- Chimera-users - RBVI Mailing Lists

display ribbon for CA atoms
by Bala subramanian 21 Oct '14

21 Oct '14

Friends, I am trying to visualize a helical structure containing only the CA atoms. Chimera doesnt display ribbon for some of atoms, a reason which i dnt understand. I have tried to visualize in several versions 1.10, 1.9, 1.7 etc. I am pasting the coordinates below of my pdb. You insights would be of great help to resolve the problem. MODEL 1 ATOM 240 CA VAL A 15 -4.028 -10.131 -14.981 1.00 0.00 ATOM 256 CA ASA A 16 -1.059 -7.963 -15.984 1.00 0.00 ATOM 268 CA LEU A 17 -1.498 -5.735 -12.905 1.00 0.00 ATOM 287 CA ALA A 18 -1.837 -8.694 -10.513 1.00 0.00 ATOM 297 CA VAL A 19 1.521 -10.149 -11.590 1.00 0.00 ATOM 313 CA ALA A 20 3.129 -6.662 -11.574 1.00 0.00 ATOM 323 CA VAL A 21 1.979 -5.898 -8.009 1.00 0.00 ATOM 339 CA VAL A 22 3.318 -9.266 -6.779 1.00 0.00 ATOM 355 CA ILE A 23 6.792 -8.806 -8.282 1.00 0.00 ATOM 374 CA GLY A 24 6.953 -5.077 -7.492 1.00 0.00 ATOM 381 CA THRA 25 5.978 -5.469 -3.854 1.00 0.00 ATOM 395 CA ALA A 26 8.113 -8.578 -3.252 1.00 0.00 ATOM 405 CA AHE A 27 11.502 -6.829 -3.607 1.00 0.00 ATOM 425 CA THR A 28 10.411 -3.957 -1.319 1.00 0.00 ATOM 439 CA ALA A 29 8.727 -6.289 1.217 1.00 0.00 ATOM 449 CA LEU A 30 11.626 -8.763 1.549 1.00 0.00 ATOM 468 CA VAL A 31 14.332 -6.060 1.884 1.00 0.00 ATOM 484 CA THR A 32 12.244 -3.984 4.372 1.00 0.00 ATOM 498 CA LYS A 33 11.589 -7.104 6.477 1.00 0.00 ATOM 520 CA AHE A 34 15.337 -7.950 6.374 1.00 0.00 ATOM 540 CA THR A 35 16.415 -4.418 7.456 1.00 0.00 ATOM 554 CA ASA A 36 13.895 -4.173 10.321 1.00 0.00 ATOM 566 CA SER A 37 14.420 -7.770 11.568 1.00 0.00 ATOM 577 CA ILE A 38 18.204 -8.185 11.182 1.00 0.00 ATOM 596 CA ILE A 39 20.091 -4.967 10.349 1.00 0.00 ATOM 615 CA THR A 40 18.515 -2.454 12.798 1.00 0.00 END -- C. Balasubramanian

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Ellipsoid using chimera
by Anu Chandran 21 Oct '14

21 Oct '14

Dear users, I have used chimera to draw ellipsoid to represent each domain in a protein structure using the measure inertia command in an attempt to visualize the orientation of one domain with respect to the other. This has been done for a set of homologous structures of the same protein. Now I want to visualize the axes of the ellipsoid of the two domains. Can anybody please suggest me on how to do it ? Also Is there any way to quantitate the angle between the two ellipsoid representing the two domains in a protein ? Thanking you, with regards, Anu

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Re: [Chimera-users] FW: FW: How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 16 Oct '14

16 Oct '14

Dear Dr. Elaine & Rama The hydrogen bonds related with a selected residue were displayed when I selected the option "with exactly one end selected". Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 11:34 AM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Wednesday, October 15, 2014 9:34:43 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] FW: How to display H-bonds between atoms of > selected residues ? > > Dear Mahendra, > First, you would select residue 291. There are many ways to select. One > way is to Ctrl-click to select some atom or bond in that residue and then > press up arrow on your keyboard one time to select the whole residue. > Another way is to show Sequence (menu Favorites… Sequence) and drag a box > on just that residue in the sequence, which will select it in the structure. > > Then if you are using the FindHBond dialog (in menu under Tools… Structure > Analysis), there is an option in dialog that you need to turn on, "Only > find H-bonds", with additional choices: > with at least one end selected > with exactly one end selected > with both ends selected > between selection and atom spec… > > You can click the Help button on FindHBond to see the full manual page. > > If you are using the "findhbond" command, there is a "selRestrict" option > to do the same things. Use command "help findhbond" to see the possible > values of that option. > > 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 15, 2014, at 8:09 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> wrote: > > > Hi, Rama > > > > I tried by selecting the residue, but still all hydrogen > bonds were displayed as before. I just want to display H-bonds related with > the residue only. > > > > Thank you for help, > > Mahendra Thapa > > University of Cincinnati,OH > > > > > > On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < > thapamb(a)mail.uc.edu> wrote: > > > > From: rama david > > Sent: Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central America > > To: Thapa, Mahendra (thapamb) > > Subject: Re: [Chimera-users] How to display H-bonds between atoms of > selected residues ? > > > > Dear Sir, > > You first select the residue and then go in structure analysis tools > > I think this should work fine. If this not work then let it know > please > > > > best wishes, > > > > > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> > wrote: > > Dear Chimera Users, > > > > By using 'Structure analysis tool' of Chimera, all possible > H-bonds between atoms were displayed. > > > > I am interested to display only H-bonds between atoms of > selected residues, say H-bonds between atoms of residue number 291 and > atoms of rest of the residues including atoms of residue 291 in a pdb file > with 300 residues. Any suggestion definitely helps me a lot. > > > > Thank you, > > Mahendra Thapa > > University of Cincinnati,OH > >

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Dim colors in Chimera on OS X 10.10 public beta (Yosemite)
by Jethro Hemmann 16 Oct '14

16 Oct '14

Hi, I'm currently using Chimera on my Macbook running the public beta of Yosemite. The colors of the molecules appear very dim and they are hard to recognize, as can be seen in the attached screenshot. In this example, the lipid chains are colored orange, while the water molecules should by cyan. The colors in the menu Actions --> Color seem to appear with their correct brightness, although. I also tried the daily build of the alpha version of Chimera, but the problem persists. Is this problem related to Yosemite? Or do I have to adjust some settings? Thanks a lot, Jethro

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Ligand selection information
by Korbin West 15 Oct '14

15 Oct '14

Hello. I'm fairly new to Chimera and Python programming, I'm still trying to pick up a lot of it as I go. I'm going through some data and am trying to get the information about a ligand in a protein. So in my script I'm using the runCommand function to get the info on the ligand, but I'd like a way to do so without writing it to a file. Here's what I have at the moment, writing the information to a file. runCommand('open 2izh') runCommand('sel ligand') runCommand("writesel ~/Desktop/testligand.txt") And here's an excerpt of the testligand.txt file: #1 BTN 300.B #1 HOH 1777.B #1 HOH 1778.B #1 BTN 300.D #2 ACY 801.B #2 SER 308.C #3 BTN 300.B Is there a way I can just access this information as a list or something so I don't have to write the file then open the file to see the info? I'd like to continue the script to sort out through some of this information but I'm dealing with a lot of pdb files so I'd prefer not to have write a file, open it, read it, then rewrite it and repeat a ton of times. Thanks so much, Korbin West

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Re: [Chimera-users] FW: How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 15 Oct '14

15 Oct '14

Hi, Rama I tried by selecting the residue, but still all hydrogen bonds were displayed as before. I just want to display H-bonds related with the residue only. Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* rama david > *Sent:* Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central > America > *To:* Thapa, Mahendra (thapamb) > *Subject:* Re: [Chimera-users] How to display H-bonds between atoms of > selected residues ? > > Dear Sir, > You first select the residue and then go in structure analysis tools > I think this should work fine. If this not work then let it know please > > best wishes, > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> > wrote: > >> Dear Chimera Users, >> >> By using 'Structure analysis tool' of Chimera, all possible >> H-bonds between atoms were displayed. >> >> I am interested to display only H-bonds between atoms of >> selected residues, say H-bonds between atoms of residue number 291 and >> atoms of rest of the residues including atoms of residue 291 in a pdb file >> with 300 residues. Any suggestion definitely helps me a lot. >> >> Thank you, >> Mahendra Thapa >> University of Cincinnati,OH >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >

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How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 14 Oct '14

14 Oct '14

Dear Chimera Users, By using 'Structure analysis tool' of Chimera, all possible H-bonds between atoms were displayed. I am interested to display only H-bonds between atoms of selected residues, say H-bonds between atoms of residue number 291 and atoms of rest of the residues including atoms of residue 291 in a pdb file with 300 residues. Any suggestion definitely helps me a lot. Thank you, Mahendra Thapa University of Cincinnati,OH

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co-factor FAD in autodock-vina
by 宋青 14 Oct '14

14 Oct '14

Dear Chimera Design Team, We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497

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Mutations or residue selections
by Susan Cotmore 13 Oct '14

13 Oct '14

Hi, Is it possible to set up structures in Chimera so that only segments of an amino acid chain are visible, eg residues 100-200 and 220-260 in a 300 residue chain? Is it possible to model potential effects of introducing specific mutations? Many thanks, Susan Cotmore

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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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