- Chimera-users - RBVI Mailing Lists

index out of range
by Francesco Pietra 06 Jun '12

06 Jun '12

Running movie for prmtop/dcd proved extremely slow at amd64, finally showing the protein in a water box, albeit offering very limited analysis. Error message: index out of range, error processing "monitor changes". The log is 16MB!, below the startr and end of the log: MDTools 1.2 Exp (2005-08-20) by James Phillips. Trajectory.DCD.MDToolsMarch97.md.help() for more info. HomoCoord 1.3 Exp (2005-08-20) - Constants 1.1 Exp (2004-05-17) - AtomGroup 1.4 Exp (2007-02-07) - local 1.1 Exp (2004-05-17) Unknown OSTYPE ??? set. Viewing and plotting are disabled. - Trans 1.2 Exp (2005-08-20) - DCD 1.10 Exp (2007-02-07) - Data 1.2 Exp (2005-08-20) using memory mapping REMARKS FILENAME=./heat-01.dcd CREATED BY NAMD REMARKS DATE: 06/03/12 CREATED BY USER: francesco Model 0 (heat-01.dcd) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Traceback (most recent call last): File "/usr/local/chimera_Nov3.2011/share/chimera/triggerSet.py", line 83, in invoke self._funcData, triggerData) File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line 1161, in _cacheCheck if len(kids) == molecule.rootForAtom(kids[0], IndexError: list index out of range Error processing trigger "monitor changes": .................................... .................................... Traceback (most recent call last): File "/usr/local/chimera_Nov3.2011/share/chimera/triggerSet.py", line 83, in invoke self._funcData, triggerData) File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line 1161, in _cacheCheck if len(kids) == molecule.rootForAtom(kids[0], IndexError: list index out of range Error processing trigger "monitor changes": IndexError: list index out of range File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line 1161, in _cacheCheck if len(kids) == molecule.rootForAtom(kids[0], See reply log for Python traceback. Thanks for the attention francesco pietra

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transparency for surface in intersurf
by Jean-Didier Maréchal 06 Jun '12

06 Jun '12

Hi guys, is there a way to change the transparency of intersurf objects? I'd like to have the surface not hiden all the object in behing one given view. thanks a lot, cheers jd Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

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fitmap
by Hernando J Sosa 05 Jun '12

05 Jun '12

HI, What is the correct syntax to run the fitmap command?. I have a pdb structure named C1 and a density map (spider format) named MV (names as appear in the Model panel). If I try in the command line: fitmap C1 MV I get the error: fitmap invalid volume argument "MV" What am I doing wrong? Thanks

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Fwd: ESP calculations
by Eric Pettersen 05 Jun '12

05 Jun '12

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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ESP calculations
by Nikolay Igorovich Rodionov 05 Jun '12

05 Jun '12

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

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Question about animated Ramachandran plot
by Trina Manalo 04 Jun '12

04 Jun '12

Hello, I would like to create an animated Ramachandran plot using an MD trajectory. One approach I've considered is using a per-frame script to save Ramachandran plot images (i.e., using the model panel, its possible to create a plot and then save the image as a png) Is there a way to do this using commands? Or is there an easier way to animate a plot of phi and psi angles over time? Thank you very much, Trina

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triggering events when findhbond finds a bond
by Anne Bowen 04 Jun '12

04 Jun '12

Hi, I currently have a "Per-Frame Command" set up (in the MD Movie dialog) that finds the H bonds (findhbond makePseudobonds true lineWidth 2.0 color green intramodel true intermodel false selRestrict any) every frame of a trajectory. Whenever a hbond is detected, I would like to turn the entire structure a different color just for that frame, and then have it go back to being colored by heteroatom. Is there an easy way to accomplish this? I tried to look through the documentation to determine if "findhbond" could return true or false if an h bond was found and it did not seem like it was possible. Is the only way to do this to change the findhbond script itself? Any help or suggestions is greatly appreciated! Thank you, Anne

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bond transparency as a function of length?
by Kersey Black 04 Jun '12

04 Jun '12

Hi, Very recent to Chimera. Trying to set the transparency of a bond to be a function of bond length in each frame of a trajectory. I have figured out how to define a transparent color, and now I am imaging the solution might use something like range color to vary the blending of the opaque version of the color and the fully transparent version based on distance, with the distance being determined as a per frame attribute of those atoms, but someplace around here I am lost. Any hints, links or suggestions would be very much appreciated. Cheers, KB

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Re: [Chimera-users] [chimera-dev] Rotating about an axis with mouse
by Elaine Meng 04 Jun '12

04 Jun '12

Hi Patrick, If I understand correctly, you can do what you want with "Constrained Move" (in menu under Tools... Movement): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/constrained/constr…> (The purpose of "Movement Mouse Mode" is different, mainly to allow moving subparts of a model. By default, mouse manipulation moves whole models.) You can also specify center and axis of rotation if using commands (turn, roll). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.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 Jun 4, 2012, at 6:28 AM, ladam wrote: > Hi all, > I have a python script that allows me to rotate a residue in a molecule > of a desired angle around a predefined vector. > Now I'd like to be able to do this graphically with the mouse on a selected > residue. > I have almost found what I want if I use the 'Move selection' option in the > 'Movement Mouse mode' but this does rotate around the center of Mass or > geometric center, not around a vector. > What I plan to do is derive the code from the corresponding /share/MoveSelection/move.py > module and try to insert a vector instead of the center_of_rotation(self.movable_groups) > but there is maybe a better, simpler idea. > Any suggestion? > Thanks a lot > -------------------------------- > Patrick Ladam > Maître de Conférence > Université Paris 13 - UFR SMBH > CSPBAT - Service RMN > 74, rue Marcel Cachin > 93017 Bobigny Cedex > Tel: 01 48 38 73 25 > Fax: 01 48 38 77 77 > mail: ladam(a)smbh.univ-paris13.fr > -------------------------------

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make selection disappear smoothly
by Thomas Evangelidis 01 Jun '12

01 Jun '12

Dear Chimera developers, Simple question: is there any way to make a selection disappear smoothly during a movie? Thanks, Thomas

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copy & paste multiple commands
by Thomas Evangelidis 01 Jun '12

01 Jun '12

Dear Chimera developers, This is an elementary question, but after searching a while in the mailing list and the documentation, I couldn't find the answer. So the question is if it is possible to copy & paste multiple commands in a single line into the Chimera command line interface. Alternatively, is the any "end of line" character that designates the end a of one command and the start of the next one? Thanks in advance, Thomas

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pH based conformational change
by Nikolay Igorovich Rodionov 01 Jun '12

01 Jun '12

Hi all, Is there any way in Chimera to model protein denaturation across various pH values? Thanks Nikolay Rodionv

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Re: [Chimera-users] Interpreting field / force direction in Coulombic Surface Coloring
by Elaine Meng 01 Jun '12

01 Jun '12

Hi Sumitro, The interaction energy of a "test" charge at some point would be the charge multiplied by the electrostatic potential. So if the test charge is -1 e (like one electron) its interaction energy at a point with potential +10 kcal/(mol.e) would be favorable, -10 kcal/mol. Positive potential favors interaction with negative charges and vice versa. I hope this clarifies, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. better to send questions to chimera-users(a)cgl.ucsf.edu because if you send to me and I'm on vacation, you might not get answered On May 18, 2012, at 12:36 AM, Sumitro Harjanto wrote: > Hi Elaine, > I have a simple question regarding the Coulombic Surface Coloring. I understand that the potential are generated by assuming a charged probe that moves along the surface of the model and as it traverses the surface the potential is picked up as the calculated electrostatic force the probe should experience (that's my understanding, correct me if I'm wrong please). > > I am just, however, a little confused about the interpretation of the value. say if I got a blue patch on the surface, which means I'm getting values in the range of ~10 (positive) kcal/(mol·e) at 298 K; does that mean the region indicated by the blue patch should potential attract or repel electron? > Thanks! > Cheers, > Sumitro

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Visualization of terminal carboxylate
by George Tzotzos 26 May '12

26 May '12

This must be really trivial but I am asking nevertheless as I tried to no avail. I'm trying to visualise the terminal carboxylate oxygens. For example, I do: select :125@O :125@OXT and get 2 atoms selected. I then try to Actions Atoms/Bonds sphere. Nothing is shown. I would be grateful for any suggestions Regards George

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PubChem Online Compound Search and Download
by Nancy 25 May '12

25 May '12

Hi All, I have been using the PubChem database to search for uncharged small molecules. However, even after specifying zero charge, PubChem still outputs compounds containing amino groups (-NH2) and carboxylic acids (-COOH); since I am interested in physiological pH, these compounds would actually be charged. Is there some way to exclude molecules containing these functional groups? I've noticed that there is an option on PubChem to include only certain atoms, but the search times out at 2 minutes if I try this. I'd like to exclude halogens and aldehydes as well, can this be specified? Finally, after searching for numerous compounds, how could all of them be downloaded into an organized compound library? If there is another online compound database besides PubChem that can be easily searched and has the same or better functionality, I'd greatly appreciate any info about it. Thanks, Nancy

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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 20 May '12

20 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 19 May '12

19 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 17 May '12

17 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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RMSD between ensemble of a protein and its paralogue crystal structure
by Thomas Evangelidis 15 May '12

15 May '12

Dear UCSF Chimera developers, I want to calculate the RMSD between a MD trajectory of a protein and the crystal structure of its paralogue protein. I have looked though the Ensemble Match and RMSD Analysis pages but these applications work for the same proteins (correct me if I am wrong). Is there any way to provide an alignment file to Chimera and calculate the time series of the RMSD between the two paralogues? Thanks in advance, Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Addition of phosphates to PDB structures
by Donado, Carlos 14 May '12

14 May '12

Hi all, I would like to learn how to add a phosphate group to a particular residue, resembling phosphorylation of a particular residue, to a PDB structure. If this is doable using Chimera I would really appreciate any hints on how to do this. Also, I am new to Chimera but I was wondering if there was a way of adding ATP to a designated ATP binding site. I would very much appreciate any responses, Thanks, Carlos Donado The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Chimera-users] semi-transparent ribbon behind semi-transparent surface
by Tom Goddard 14 May '12

14 May '12

Hi Sumitro, I made an image in the style of your image (1a0m.jpg below) using Chimera 1.6.1 and I think it captures the effect of your Chimera 1.5 image (ep.png) very well. The difference is that in your image where the ribbon crosses itself you can sometimes see through the top ribbon. Actually the top ribbon is only transparent in your image in about half of the crossings due to a Chimera 1.5 ribbon transparency bug. In the Chimera 1.6.1 image the ribbon is fully opaque so you do not see through it at places where it crosses itself. I think this produces a better image with less visual depth confusion. Also I think adding silhouette edges as I did in 1a0m_edges.jpg below improves the perception of ribbon crossovers further. I think the main virtue of your image is that the ribbon that is further back is lighter in color so it draws less attention. That is achieved by depth cueing which is the same in Chimera 1.6 and 1.5. My image perhaps does not illustrate depth cueing as well as yours since I used a different PDB model (didn't have yours) and in my view it doesn't vary as much in depth. Tom -------- Original Message -------- Subject: Re: [Chimera-users] semi-transparent ribbon behind semi-transparent surface Date: Sun, 13 May 2012 18:19:39 +0800 From: Sumitro Harjanto To: Tom Goddard Hi Tom, I've attached an image, it's something like this, can you view it? thanks! cheers, Sumitro On 12 May 2012 00:58, Tom Goddardwrote: Hi Sumitro, It is hard to completely understand your problem without seeing an example image made with Chimera 1.5 using the technique you described. If you provide such an image we might have suggestions about how to make something very similar in the latest Chimera. The image link you send before gives permission denied. Tom > Hi Elaine, > > thanks for the reply. I believe you exactly described what I did > with this paragraph: > "In Chimera 1.5 each surface could have its own single-layer > transparency. Thus you could still have multiple transparent > layers overall, but only the top layer of each surface. I'm > guessing the image is something like that (I don't have permission > to view it)." > Sadly, I resorted to re-installing CHIMERA 1.5 cos even if I use > pastel colours in Chimera 1.6, the effects were far from what I've > got using the multiple-single layer transparency previously. Is > there any plan to make the transparency setting more customisable > in the future? that will be of great help! thanks! > > Cheers, > Sum > > On 4 May 2012 00:18, Elaine Meng wrote: > > > On May 3, 2012, at 8:05 AM, Sumitro Harjanto wrote: > > > Hi Elaine, > > I used to use CHIMERA 1.5 to generate some molecular images. > and I was able to show a "hint of shadow" of ribbon behind a > semitransparent molecular surface. but I realised that I can > no longer do that from Chimera 1.6 onwards. I have tried > fiddling with the new "single layer transparency" value, but > either option did not provide me with the visual effect that I > could previously get in chimera 1.5. when I turned off the > single layer transparency, the molecular surface became very > messy with multiple shades and the color is visibly darker. > but If I leave it on, the semi-transparent ribbon was not > displayed at all. is there anyway that I can achieve a similar > effect in Chimera 1.6? i.e if you're wondering what effect I > am talking about here is an example: > http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/n… > <http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/n…> > > Thanks, Elaine! > > Cheers, > > Sumitro > > Hi Sumitro! > In Chimera 1.5 each surface could have its own single-layer > transparency. Thus you could still have multiple transparent > layers overall, but only the top layer of each surface. I'm > guessing the image is something like that (I don't have > permission to view it). > > In Chimera 1.6 the choices are only either a single layer of > transparency, or all transparent layers. > > In Chimera 1.5 if you turn off single-layer transparency for > each surface, the result is the same as in Chimera 1.6 if you > turn off global single-layer transparency. However, I realize > that does not help, since you don't want to show all layers > (it's often ugly, as you describe). > > I don't know if there is any way to get exactly what you had > before, but in 1.6 I suggest trying this: use single-layer > transparency (which is the default), make only the surface > transparent, keep the ribbon opaque. If you want the ribbon > to be less bold, try making it a pastel color. > > I am not involved in the graphics programming -- I CC'd the > list since the other developers may have suggestions (and > other users might find the discussion informative). > 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 > >

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Surface atoms and charges
by Nikolay Igorovich Rodionov 14 May '12

14 May '12

Hi all, I was wondering if any of you knew of a way to determine exactly what atoms occur on the surface of a molecule or how to get the exact charge at a point on a surface. Thank you, Nikolay Rodionov

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AMBER ff99SB Documentation
by Nikolay Igorovich Rodionov 12 May '12

12 May '12

Hi all, Could someone point in the direction of some good documentation on ff99SB, how it functions, and what calculations it performs? Thank you, Nikolay Rodionov

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Using Chimera from non-chimera python scripts
by Dan Cohen 11 May '12

11 May '12

Hello, I would like to use Chimera python classes from a python script running outside Chimera (part of a larger python project). I saw another post that explained that this could be done but I was unclear which of the Chimera functionality can be used in this case. In case I want to create an image (e.g. load pdb files, do some editing and then create an image to a file) - can I use the "chimera" class or do I need to use something else? (I saw a reference to "midas" classes) Is there an example for doing that? Processing a file and creating an image in a non-GUI scenario running outside chimera? Thank you, Dany

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Re: [Chimera-users] semi-transparent ribbon behind semi-transparent surface
by Elaine Meng 11 May '12

11 May '12

On May 3, 2012, at 8:05 AM, Sumitro Harjanto wrote: > Hi Elaine, > I used to use CHIMERA 1.5 to generate some molecular images. and I was able to show a "hint of shadow" of ribbon behind a semitransparent molecular surface. but I realised that I can no longer do that from Chimera 1.6 onwards. I have tried fiddling with the new "single layer transparency" value, but either option did not provide me with the visual effect that I could previously get in chimera 1.5. when I turned off the single layer transparency, the molecular surface became very messy with multiple shades and the color is visibly darker. but If I leave it on, the semi-transparent ribbon was not displayed at all. is there anyway that I can achieve a similar effect in Chimera 1.6? i.e if you're wondering what effect I am talking about here is an example: http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/n… > Thanks, Elaine! > Cheers, > Sumitro Hi Sumitro! In Chimera 1.5 each surface could have its own single-layer transparency. Thus you could still have multiple transparent layers overall, but only the top layer of each surface. I'm guessing the image is something like that (I don't have permission to view it). In Chimera 1.6 the choices are only either a single layer of transparency, or all transparent layers. In Chimera 1.5 if you turn off single-layer transparency for each surface, the result is the same as in Chimera 1.6 if you turn off global single-layer transparency. However, I realize that does not help, since you don't want to show all layers (it's often ugly, as you describe). I don't know if there is any way to get exactly what you had before, but in 1.6 I suggest trying this: use single-layer transparency (which is the default), make only the surface transparent, keep the ribbon opaque. If you want the ribbon to be less bold, try making it a pastel color. I am not involved in the graphics programming -- I CC'd the list since the other developers may have suggestions (and other users might find the discussion informative). 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

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Partial Charge and Electrostatic Potential Maps
by Nikolay Igorovich Rodionov 10 May '12

10 May '12

Hi Everyone, I was wondering if there is a way to create a maps of partial charge and electrostatic potential that I could then overlay on top of a similar structure. The biological assembly I am working with is too large for good surface calculations so I would like to overlay these maps on the surface of a condensed structure that only includes the regions I am concentrating on. Thank you, Nikolay Rodionov

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Recording actions
by Nikolay Igorovich Rodionov 10 May '12

10 May '12

Hi all, Is there any way to get a read out of all of the operations I have performed within a session? I know of the command history option but that only record the commands I have entered in the command line. I would like to be able to record my command line and non-command line actions, in the order they occurred. Thank you, Nikolay Rodionov

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Writing image to a file using Chimera python script
by Dan Cohen 10 May '12

10 May '12

Hello all, Is there a python interface for exporting images to a file in the UCSF Chimera. I understand I can use runCommand("copy") or runCommand("export"). Is there a python class for doing such commands? Thank you, Dany

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Re: [Chimera-users] [chimera-dev] Dividing a model into seperate models - one for each chain
by Tom Goddard 09 May '12

09 May '12

Hi Mateusz, The "split #0" command produces separate models for each chain. They are numbered #0.1, #0.2, #0.3, ... with the same primary id number (0) and different secondary id numbers. You can use these two-part id numbers in any Chimera command (e.g. color blue #0.2), or you can refer to all the models using #0. There is currently not a way to change the id numbers of models. Tom > Hello, > > Is there a command / a way to split a model into seperate models (one > for each chain)? I know there is the "split" command, but it divides > the model into submodels. > > Mateusz >

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keyboard accelerator "es" doesn't not work after open the command box
by Weimin Wu 09 May '12

09 May '12

A command box was open to input a sym command to generate 60 copies of a pdb structure on the virus capsid surface. Does anybody know how to close this command box? because the keyboard accelerator "es" always goes to command line instead of erasing the density I specified. It is really annoying. Weimin

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Add-H to water O
by Francesco Pietra 09 May '12

09 May '12

Is it possible with CHIMERA to add-H selectively to O atoms to get H-bonded water molecules? I used REDUCE to add-H (-build flag) but was unable to get H2O from O atoms, although het database is in place. What I am trying to get is a reasonable H-bonded water for a highly hydrated protein, before submitting to MD to actually see h-bonding. thanks francesco pietra

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hydrogen bonds in Chimera
by Beale, John 09 May '12

09 May '12

I have a model of a ligand docked in the active site of a receptor protein. I want to visualize only the hydrogen bonds between ligand and receptor- not for the entire protein. Is this possible in Chimera? John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110-1088 Office: 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 John.Beale(a)stlcop.edu<mailto:John.Beale@stlcop.edu>

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Glassy surface in Chimera
by John Squire 08 May '12

08 May '12

Hello, I am trying to show a density map as a glassy surface within which various molecular chains have been fitted. Can anyone please tell me how to produce such a glassy surface for the density map in Chimera? Thanks, John Squire Professor John M Squire, Muscle Contraction Group, School of Physiology and Pharmacology, University of Bristol, University Walk, Bristol BS8 1TD. United Kingdom. Visiting Professor Imperial College London (44) (0)1722 421734 j.squire(a)imperial.ac.uk j.m.squire(a)bristol.ac.uk -------------------------------

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NMR
by MESHAL ALMUALLIMI 07 May '12

07 May '12

Hello, How can I show only the average of my NMR solved structure? As when I fetch the PDBID 1YJR it shows all the structures aligned and I only need the average. I figured out how to eliminate as much structures as I can but I am interested in taking the average of all. Regards Meshal MS candidate Georgetown University

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Chelation of Calcium with Citrate
by Nancy 05 May '12

05 May '12

Hi All, I would like to find the stoichiometry for the chelation of a calcium ion (Ca 2+) with a citrate ion (citrate 3-), as well as the equilibrium constant or free energy of calcium-citrate complex formation. x*Ca2+ + y*citrate3- <=> z*calcium-citrate-complex (x, y, and z are the stoichiometric coefficients) Thanks in advance, Nancy

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Amber Force Field
by Forbes J. Burkowski 04 May '12

04 May '12

Hi: I have noticed that scripts can start with: import MMTK import MMTK.ForceFields from MMTK.ForceFields import Amber94ForceField We are doing some side chain packing studies that would benefit from the availablity of "easy" force field calculations. Currently, the algorithm works with useRotamers() to set two neighbouring rotamers and this is followed by a simple energy calculation to evaluate the interaction energy between the two rotamers. Right now, the energy calculation is only a bit more sophisticated than a steric collision detector. Question: Can we use some functions in the MMTK.ForceFields module to get an improved energy calculation? Any suggestions would be appreciated. Cheers, Forbes

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Re: [Chimera-users] transform coordinates of multiple volumes
by Elaine Meng 03 May '12

03 May '12

On Apr 27, 2012, at 9:26 AM, Ludovic Renault wrote: > Hi Elaine, > I have 120 or so 3d volumes (EM maps). They are all equivalent and are centered at the same position. > I would like to move each one of these 120 volumes by a specific value in terms of euler angles and shift (in pixels I assume). I can use the 'trAnsform coordinates' tool but then if I save the map, it is not saved with the new coordinates. > So > 1- How to (Or can I) save the new coordinates for each volume? > 2- Can I use command lines to automate the process for example by giving the command a text file with the specific coordinates for each volume? > > I did do the rotation with spider software, but the shifting doesn't work because the volume(s) go outside of the box. So if all the above is not doable, is it possible to increase the volumes boxe size in chimera, then I could use the shift function in spider? > > I hope I'm clear enough. > Thanks, > Ludovic Hi Ludovic, It is recommended to send Chimera questions to the chimera-users list (CC'd) -- I'm not the top expert on volumes, so others may have better answers! I think the shift in Transform Coordinates is not in pixels but in units of length. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor…> How the volume grid units map to units of length can be viewed by using Features...Coordinates in the Volume Viewer menu. Chimera has commands for translation (move) and rotation (turn) in X,Y,Z coordinate systems, but I don't know of a command to apply Euler rotations. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> About saving a transformed map: The map formats don't include transformation information, so there is no way to save EXACTLY the same data, except transformed. However, you can resample the map onto a new grid, and then save the new map. The values at the new grid points are determined by interpolation, so there will be some (generally minor) data loss. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> The resampling of one map onto the grid of another can be done with command "vop resample", for example: vop #1 resample onGrid #0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> To save the new resampled volume to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its "save" option. However, I see that "vop resample" is most pertinent for saving a map that has been fitted to another. In your case you are simply transforming the map, so it is unclear on what grid you could resample. Maybe there is some way to make a "dummy" grid in the right place. Although "vop cover" extends a map, it assumes periodicity of that map, whereas I assume you want zeroes in the expanded parts. Perhaps expanding a map with zeroes could be done using "vop add" to add a dummy zero map to your data set of interest. Sorry I couldn't give a more complete solution, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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About resolution and origin
by Yuhong Li 02 May '12

02 May '12

Hi friends, Firstly, I was wondering how to know the resolution of my map since one day I opened volume viewer...tools...fit to segments. And I found that there displaying "density map resolution". So my question is whether that number is the correct resolution of my map? Secondly, in the volume viewer...corrdinates I can know the origin index, but how can I know the origin? These questions may seem to be stupid, but I just want to know. So hope to hear from you very soon! Best Wishes, Yuhong Lee

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changing map dimensions
by Elaine Meng 01 May '12

01 May '12

On Apr 30, 2012, at 6:56 PM, Yuhong Li wrote: > Hi Elaine, > Thanks for your help, now I've understood what those numbers mean. But I was wondering if you could tell me how I can change those gird points, such as change 88 66 94 to 94 94 94 or any cubic numbers ? > Best Wishes, > Yuhong Lee > Hi Yuhong, Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of directly to me. Those numbers are the size of your input data file, so I'm not sure what you mean. You can't just change the numbers arbitrarily. It is possible to make a new data set by cutting off part of the original data set. One way to do that is to use the "volume" command to save a new map file, using the "saveSubregion" option to include only part of the original map. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> However, it sounds like you want to make a new data set that is bigger than your original map. There is a "vop cover" command that will make a bigger map, but it assumes periodicity of the input map. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> If instead you wanted values of zero at the additional grid points, however, I don't know how to do that -- maybe the others have ideas. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Just want atom distances
by Patricia LiWang 30 Apr '12

30 Apr '12

Hello users group, I don't want anything complicated-- I just want to get some rough distances between atoms. So I go to Tools Structure Analysis Distances A window comes up with an empty table. (No instructions on how to pick atoms) A search of the Chimera documentation tells me I have to Control-leftclick to pick two atoms But no matter how often I click and click and click, it never gives me anything. I can't get even one atom to show up in the panel, let alone two. The side chains are sitting right there, getting clicked away, with nothing happening in the table. I am reading so many similar documentation pages, and apparently there is a difference between "selecting" and "picking" So I figure I'll just use the command line. But the instructions don't even bother to tell you how to use the command line to get the distance between two atoms. There is documentation on how to get distances between something and a "plane". Why do they make this so hard? Surely this is the main "simple" thing people want to do with this program. Would someone please tell me how to Pick or Select or Whatever two amino acids (any atom in them would be fine) and get a distance? Or better yet, please tell me the exact command line command I can use to get the distance between Asparate 234 carboxyl oxygen and Aspartate 295 carboxyl oxygen, both from chain "G"? Thanks! Patti ---------------------------------------------------------------------------

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Measure contact between copies of the same map
by Giovanni Cardone 30 Apr '12

30 Apr '12

Hi, I can use the tool measure contactArea on the surface models of two different maps, but I can not make it work when using it on two copies of the same map: no matter how much I move one map with respect to the other, the first surface listed in the command line will always be entirely colored in red (using offset 0). It looks like the command ignores the transformation. Is this the expected behavior? I can work around it by resampling the maps after the transformation (vop resample # onGrid #), but I liked more the idea of doing the measure without this additional step. Tested it with the latest alpha version 1.7 (build 36320). Thank you, Giovanni

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Contour mapping
by Nikolay Igorovich Rodionov 30 Apr '12

30 Apr '12

Hi all, I was wondering if anyone could help me create an accurate contour map based on surface charge. I've tried rendering my molecule by charge, then using the surface clipping, capping, and the color zone tools. However, the coloring varies based on how I orient the plane. Does anyone know a better and more accurate way to creating a contour map? Nikolay Rodionov

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gaussian filter
by Mike Strauss 30 Apr '12

30 Apr '12

Hi, I've been using the gaussian filter for a number of years to help me display my noisy data. I'd like to understand what it's doing a bit better, and so I need help with the following code: ijk_linewidths = map(lambda step: linewidth / step, g.step) what is the resulting length of ijk_linewidths? I can't seem to figure out what type of data type g.step is. Is it a feature of the image itself, or where does it come from? Best Regards, mike

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