October 2014 - Chimera-users - RBVI Mailing Lists

question
by JESSE JAYNES 22 Oct '14

22 Oct '14

Folks: I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse

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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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