 *43718136.95711854 5.23606797749979 >>> =95379640.39879936 >>> --------------------------------- >>> or 95 million cubic Å >>> --------------------------------- >>> >>> >>> >>> Method B >>> R(e)- Exsphere radius- 285 >>> >>> R(e) = a / 4 * √(10 + 2 * √5) >>> ---------------------------------- >>> writing in python was easier for me here: >>> >>> 285=a/4 * math.sqrt(10+2*math.sqrt(5)) >>> 285=a/4 * 3.804226065180614 >>> ---------------------------------------------- >>> >>> solve for a: >>> a=(285/ 3.804226065180614)*4 >>> a=299.6667339079062 >>> >>> -------------------------------------------- >>> Now that we have the icosahedral edge length (a), we can calculate the volume of the virus with: >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> -------------------------------------------------- >>> writing in python is a little easier here: >>> >>> V= ((5/12.0)*(299.6667339079062**3)*(3+math.sqrt(5))) >>> >>> = 58709669.80741614 >>> -------------------------------- >>> or 58 million cubic Å >>> --------------------------------- >>> >>> >>> >>> Method C >>> R(i)- Insphere radius (tangent to face of icosahedran) >>> >>> R(i) = a / 12 * √3 * ( 3 + √5 ) >>> >>> ----------------------------- >>> >>> 285 = a/12 *((math.sqrt(3))*(3+math.sqrt(5))) >>> >>> 285= a/12 * 9.069135768914048 >>> >>> a= (285/9.069135768914048)*12 >>> = 377.1031868022763 >>> ---------------------------------------- >>> >>> Use edge of 377.1031868022763 to calculate volume >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> ------------------------------------------- >>> >>> V= ((5/12.0)*(377.1031868022763**3)*(3+math.sqrt(5))) >>> V= 116996977.425189 >>> --------------------------------------------- >>> >>> or 116 million cubic Å >>> >>> ------------------------------------------ >>> >>> Reggie McNulty >>> >>> On Oct 9, 2014, at 4:49 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>> >>>> When you use the “measure volume” command on an icosahedral cage it is measuring the volume enclosed in the polygonal solid defined by the cage, not the volume of a sphere. I don’t know what you mean by “exsphere”, “midsphere”, “calculate by hand”. >>>> >>>> Tom >>>> >>>> >>>> On Oct 9, 2014, at 1:01 PM, Reginald McNulty wrote: >>>> >>>>> I manually fixed the cage and shrunk it to encompass the internal DNA using a radius of 285. I used the measure volume command to measure the volume inside the cage. Can Chimera show sphere it is using to calculate calculate the volume? A cage with radius 285 angstroms gives a volume of 58 million cubic angstroms. By hand, I can calculate volume of also 58 million cubic angstroms using an exsphere radius of 285; edge is 300 angstroms. However, a midsphere radius of 285 gives me an edge of 352 angstroms and volume of 95 million cubic angstroms. >>>>> Reggie >>>>> >>>>> On Oct 8, 2014, at 2:24 PM, Tom Goddard wrote: >>>>> >>>>>> Yes you could probably fix the alignment of a cage by hand in Chimera so it looked decent. If you want to do some analysis using the symmetry that is harder. >>>>>> >>>>>> Tom >>>>>> >>>>>> On Oct 8, 2014, at 2:14 PM, Reginald McNulty wrote: >>>>>> >>>>>>> Never mind. I think it’s close enough with 2fold on x, 3 fold on z, with extra rotation. >>>>>>> On Oct 8, 2014, at 2:07 PM, REGINALD MCNULTY wrote: >>>>>>> >>>>>>>> Thanks. It works. >>>>>>>> I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map? >>>>>>>> Reggie >>>>>>>> On Oct 8, 2014, at 11:34 AM, Tom Goddard wrote: >>>>>>>> >>>>>>>>> Hi Reggie, >>>>>>>>> >>>>>>>>> I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. >>>>>>>>> >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> open 2xyz >>>>>>>>> rainbow chain >>>>>>>>> sym #0 surf true >>>>>>>>> >>>>>>>>> # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). >>>>>>>>> >>>>>>>>> shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 >>>>>>>>> molmap #0 10 sym i,n25r >>>>>>>>> >>>>>>>>> >>>>>>>>> <2xyz.jpg> >>>>>>>>> >>>>>>>>> On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: >>>>>>>>> >>>>>>>>>> Dear Tom, >>>>>>>>>> >>>>>>>>>> I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? >>>>>>>>>> I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html >>>>>>>>>> >>>>>>>>>> All the best, >>>>>>>>>> -Reggie >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Reginald McNulty, Ph.D. >>>>>>>>>> Postdoctoral Research Associate >>>>>>>>>> The Scripps Research Institute >>>>>>>>>> Johnson Lab >>>>>>>>>> Department of Integrative Structural and Computational Biology >>>>>>>>>> 10550, N. Torrey Pines Road, MB-31 >>>>>>>>>> La Jolla, California 92037 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> All the best, >>>>> -Reggie >>>>> >>>>> -- >>>>> Reginald McNulty, Ph.D. >>>>> Postdoctoral Research Associate >>>>> The Scripps Research Institute >>>>> Johnson Lab >>>>> Department of Integrative Structural and Computational Biology >>>>> 10550, N. Torrey Pines Road, MB-31 >>>>> La Jolla, California 92037 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >> > >

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command @/serialNumber=#
by Francesco Pietra 12 Oct '14

12 Oct '14

Hello: I wonder whether it is possible to extend the command sel @/serialNumber=18801 (as an example of a particular serial number) to comprise a range of atoms. So as to cover, for example, an entire ligand, may be dioxygen, 18801-18802. And whether that could be extended to define a centroid. it is implied that I have prepared a large system based on segname (charmm ff with namd), which is not dealt with by chimera. thanks francesco pietra PS: I can follow the ligand by defining the centroid for a single atom of the ligand. This would be my last resource.

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measuring distance between an atom and centroid of an aromatic ring
by Aswani Kumar Kancherla 10 Oct '14

10 Oct '14

Hello Chimera Users, I need to measure and mark the distances of a few atoms to the center of an aromatic ring. I could define and create a centroid and plane for the ring. However, I am unable to measure or mark the distances of the surrounding atoms from the centroid of the ring (This is an exercise to show the ring current effect of the aromatic ring on the chemical shifts of the neighboring protons). Could anyone please give a hint on how I can go about this? thanking you in advance, best wishes, Aswani -- K.Aswani Kumar Graduate Student Molecular Biophysics Unit Indian Institute of Science Bangalore-560012 Karnataka, India.

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please give advice
by Jane Norman 10 Oct '14

10 Oct '14

Hello I am new to using chimera and I have been struggling with one aspect. I'm trying to mutate one residue in my protein, by using the command swapaa leu :310, this seems to work nicely, To show the amino acid I then go in to "tools" then "sequence" and select this mutated residue and then go to "actions" then "atoms/bond" and "show" and the residue is displayed, however it is displayed as a block colour which I can't seem to change the colour scheme of the amino acid to match other residues which I've displayed nearby (e.g showing different colours (white/blue/red for different groups on the amino acid). i can easily change the block coulr of the whole reside but not to match the helpful scheme of he other displayed residues. However If I just pick an unmutated residue to display it shows it in the same style as the other residues (which is what I want for my mutated one) I hope that makes sense I couldn't find the answer in the help section Thank you very much for your time Jane

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Failed to prepare receptor for AutoDock Vina
by William McDonald 09 Oct '14

09 Oct '14

Hello Chimera users, I am attempting to learn ligand docking using autodock vina in Chimera. I am using a local copy of AutoDock Vina, and Chimera 1.9 (64 bit) for mac os 10.9.5. I have added H atoms to the ligand prior to loading the structure into Chimera. I added H atoms to the protein within Chimera. However, when I run AutpDock Vina I receive the error: ValueError: Could not find atomic number for Ha Ha failed to prepare receptor for AutoDock Vina; please look in Reply Log to see errors. I thought that this could be because of the H atoms added to CA atoms are named HA by default, however if I change the HA atom names to H, I still get the same error. I can verify that there are no atoms named "Ha" in the structure. What am I doing wrong? Thanks for your time. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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color zones with multiple markers
by Revyakin, Andrey (Dr.) 09 Oct '14

09 Oct '14

Hi Chimera folks, I am a new user of Chimera; trying to simultaneously color different features of a Cryo-EM structure (EMD-2305) with different colors. I select volume tracer and make a marker (looks like a tumour on the structure), and select color zone. The features are large, so I select another marker nearby to expand the color zone (another tumour appears next to the first tumour), but then the color zone associated with the first marker disappears and moves to the next marker. How can I preserve the previously created color zone? I seem to be unable to select multiple markers by holding ctrl and clicking/dragging-- either the whole structure is selected, or only one marker can be selected at a time. I spent an hour looking on the web for a solution, but did not find any. Windows 7, 64 bit. I apologize if this is too trivial of a question. Cheers, Andrey R.

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Energy calculation
by bobo2412＠gmail.com 09 Oct '14

09 Oct '14

Hi, Do you know if chimera can do energy calculation? I have a protein I want to mutate some residues and calculate the energy difference before and after the mutation. Do you know if I can do that in chimera? Thanks, Bobo 发自我的 iPhone

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Re: [Chimera-users] measure symmetry
by Tom Goddard 08 Oct '14

08 Oct '14

Hi Reggie, You are right that the EMDB 1220 virus capsid has none of the standard icosahedral orientations. It is approximately 3-fold axis along z, and 2-fold axis along x (Chimera orientation 2n3r) but it is maybe 5 degrees off from that. If this capsid was refined with C1 symmetry then there is no reason for it to have a standard orientation. It will be difficult to compute the icosahedral symmetry matrices. I suggest you talk to the author of that map Gabe Lander who has a lab at Scripps, right where you are located. Tom On Oct 8, 2014, at 2:07 PM, Reginald McNulty wrote: > Thanks. It works. > I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map? > Reggie > On Oct 8, 2014, at 11:34 AM, Tom Goddard wrote: > >> Hi Reggie, >> >> I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. >> >> Tom >> >> open 2xyz >> rainbow chain >> sym #0 surf true >> >> # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). >> >> shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 >> molmap #0 10 sym i,n25r >> >> >> <2xyz.jpg> >> >> On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: >> >>> Dear Tom, >>> >>> I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? >>> I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html >>> >>> All the best, >>> -Reggie >>> >>> -- >>> Reginald McNulty, Ph.D. >>> Postdoctoral Research Associate >>> The Scripps Research Institute >>> Johnson Lab >>> Department of Integrative Structural and Computational Biology >>> 10550, N. Torrey Pines Road, MB-31 >>> La Jolla, California 92037 >>> >>> >>> >>> >>> >>> >> > >

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Re: [Chimera-users] Analysis of the multiple alignments + structures
by James Starlight 08 Oct '14

08 Oct '14

Dear Chimera users! I've been interested in the possibility to make some sort of evolutional analysis in Chimera using MSA of the protein under study, its X-ray structures and its superimpositions as well as obtained projections of the sequence conservation in key (functionally-important) hot spots made by means of mutalign plugin. For my particular case I have MSA for the big number of olfactory receptors sequences (including receptors from different sub-groups associated with different specificity towards different odors). As the result I should to find possibility to sort these sequences of each ORs based on some phylogenetic study (I thinks to obtain tree-like view of the sequences) considering explicitly residues of the receptor's binding site. One of the possible idea is to keep only those residues of interest (from the ligand binding cavity) and rerun the alignment on these mini sequences to make prediction of new family of Or that may interact with the same kind of odorants. Would this idea is better realized by means of differential evolutional tracing method (because In fact we need to subtract conservative residues of one sub-branch of the whole phylogeny tree from those of all (root) OR) or there are any trivial alternatives? Thanks for help, James 2014-09-19 22:04 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: > Dear Elaine, > > thanks you very much for the suggestions! It's always a big pleasure to > get advise from the experienced person :) BTW may be the next question will > be more in connection with your present job (Chimera software developer). I > wounder whether it *in principle* possible to find an academic post-doc job > focused mainly on molecular visualization and animation (as the trivial > example os such job in my mind is to make a pictures and movies of the > proteins and it's complexes using data from different resolution's > experimental techniques and modelling). How do you think will it be easily > to obtain such job for the person who's PhD was based on structural biology > (experimentalist) or alternatively focused on molecular modeling and > bioinformatics ? > > Kind regards, > > Gleb > > 2014-09-16 23:36 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > >> Dear Gleb, >> I really don't know the answer! I've never searched for such a position >> myself. I could only guess that you would try to search for "teaching" in >> addition to the keywords about molecular modeling and structural >> bioinformatics. >> >> For postdocs at least, most people are looking for research lab positions >> rather than teaching. In that case they identify research papers that >> describe the types of work that they want to do, then contact the labs of >> the authors about possible postdoc opportunities. >> >> The only other idea I have is to try to figure out (by online searching) >> what institutions offer classes in chemistry and biology that include >> structures/modeling, then see if they have openings for instructors. >> >> I'm sorry, I don't think these are very bright ideas, or anything that >> you wouldn't have thought of yourself already. >> 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 Sep 16, 2014, at 12:09 PM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> >> > Hi Elaine, >> > >> > thank you for the suggestions again! By that time I've noticed that to >> find structural bioinformatics position is much complicated than to find >> positions in fields of theoretical biophysics, computational biology or >> even genome bioinformatics. BTW according to your experience what keywords >> might be to seek position focused rather not to the research but to make >> some teaching practice, workshops and tutorials (focused on structural >> bioinformatics and modeling)? >> > >> > Kind regards, >> > >> > Gleb >> > >> > 2014-09-10 2:52 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: >> > Glad it was useful! I don't know if there is a specific name other >> than "structural bioinformatics," but especially now that more and more >> structures are known (in combination with perhaps too many sequences!), it >> should be a fruitful and interesting area of research. >> > Best, >> > Elaine >> > >> > On Sep 6, 2014, at 12:00 AM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> > >> > > Hi Elaine, >> > > >> > > thank you very much It was really useful for me! I plan to look for >> the post-doc for myself on next year switching from the modeling and >> theoretical chemistry to structural bioinformatics coupled with the >> phylogenetic analysis (I don't know yet precise name of this discipline in >> the computational biology) so It will be very helpful! >> > > >> > > All the best, >> > > >> > > James >> > > >> > > >> > > 2014-09-05 20:59 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: >> > > HI James, >> > > Sorry, Chimera does not do evolutionary trace calculations. I would >> definitely have mentioned it if it did! In Chimera, if you input a tree >> along with your alignment, you can click a node on the tree and easily >> extract only the sequences for that node, but there is nothing to compare >> the residues from one set of sequences with those from another set of >> sequences, other than looking at the separate alignment windows yourself. >> Also, Chimera cannot create the tree, it must be read in from a file. >> > > < >> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f… >> > >> > > … see the section on Trees: >> > > < >> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m… >> > >> > > … example image of tree+alignment in Chimera: >> > > < >> http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/redoxin/ConSurf-1hd… >> > >> > > >> > > Although I’m still very interested in GPCRs, I have not actively >> worked on them for >10 years, so I’m not the best person to ask for >> current information. I know there is a GPCRdb, but I don’t know if it has >> been kept up to date. You could try googling or pubmed-searching for “gpcr >> alignments” or similar terms. >> > > >> > > Two ideas for evolutionary trace: >> > > >> > > (1) The Lichtarge group has an evolutionary trace server. >> > > <http://mammoth.bcm.tmc.edu/ETserver.html> >> > > >> > > At first I thought you could only put in a PDB ID and not have any >> control over what sequences are used (which might not be useful for your >> research), but then I noticed a “GPCRs” link on the left-hand side. Click >> that and it lets you choose specific GPCR subsets, which sounds exactly >> like the kind of calculation you wanted. I don’t know if it includes your >> specific groups of interest, however, and I don’t see a way to use your >> own alignments. >> > > <http://mammoth.bcm.tmc.edu/gpcr/diff_GPCRA.html> >> > > >> > > (2) JEvTrace, a Java implementation of evolutionary trace. >> > > <http://compbio.berkeley.edu/people/marcin/jevtrace/> >> > > >> > > I have one correction to that page. It says you can show results >> using the MSF Viewer tool in Chimera, which no longer exists. You can >> still use Chimera, just the Multalign Viewer tool instead (Multalign Viewer >> menu: "File… Load SCF/Seqsel File” will open the file from JEvTrace). I’ll >> email the author and tell him to update that information. >> > > >> > > Those are all my ideas. If neither helps you, you may have to >> continue searching for programs or other tools and instructions on how to >> do the steps of the analysis yourself. >> > > I hope this helps, >> > > 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 Sep 4, 2014, at 11:39 PM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> > > >> > > > Elaine, >> > > > >> > > > onequestion about your 2003 GPCRs study: in this paper you've used >> the method called differential evolution tracing to detect >> functionally-relevant amino acids for rhodopsin only (substration of the >> conservative residues found in rhodopsin from those found in whole set of >> A-class GPCRs). I wounder if there any possibility for this method in >> Chimera's mutalign (in case where I have big alignment with thesequences of >> all olfactory receptors) to substract residues found in one philogenetic >> branch (corresponded to specified sub-class or group of those receptors) >> from the residues common to all olfactory receptors or (ii) substract >> residues common for the all olfactory receptors from those common to all >> A-class GPCRs? BTW do you know open-access data-bases consisted of the >> evolutional (alignments) information to the GPCRs? it's intresting to >> compare my alignment with some references. >> > > > >> > > > Thanks for help, >> > > > >> > > > James >> > > >> > > >> > > _______________________________________________ >> > > Chimera-users mailing list >> > > Chimera-users(a)cgl.ucsf.edu >> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >> > >> >> >

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Chimera-users October 2014