- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] deleting entries from rapid access list (plain text format)
by Jaime Rodríguez-Guerra Pedregal 06 Jun '16

06 Jun '16

Hi, I was searching for a Chimera function that did this very same thing, but found nothing, so I created a little script to do that from the terminal. I know this is old, but maybe somebody finds it useful after all! Get it here https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768 Jaime Rodríguez-Guerra Pedregal Molecular modeling of transition metal systems group Department of Chemistry, Faculty of Sciences Edif. C · C7/153 Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 93 581 28 57 www.uab.cat<http://www.uab.cat/> [http://www.uab.cat/vcard/Logo_ORCID_0.png] <http://orcid.org/0000-0001-8974-1566> [http://www.uab.cat/vcard/Logo_LinkedIn_0.png] <https://www.linkedin.com/in/jaimergp> This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. Please consider the environment before printing this email.

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coloring by RMSD (conformational variability)
by George Tzotzos 06 Jun '16

06 Jun '16

Following PC analysis, I have obtained pseudo trajectories for each of the first 3 principal components. I used Chimera to colour the regions exhibiting the largest structural variations as per instructions of Elain Meng, which I attach for easy reference. I have placed side by side, say the 1st PC, of two independent pseudo trajectories (see attached image). As the structure is disordered between residues 1-10 and 124-125, I’d like to render these ranges of residues semitransparent. I’ve tried to do this with the transparency command but this applies to ribbons only (I think). I’d appreciate any suggestions as to how this can be done. Thank you in advance George From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: coloring by RMSD (conformational variability) Date: 25 March 2014 at 19:32:47 GMT+1 To: George Tzotzos <gtzotzos(a)me.com> Cc: chimera List <chimera-users(a)cgl.ucsf.edu> Reply-To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Hi George, Sure, you can do it by having Chimera calculate the CA-RMSD at each position and then mapping that value to color. The file is a little strange in that it has only CA atoms and all the residues are ALA, but it will still work: (1) show the sequence (menu: Favorites… Sequence). Just choose any one of the 34 -- it doesn't matter which one, since they all have the same sequence. (2) associate all 34 copies of the structure with the one sequence: in the sequence window menu, choose Structure… Associations. In that dialog, change all the "none" to the same sequence, then click OK. This is somewhat tedious, but I just did it, so you can too! Now, all of the structures will be connected to that one sequence. (3) tell Chimera to calculate the RMSD at each position: in the sequence window menu, choose Headers… RMSD. Now the sequence window will have an RMSD histogram above the sequence. It may almost look like a line because most of the bars in the histogram (the RMSD values) are very low. (4) color the structures by the RMSD values with Render by Attribute (in main Chimera menu under Tools… Depiction). In that tool, choose attributes of "residues" and attribute name "mavRMSD" (the "mav" part stands for Multalign Viewer, which is showing the sequence). It will show a histogram of the values with some vertical colored bars. You use those bars to define how the values are mapped to color. The bars can be dragged left and right, and you can delete bars or add more bars with Ctrl-click. You can change the color of each bar by clicking it and then clicking the "Color" square below the histogram and using the Color Editor, or you can just use one of the Palette options below that. You can keep clicking Apply and then adjusting the coloring until it is how you like it. For example, I show coloring by RMSD from blue->red->yellow (and then menu: Presets… Publication 1) in the attached image. I hope this helps, Elaine

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Chimera-win10-install
by Mitja Ogrizek 06 Jun '16

06 Jun '16

Dear all, I tried to install a new version of chimera on my laptop with win10, but it doesn't want to load and start the setup. Has anybody else reported or had the same troubles? Kind regards, Mitja Ogrizek

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Cap color precedence when global clip planes slice through multiple volumes?
by Oliver Clarke 06 Jun '16

06 Jun '16

Hi, When slicing through multiple superimposed volumes with caps shown, the color of the resulting cap seems to be a bit of a patchwork - sometimes dominated by one volume, sometimes by another, sometimes a mix of the two It would be good if there were a way to control the precedence of the caps, to make a cleaner and more interpretable picture - it is often good to be able to see the outline of both overlayed volumes. I know there is one way to do this, by using per model clipping planes and changing the offsets such that one per model clip plane is just slightly in front of the other, but it might be helpful in ChimeraX to have more granular control over this. Cheers, Oli

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Cut asymmetric unit from volume
by Morris, Kyle 03 Jun '16

03 Jun '16

Hi Chimera team and users, Is there a way to extract the asymmetric unit from a volume which has been 'symmetrised’ from, say for instance, Relion? In this case what are the conventions used by chimera to define the bounds of the sub-volume to extract? Thanks for your help! Best wishes, Kyle

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Request for support
by Mendoza Wilson, Ana Maria 03 Jun '16

03 Jun '16

Hello, How I can select an isodensity value in the Chimera software (1.11rc) for calculating molecular surface and molecular volume from one cube data file or fchk file previously generated in Gaussian 09? Thanks in advance -- Dra. Ana María Mendoza Wilson Investigador Titular Centro de Investigación en Alimentación y Desarrollo, A.C. Coordinación de Tecnología de Alimentos de Origen Vegetal Carretera a La Victoria Km. 0.6 Hermosillo, Sonora, México C.P. 83000 Tel +52 (662) 289 24 00 Ext. 354

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FW: Chimera Log File
by Williams, Joanne 03 Jun '16

03 Jun '16

From: Erin Coppola <erincoppola8(a)gmail.com<mailto:erincoppola8@gmail.com>> Date: Friday, June 3, 2016 8:10 AM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: Chimera Log File Hi, When using Chimera, is there a way of tracking the script command versions of GUI actions performed?

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Creating maps from models for map/model FSC calculations
by Ardan Patwardhan 03 Jun '16

03 Jun '16

Dear all We are using Chimera to align PDB models to maps, then creating maps from the models using the following command (as an example): molmap #0 5 gridSpacing 1.3 This should create a map with the voxel spacing of 1.3A and a gaussian atom spread function with the width related to 5A resolution (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html) Our problem is a) the map that is created can have an arbitrary size - we need it to be cubic and have the same (known) dimensions as the second map against which it will be compared b) we have tried padding it in other programs like bsoft but then we sometimes run into problems of centring the model. I was wondering if there was a way to get a centred map of a certain size from a model directly from Chimera? Perhaps there are certain parameters that can be used in molmap? You thoughts and advice on this issue are much appreciated! Many thanks and best wishes Ardan Patwardhan Coordinator - cellular structure & PDBe production Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: +44 1223 492649

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mask
by Dougherty, Matthew T 02 Jun '16

02 Jun '16

I have a volume whose density values are -127 thru 127. Zero is a valid density & approximately the peak of the Guassian distribution. I would like to use the command mask. It sets the unmasked density values to zero. How can I set the unmasked density values to -128 using the mask command? Will I need to hack the code? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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finding residues with large effects on local electrostatic potential
by Elaine Meng 01 Jun '16

01 Jun '16

Hi Deniz, No need to apologize, that’s why we have an address for questions. :-) I am guessing you were coloring by electrostatic potential and want to figure out which residues are having large effects in some places. The question is not that simple because electrostatic interactions are long-range, meaning that the potential at a point is based on many atoms in many residues, including those farther away. However, the largest contributions at a surface point will generally be from the residues with net positive or negative charges that are not too far away. In other words, if you see a blue patch, you could then try to figure out positively charged residues are near it, or if a red patch, which negatively charged residues are near it. The problem in Chimera that you may be having is that when you put the mouse over the surface, the surface is blocking the atoms, so it does not tell you what residue is under that surface. One way to try to figure it out is to temporarily hide the surface (Favorites… Model Panel, uncheck the “Shown” button for the surface), then click back into the main window *without moving the structure* and put the mouse over the same area to see what residues are there, using the pop-up balloons with residue information. You would probably want to show all the sidechain atoms first (e.g. command: display protein), and maybe select residues that are known to be positive (or negative) to help guide yourself to the right place. Command: select :lys,arg,his (… the ones likely to contribute to positive patches…) Command: select :asp,glu (… the ones likely to contribute to negative patches…) You can keep turning the surface on and off with the checkbox in the Model panel. This is interactive guessing and may not be that easy. Just keep in mind that you can’t say that some patch is all from one or two residues, only that they have significant contributions. 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 1, 2016, at 3:44 PM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > Hi Elaine, > I am sorry for bothering you. But, I need urgent help. > If I tell chimera to find the surface charge, negative and positive, and if I want to know which residues are responsible for this charge, what do I do? > > thank you so much, > deniz

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