February 2012 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! 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 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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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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Re: [Chimera-users] [Dock-fans] Help with antechamber
by Trent E. Balius 10 Apr '12

10 Apr '12

Hi Brad, I am cc'ing this to the chimera list. I think that you should write a python script to run DOCK prep on the command line. See the following: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html For other example scripts see the following: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html You should not have to specify the AMBERHOME path. This is done internally to chimera. as an aside, It is unnecessary to run antichamber with sudo. I hope this helps, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/ -----Original Message----- From: Brad Ridder <clustro(a)gmail.com> To: dock-fans <dock-fans(a)docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber Hi Dockfans, My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University. We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI. Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens. Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running: sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/3GLRcharged.mol2 -fo mol2 Which returns the error: Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder. Here is what I have in my .bash_profile file in my home folder. export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6' I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect. I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem. I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files. What am I doing wrong that is preventing antechamber from executing correctly? -- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University _______________________________________________ Dock-fans mailing list Dock-fans(a)docking.org http://mailman.docking.org/mailman/listinfo/dock-fans

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how to copy partial charges from a .mol2 file to another
by Thomas Evangelidis 29 Feb '12

29 Feb '12

Dear Chimera community, Is there any straight forward way to copy the partial charges from one .mol2 file to another? 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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partial conservation coloring
by Eric Pettersen 28 Feb '12

28 Feb '12

Jill Voreis wrote: > I'm trying to use chimera to show conservation maps. Using pdb files > that I fetch from the database using the pdb id number and > alignments created in clustal that contain the sequence of the pdb > file, I select render by conservation. For some reason, the > conservation colors only go onto my model when it's in ribbon form. > When I try to show the surface representation or use spheres so that > I can use commans to show the SAS, the colors of my model do not > match the conservation model but rather are stuck on some sort of > coloring scheme related to the compounds that are there. The > majority of the map looks brown, like the default color before > rendering by conservation. If you could help me, I'd really > appreciate it! Hi Jill, There are a few possibilities here, though it's impossible to be certain what the problem without access to a concrete example. My best guess is that much of the surface region of your protein is poorly conserved and those areas have columns where the rows are more than 50% gap characters. For such columns no conservation score is assigned. That means that when you use Render By Attribute with default settings, those atoms / surface parts will retain their original colors. If in Render By Attribute you use the "No-value color" color well to assign a color to such regions (perhaps gray) you will be able to tell if this is what is happening. Two other possibilities are that you don't have the "Color atom" and "Color surfaces" check boxes checked [though I image you would have noticed this!] or that your protein has multiple chains and that only one is associated with the alignment and only that one is getting colored. If none of these are "it", if you can provide me with a specific example so I can reproduce the behavior then I will investigate. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Not crossfade but coinciding bond command...
by Kevin D. Walker 28 Feb '12

28 Feb '12

I temporarily disabled a bond command and found this to be the cause of the selected bond problem I am having. I don't think crossfade has anything to do with it.

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Animate a Reacton Mechanism?
by Kevin D. Walker 28 Feb '12

28 Feb '12

I constructed a movie for the first part of a reaction mechanism (substrate docking). I would like the animated mechanism to continue as follows. The substrate donates a proton to a tyrosine residue of the enzyme, forming an intermediate. The intermediate rotates 180 (I have accomplished this part) and the proton rebounds to the intermediate forming a new product, which is released. I can animate the product release -- it's the reverse of substrate docking. The part of the animation I cannot envisage is how to smoothly show or morph the bond transitions (bond breaking and making) during the reaction progression. IAny advice on whether Chimera or other ancillary software can do this is appreciated.

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using CalcAttr from a Python script
by Roger L. Chang 28 Feb '12

28 Feb '12

Hi, 1) I need to get residue.areaSES for two separate selections (all polar amino acids and all nonpolar amino acids). I have successfully generated a list of residue.areaSES using the GUI simply by selecting the residues of interest and then using the attribute calculator typing "residue.areaSES" in the formula box of the Attribute Calculator, which outputs the list to the Reply Log. This is the data that I need, but I need to get it for >2000 PDB structures and would like to automate this analysis through a Python script. I am somewhat new to Python and Chimera and don't yet know all the ins and outs yet. I dug through the code and found a method "getResidueAttr" in the "ResidueDataWrapper" class from "CalcAttr". This seems to be what I need, but I don't know the proper syntax to call it from my Python script. Could someone please provide an example? 2) I would like to sum the residue.areaSES values once I have them. I tried "sum(residue.areaSES)" in the formula box of the Attribute Calculator in the GUI, but this returns the error "Formula evaluation error: expecting vector argument in function". I'm not sure again on the proper syntax to use "sum()" in the Attribute Calculator. If I knew how to generate/save the residue.areaSES data from the command line, I could just parse the saved file and sum the values in Python. How can Attribute Calculator formulas be used from the command line, and if they can't, how can I save the residue.areaSES data to file from a Python script? Thanks in advance, Roger -- Roger L. Chang Graduate Student Bioinformatics and Systems Biology Graduate Program University of California, San Diego

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