April 2011 - Chimera-users - RBVI Mailing Lists

trying to add charges
by Irene Newhouse 28 Apr '11

28 Apr '11

I'd like to do a PDB2PQR run of my protein with its 'ligands' - actually substrates & am having problems getting the server to recognize my mol2 file. So I thought I'd use chimera to add charges & write, hopefully, a compatible mol2 file. I'm having problems with that as well. This is a pdb of the ligands:HETATM 8225 MG MG A 291 25.874 25.146 58.617 1.00 0.00 Mg2+ HETATM 8226 C4 FPS A 292 25.754 19.949 62.737 1.00 0.00 C HETATM 8227 C3 FPS A 292 26.088 21.273 63.475 1.00 0.00 C HETATM 8228 C2 FPS A 292 26.021 22.571 63.132 1.00 0.00 C HETATM 8229 C1 FPS A 292 25.656 23.447 61.998 1.00 0.00 C HETATM 8230 S1 FPS A 292 27.204 24.181 62.219 1.00 0.00 S HETATM 8231 P1 FPS A 292 27.928 23.762 60.771 1.00 0.00 P HETATM 8232 O1 FPS A 292 28.873 24.955 60.385 1.00 0.00 O HETATM 8233 P2 FPS A 292 28.554 26.180 59.405 1.00 0.00 P HETATM 8234 O2 FPS A 292 28.206 25.713 57.968 1.00 0.00 O HETATM 8235 O3 FPS A 292 27.331 26.943 59.830 1.00 0.00 O HETATM 8236 O4 FPS A 292 29.622 27.136 59.149 1.00 0.00 O HETATM 8237 O5 FPS A 292 26.862 23.528 59.683 1.00 0.00 O HETATM 8238 O6 FPS A 292 28.976 22.661 61.190 1.00 0.00 O HETATM 8239 C5 FPS A 292 26.754 21.192 64.778 1.00 0.00 C HETATM 8240 C6 FPS A 292 26.118 20.990 66.155 1.00 0.00 C HETATM 8241 C7 FPS A 292 27.084 20.015 66.840 1.00 0.00 C HETATM 8242 C8 FPS A 292 28.144 20.342 67.618 1.00 0.00 C HETATM 8243 C9 FPS A 292 28.586 21.777 67.991 1.00 0.00 C HETATM 8244 C10 FPS A 292 28.618 19.212 68.506 1.00 0.00 C HETATM 8245 C11 FPS A 292 27.622 19.162 69.634 1.00 0.00 C HETATM 8246 C12 FPS A 292 27.899 18.054 70.615 1.00 0.00 C HETATM 8247 C13 FPS A 292 28.127 18.187 71.942 1.00 0.00 C HETATM 8248 C14 FPS A 292 28.131 19.492 72.723 1.00 0.00 C HETATM 8249 C15 FPS A 292 28.358 16.835 72.549 1.00 0.00 C HETATM 8250 H4 FPS A 292 24.677 19.881 62.580 1.00 0.00 H HETATM 8251 H5 FPS A 292 26.263 19.931 61.773 1.00 0.00 H HETATM 8252 H1 FPS A 292 25.472 22.838 61.113 1.00 0.00 H HETATM 8253 H11 FPS A 292 24.694 24.092 62.300 1.00 0.00 H HETATM 8254 H14 FPS A 292 28.310 18.659 67.618 1.00 0.00 H HETATM 8255 H15 FPS A 292 29.626 18.910 68.790 1.00 0.00 H HETATM 8256 H141 FPS A 292 28.344 19.287 73.772 1.00 0.00 H HETATM 8257 H142 FPS A 292 28.897 20.155 72.320 1.00 0.00 H HETATM 8258 H143 FPS A 292 27.155 19.970 72.638 1.00 0.00 H HETATM 8259 H91 FPS A 292 29.470 21.732 68.628 1.00 0.00 H HETATM 8260 H92 FPS A 292 28.821 22.333 67.083 1.00 0.00 H HETATM 8261 H93 FPS A 292 27.779 22.279 68.525 1.00 0.00 H HETATM 8262 H7 FPS A 292 26.852 18.977 66.652 1.00 0.00 H HETATM 8263 H61 FPS A 292 26.054 21.948 66.670 1.00 0.00 H HETATM 8264 H62 FPS A 292 25.117 20.575 66.036 1.00 0.00 H HETATM 8265 H51 FPS A 292 27.451 20.354 64.779 1.00 0.00 H HETATM 8266 H52 FPS A 292 27.298 22.117 64.967 1.00 0.00 H HETATM 8267 H4 FPS A 292 26.087 19.103 63.338 1.00 0.00 H HETATM 8268 H12 FPS A 292 27.905 17.074 70.162 1.00 0.00 H HETATM 8269 H151 FPS A 292 28.547 16.946 73.646 1.00 0.00 H HETATM 8270 H152 FPS A 292 27.455 16.195 72.388 1.00 0.00 H HETATM 8271 H153 FPS A 292 29.246 16.355 72.064 1.00 0.00 H HETATM 8272 H111 FPS A 292 27.646 20.103 70.183 1.00 0.00 H HETATM 8273 H112 FPS A 292 26.622 19.003 69.230 1.00 0.00 H HETATM 8274 H2 FPS A 292 26.305 23.333 63.843 1.00 0.00 H HETATM 8348 O3 IPE A 586 21.257 22.023 59.139 1.00 0.00 O HETATM 8349 C1 IPE A 586 21.725 22.610 60.331 1.00 0.00 C HETATM 8350 C2 IPE A 586 21.891 21.539 61.401 1.00 0.00 C HETATM 8351 C3 IPE A 586 22.135 21.746 62.732 1.00 0.00 C HETATM 8352 C4 IPE A 586 22.476 23.125 63.351 1.00 0.00 C HETATM 8353 C5 IPE A 586 22.090 20.534 63.651 1.00 0.00 C HETATM 8354 P1 IPE A 586 22.541 22.279 58.101 1.00 0.00 P HETATM 8355 O1 IPE A 586 23.289 23.718 58.505 1.00 0.00 O HETATM 8356 O2 IPE A 586 23.635 21.031 58.224 1.00 0.00 O HETATM 8357 O7 IPE A 586 21.980 22.381 56.596 1.00 0.00 O HETATM 8358 P2 IPE A 586 22.517 20.944 55.933 1.00 0.00 P HETATM 8359 O4 IPE A 586 24.120 21.122 55.494 1.00 0.00 O HETATM 8360 O5 IPE A 586 22.398 19.740 57.082 1.00 0.00 O HETATM 8361 O6 IPE A 586 21.597 20.552 54.601 1.00 0.00 O HETATM 8362 H6 IPE A 586 20.970 20.939 61.359 1.00 0.00 H HETATM 8363 H7 IPE A 586 22.711 20.896 61.047 1.00 0.00 H HETATM 8364 H4 IPE A 586 22.660 23.213 64.432 1.00 0.00 H HETATM 8365 H5 IPE A 586 22.534 24.017 62.710 1.00 0.00 H HETATM 8366 H1 IPE A 586 21.090 20.076 63.606 1.00 0.00 H HETATM 8367 H2 IPE A 586 22.843 19.801 63.329 1.00 0.00 H HETATM 8368 H3 IPE A 586 22.303 20.848 64.684 1.00 0.00 H HETATM 8369 H11 IPE A 586 22.687 23.089 60.148 1.00 0.00 H HETATM 8370 H12 IPE A 586 21.008 23.356 60.675 1.00 0.00 H END When I try to add charges, chimera chews on it for a bit, then gives me a message that amber has stopped running, check the log file. When I click on the log file, the only message is that I've had a crash. In the older version of chimera I was running, I also tried this with only the IPE & got the same behavior. Are my compounds just too nonstandard? Thanks! Irene Newhouse

2 6

3D labels
by matheus froeyen 26 Apr '11

26 Apr '11

Dear all, I try to change the size of the 3D labels in my structure via the preferences/background menu but there is no effect! Strange but changing the font type & bold, italic etc works. I tried a previous version of chimera and there I have the same problem. The font is always small (about 12?) The 2D labels I can change font size without problem. But I know it has worked before. I have no idea what is going on. I work on A Macintosh G5 with Leopard. Thanks for any suggestions mathy

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labels
by Jean-Paul Armache 26 Apr '11

26 Apr '11

hello, i was wondering, whether there is a way to make the 2d labels appear slowly, stepwise (meaning, through some rounds of opacity to the normal text) ? best regards, jean-paul

2 2

how to make simmetric dimer
by Francesco Biagi 26 Apr '11

26 Apr '11

Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results.I would like to know if there is a method or a script that can help me. Thanks to all.Francesco

2 3

PDB reference frame
by Roberto Kopke Salinas 25 Apr '11

25 Apr '11

Dear All, Is there a way to draw and visualize the three axes of the PDB reference frame in Chimera? Thank you for your help, Roberto

2 2

Re: [Chimera-users] Changing charge of protein
by Elaine Meng 22 Apr '11

22 Apr '11

Dear Monisha, If you get a Chimera daily build (version 1.6, whereas you probably have 1.5), there will be AddH options for all those residue types I mentioned. The options in AddH are for the side chains. The N-terminus of the backbone will already get a +1 charge, and the C-terminus -1. If the backbone N is not the N-terminus, it is in an amide group and will not be formally charged. However... There is a limit as to what total charge is reasonable for a given protein sequence. If you just arbitrarily increase positive charges everywhere to try to reach some value (why??), it will become less representative of reality. Another approach you might consider if you are trying to make your "system" more neutral is to add counterions (see Tools... Structure Editing... Add Ions). 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 Apr 22, 2011, at 11:47 AM, Monisha Hajra wrote: > Dear Elaine, > > Thank you for your reply. > > However I find in AddH option, its only Histidine specific, what should I do if I want to alter specific protonation state of Lys, Arg. > > Also, read from the link that you had send is that > "lysine positive or neutral > • charges for the neutral LYN residue are assigned if the atom named NZ has atom type N3 and thus two attached hydrogens rather than three" > Is that mean that I can't create +2 charge for Lys, by adding another H to N (which is attached to alpha C)? > > I tried even by command line " addh #0: 34@N", its showing error, though chain #0: 34@N is showing the N atom. > > Kindly provide some solution. Right now charge of my protein is -22, I have to bring it up to +10. Really appreciate on general comment of yours on how do do that? > > Regards > Monisha > > On Fri, Apr 22, 2011 at 9:38 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Dear Monisha, > The charge of the protein is the sum of the charges of its residues, but charges are not saved in PDB format. > > Maybe you mean you want to control the protonation state and thus the formal charges of certain residues (for example, specifying which histidines should be positive and which should be neutral)? That can be done when you are adding hydrogens. In the AddH tool (under Tools... Structure Editing) there is "Protonation states for" setting for controlling protonation states of histidine, glutamic acid, aspartic acid, lysine, and cysteine residues. You would have to decide yourself which residues should be in which states. You could indicate that by editing the input PDB file to contain special residue names, or just choose "specified individually" for it to go through and ask you about each one. Details: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> > > Then, you could save the PDB file including the hydrogens using "File... Save PDB" in the Chimera menu. > > Charges are a somewhat separate matter, and are not saved in PDB files. There would not be any charge assignments until after you used Add Charge (under Tools... Structure Editing). Then, you could see the atom and residue charges in histograms in Render by Attribute, or save them to a file using that tool. If you really meant you wanted to assign specific charges to specific atoms yourself, you could do that with Define Attribute or the command setattr. You can label atoms with their charges as described here > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharg…> > but we don't have that for whole residues. > > 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 Apr 22, 2011, at 5:20 AM, Monisha Hajra wrote: > > > Dear User, > > Is there any way to increase or decrease total charge of the protein in Chimera? Can I see the residue wise (not atom wise) charge and modify, and should be able to save the modified protein in pdb. Trying to look to add charge / "render by attribute" section, but didn't get much help. > > Any help will really be appreciated. > > Regards > > Monisha > >

1 0

Why sym # group h did't work
by Fang, Shunming (NIH/NIDDK) [C] 22 Apr '11

22 Apr '11

Hello, There, I tried several time to use the commend sym #1(or 2,3..), group h, 11.75, 101.32 to my em map, it always show errors saying unknown keyword 11.75, 101.32? Please help me, Thanks Shunming

2 1

Changing charge of protein
by Monisha Hajra 22 Apr '11

22 Apr '11

Dear User, Is there any way to increase or decrease total charge of the protein in Chimera? Can I see the residue wise (not atom wise) charge and modify, and should be able to save the modified protein in pdb. Trying to look to add charge / "render by attribute" section, but didn't get much help. Any help will really be appreciated. Regards Monisha

2 1

Command line
by Ryan Doherty 21 Apr '11

21 Apr '11

I searched the online documents and was unable to find out how to perform certain actions via the command line. Can you let me know how to perform the following commands via the command line: Color secondary structure (and set color for Helix, Strand & Coil) Create a text file with a summary of attributes (ie. # of ions, # of ligands, # of chains, areaSAS for each selected residue) Color surface based on hydrophobicity Thanks! Ryan

3 2

help with command line selections
by Corey Fugate 21 Apr '11

21 Apr '11

I'm having a hard time figuring out how to select secondary structural elements from the command line. Can someone help me with this? Corey

2 2

Chimera-users April 2011