May 2012 - Chimera-users - RBVI Mailing Lists

water around protein
by Bala subramanian 25 May '12

25 May '12

Friends, I guess when i select no. of water as "sel ::WAT & protein z<3", i the distance of water is chosen as distance from atom protein atom centres. Instead i want to calculate no. of water around the protein Vdw surface with same distance value. Any idea would be of great help. Thanks, Bala

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Re: [Chimera-users] Chimera-users Digest, Vol 109, Issue 28
by Boaz Shaanan 24 May '12

24 May '12

Hi, In answer to Nikolay's question about ESP values in various positions: 1) Elaine is absolutely right in pointing you to the APBS bb. If you look in their FAQ you'll notice that the question has been addressed several times. 2) There is an 'atompot' command that you can use when you run apbs. It'll print the values for each atom in the pdb, the only problem is that last time I tried it there were no atom names in output which was difficult for me (apbs team were supposed to add that feature) but x,y.z were there. 3) If atompot is not what you need somebody in the abps team will surely help you. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Thursday, May 24, 2012 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 109, Issue 28 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. Fwd: ESP calculations (Eric Pettersen) 2. APBS output format (Elaine Meng) 3. Hydrogen bond energy calculation (Aditya Padhi) 4. Re: Hydrogen bond energy calculation (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 23 May 2012 13:18:14 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Fwd: ESP calculations Message-ID: <4C557064-D2EC-45A5-9523-B35E683C76D5(a)cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii"; Format="flowed"; DelSp="yes" Begin forwarded message: > From: Nikolay Igorovich Rodionov <nirodion(a)syr.edu> > Date: May 21, 2012 12:43:34 PM PDT > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] ESP calculations > > Thank you both, > > Can either of you tell me how the information in a volume data set > is organized? I am looking at a .dx file that I created using APBS > which I would assume to be very similar to the volumetric data sets > created by Chimera. What does each column of data represent? Is > there any way for me to sort the ESP data based on position using > Excel or Matlab? I am only concerned with ESP data for one region of > molecule. If you could point me in the direction of some good > documentation on this file type it would be great. I don't know, so I'm forwarding this out to chimera-users land, where someone might have an answer... --Eric > > Thanks again, > Nikolay Rodionov > > -----Original Message----- > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Monday, May 21, 2012 2:57 PM > To: chimera-users(a)cgl.ucsf.edu BB > Cc: Nikolay Igorovich Rodionov > Subject: Re: [Chimera-users] ESP calculations > > Also, if you compute a volume, you can use the "Values at Atom > Positions" tool to, um, get the values at atom positions (say, a > ligand), if that's relevant to what you're doing. > > --Eric > > On May 21, 2012, at 9:09 AM, Elaine Meng wrote: > >> Hi Nikolay, >> You can generate a grid of values with the "Compute grid" option of >> Coulombic Surface Coloring (or corresponding option of the >> "coulombic" >> command). The grid is a volume data set, and when it is generated >> the >> Volume Viewer and Surface Color dialogs will automatically appear. >> >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/ >> co >> ulombic.html >>> >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/ >> co >> ulombic.html#volume >>> >> >> You can save the grid to a file with the FIle menu of Volume Viewer. >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ >> volumeviewer >> /framevolumeviewer.html >>> >> >> As for the values at each point of the surface, I don't know of a way >> to write these all to a file, but in Surface Color if you click the >> Options button and then turn on the option to "Report value at mouse >> position" it will report the values in the status line at the bottom >> of the Chimera window when you click into the graphics window and >> then >> mouse over the surface. I just noticed that to make this work it is >> necessary to recolor the surface first by clicking the Color button >> on >> this dialog, which may be a bug, but that's the workaround! >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ >> su >> rfcolor.html >>> >> >> If you have the grid file saved you can reopen it in Chimera later >> and >> use it in Surface Color without rerunning the ESP calculation. >> >> However, keep in mind that Coulombic ESP is more for qualitative >> purposes of visualization or making comparisons between related >> structures than for absolute quantitative accuracy. For example, you >> could easily make all the ESP values half as large simply by doubling >> the dielectric constant used in their calculation, as shown in the >> equation in the Coulombic Surface Coloring manual page. >> >> 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 May 21, 2012, at 8:05 AM, Nikolay Igorovich Rodionov wrote: >> >>> Hi all, >>> I was wondering if there was a way to get an output data file >>> regarding ESP coloring and calculations based on Coulomb's law. The >>> visualization is great but I would also like to quantify the data. >>> Thank you, >>> Nikolay Rodionov >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > >

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Hydrogen bond energy calculation
by Aditya Padhi 24 May '12

24 May '12

Dear Chimera users, I want to calculate the "energy or force" exerted between amino acid residues interacted by Hydrogen bonds throughout a total trajectory from MD simulation of a protein performed using Amber 10. (Example: H-bond between Isoleucine17-Asp15, Asp15-Ile46, Ile46-His13 etc, I want to calculate the H-bond interaction energy between these pair of residues and hence the net energy). I searched in the tutorials and literature but could not able to find any appropriate solutions. If anyone has the idea, please assist me finding the solution of this problem. Thanking you, Regards Aditya.

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How to change the style of Hbonds
by Wendy Chu 21 May '12

21 May '12

Hello all, I am doing the Hbond analysis for my investigation. I found that the Hbonds are labeled as the solid line in the Chimera. But I prefer the dashed line. How to change it? Thank you~~~ -- Wen-Ting Chu State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China

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In Silico Compound Library Search
by Nancy 20 May '12

20 May '12

Hi All, Does anyone know of a free cheminformatic service from which it's possible to narrow down a search for molecules by inputting limits on their molecular parameters, such as molecular weight or the number of hydrogen bond donors, etc? Such a resource would be of great help. Thanks in advance, Nancy

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How to place a metal ion in protein model
by Suneel N.A. 18 May '12

18 May '12

Hi Its my pleasure to introduce myself, I am Suneel, graduate student from India. I am not a bioinformatician by profession but a eager aspirant of learning bioinformatics. I am new to Chimera, but as I started using it, the desire for leraning Bioinformatics increased more and more. Chimera is such an awesome tool packed with so many options. I love it . I have small question for you. I have a predicted the structure of protein using in silico tools (based on homology modeling). Literature sates that this protein binds to Magnesium. Now I would like to know if I can use chimera to place the metal in the modeled structure and prove/validate it based on metal geometry. Please do the needful. Thanking you in anticipation yours sincerely suneel -- *Suneel Narayanavari. A* Graduate Student Prof. Manjula Sritharan's Laboratory of Infection Biology Department of Animal Sciences School of Life Sciences University of Hyderabad Hyderabad-46

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Minimize Structure While keeping charges
by Michael Tomasini 18 May '12

18 May '12

Hello, I was wondering if there was a way to read in charges from a .mol2 file in order to use those charges in the minimize structure utility. By default, it seems that minimize structure adds charges which can be a rather time-consuming step. If I already have the charges in a .mol2 file, can these charges simply be used for the minimization? Thanks, Mike

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Re: [Chimera-users] [Dock-fans] cofactors in dock
by Scott Brozell 17 May '12

17 May '12

Hi, On Wed, May 16, 2012 at 03:22:11PM +0530, Mary Varughese wrote: > I have to include the cofactor GTP as part of my receptor protein and dock > with a ligand. But chimera is not allowing to prepare rec_charged.mol2 file > since it fails at finding amibcc charge method for GTP residue. Then i > separately prepared the mol2 file for GTP (using gtp.prep and gtp.frcmod) > and after performing dockprep on the receptor i opened the GTP.mol2 file in > the same window and write the mol2 file. but again at grid generation it > fails "Reading in coordinates of receptor. > WARNING assign_vdw_labels: Atom valence violated for 1SA0.pdb (combined) > **** GTP 848 C8 13145. > Error reading in receptor." Which version of chimera are you using ? There was some recent activity for GTP but using Gasteiger charges: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-October/006846.html Are you saying that you ran antechamber separately from chimera and got the am1bcc charges for gtp ? scott

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PDB column overlap --PDB2PQR,APBS
by Nikolay Igorovich Rodionov 17 May '12

17 May '12

Hi all, I am trying do Poisson-Boltzmann calculations through outside software, PDB2PQR and APBS. I am prepare my initial pdb file in chimera using the 'write pdb' method. The final structure is quite large, 737058 atoms, so I am getting overlaps in the data columns after I write the PDB file. This doesn't create a problem for rendering the PDB file but I get parsing errors and other strange occurrences when I try to create a complementary PQR file. Does anyone know of a work around? Here are links to my structures, if you look you will see that a significant portion of the structure is getting cut off in the PQR. I can't seem to generate more than about 99760 atoms, no matter what I try. http://dl.dropbox.com/u/42179401/2TMV.18H.pdb http://dl.dropbox.com/u/42179401/2TMV.18Ha.pqr Can anyone think of a potential fix? I've experienced this same problem with smaller helix pdb files. Thank you, Nikolay Rodionov

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improved movie tools
by Martin de Jonge 16 May '12

16 May '12

Hi, I recently published a tomographic reconstruction that was rendered using Chimera (see: http://www.pnas.org/content/107/36/15676.abstract) The movie that we were able to build using Chimera was excellent, but had to be recorded entirely in real time. That is, we had to turn on recording, manipulate the model, and turn off recording. I feel that it would be much easier if there was a nice interface to sequencing functionality. In this (as I imagine it) a sequence of particular views could be stored, and times specified for smooth transition from one element in the sequence ('view') to the next. These views could even be stored as saved sessions (if that helps with implementation). Please let me know if this functionality is already possible and (if so) please send me a sample! I note that my licence has expired; but when I try to renew it I run into problems with the server. Looking forward to your reply, Martin de Jonge Senior Scientist - XFM Australian Synchrotron p: (03) 8540 4195 | f: (03) 8540 4200 | m: 0488 338 594 800 Blackburn Road, Clayton, Victoria 3168 <br>This message and any attachments may contain proprietary or confidential information. If you are not the intended recipient or you received the message in error, you must not use, copy or distribute the message. Please notify the sender immediately and destroy the original message. Thank you.

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