- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] solvent-accessible surface area
by Amit Goyal 02 Dec '13

02 Dec '13

Hi Elaine, Today I subscribe to Chimera mailing list, but unable to get the proper way to post a query on it. So I am sending the query this way. I have been reading this post about how to get the areaSAS and areaSES values for any residues. http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002617.html Still, I think, is there any specific values/range for the areas AS to decide whether a particular amino acid residues is buried or exposed to the solvent. Hoping for Thanks for your help. Sincerely, AMIT -- AMIT GOYAL, Pusan National University, Korea south. amitgsir(a)pusan.ac.kr

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translation matrix
by Antón Vila Sanjurjo 02 Dec '13

02 Dec '13

Hi, I'm trying to get a translation matrix for two different crystal structures of ribisomal subunits. I've been trying to use the "measure rotation" command but I can only get it to display the following message "rotation angle is near zero (0 degrees)". I was wondering whether the command might be failing due to the fact that the ribosome contains numerous chains, or perhaps because the command does not deal with RNA. At any rate, how would one go about obtaining a translation matrix that can be applied to any model? best, Antón -- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s(a)gmail.com

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colouring according to hydrophobicity
by Dieter Blaas 29 Nov '13

29 Nov '13

Hi, I am wondering whether there is any (easy) way of colouring a volume (e.g. an MRC file made from a pdb file and filtered to say, 10 A with e.g. xmipp) according to hydrophobicity (using the values derived from the amino acid residues in the pdb file)? I am aware of the way to colour the van der Waals surface but the resolution is somewhat too high not allowing to get a more general view, for example whether the molecule is more hydrophobic on one side than on another side. The same question applies to the charge distribution.... Thanks, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Overlay binding sites
by Markus Heller 28 Nov '13

28 Nov '13

Hello all, I'm pretty sure this has been done before, so before re-inventing the wheel or failing miserably and doing everything by hand, I thought I'd ask here first :) I have a protein that has been crystallized with about a dozen ligands of different sizes. I'd like to overlap the protein residues forming the binding site. My plan was to pick the 2 largest ligands, select all protein residues within say 7 A, and consider these to be the residues forming the binding site. Then, I'd like to match this set of residues for all proteins to the same reference. I suppose I could do this all manually, but I'm hoping that there is a quicker, more efficient way! Any tips are appreciated! Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CEEC32.879D5C80] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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features/question: stereo3d and volume rendering
by Dougherty, Matthew T 28 Nov '13

28 Nov '13

1) I have been doing S3D animations. One of things I am realizing is that I need to frequently adjust the interaxial and screen distances. Sometimes my IA might be 1mm or it might be 23 inches depending on the shot. Currently chimera does not maintain this camera metadata, so every session I need to reset the values which makes my animations slightly different. Since rendering can take several hours, one typo can trash the effort. Any suggestions on a workaround? There is also a linkage between IA, horizontal field of view, and screen distance, sometimes I think I get caught in a hysteresis loop trying to converge to the desired shot. As a note, I pretty much stopped using the zoom and have gone to dolly, keeping the scale to one. 2) when doing volume rendering of electron tomograms I am finding it useful to load the same mrc map file in multiple times, such that each model has a different transfer function relating to different densities or structures. I can currently load seven, but four must be changed from floating point to byte in order to prevent memory lockout thrashing, error messages, etc. Is there a way to load a single map file in and have multiple models and transfer functions for the solid viewing? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Protonation of selected atoms ?
by Marek Maly 28 Nov '13

28 Nov '13

Dear all, I would like to protonate just several nitrogen atoms (tertiary amines) of my hyperbranched polymer. I tried Structure "Editing -> Add hydrogens" but it protonised all my tertiary amines in the structure ignoring the fact that only few of them were selected and considered for protonation. So is there any way how to protonate only selected N atoms ? If not would be a good idea to add this possibility into Add Hydrogens panel (function). Thank you, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Automatic setting of suggested contour level
by Hurt, Darrell (NIH/NIAID) [E] 27 Nov '13

27 Nov '13

Hi Chimera team, I love how Chimera seems to intelligently and automatically choose a contour level for fetched EMDB files. However, I have noticed that most EMDB files have a "suggested contour level" associated with them. It can be obtained in the "header" XML files under the tag <contourLevel>. How much more work would it be to automatically fetch this information when fetching the map and then set the contour level to the recommended setting? Would you consider doing it? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Fwd: generate raised cosine smoothed mask with "mask ones" and "vop falloff"
by Tom Goddard 26 Nov '13

26 Nov '13

Hi Dieter, Chimera does not make masks with cosine falloff. The only mask smoothing in Chimera is "vop falloff". The algorithm is completely described in the Chimera manual (copied below) and basically amounts to a "heat equation" falloff -- the grid points outside the mask are assigned the average of the neighboring values, essentially the diffusion of heat from the masked ones region to the outside zeros region. This works for any shape. Tom "vop falloff volume-spec [ iterations M ] general-options Smooth the boundaries of a masked map by replacing the value at each grid point outside the boundary with the average of the values of its six nearest neighbors, for M iterations (default 10). All grid points with values of zero before the first iteration are taken to be outside the boundary, thus assigned a new value at each iteration. Thanks to Greg Pintilie for the initial implementation." Begin forwarded message: > From: Dieter Blaas > Subject: Re: [Chimera-users] generate raised cosine smoothed mask with "mask ones" and "vop falloff" > Date: November 26, 2013 8:34:17 AM PST > To: Tom Goddard > > Hi Tom, > > thanks for these explanations! I am still not sure whether such a mask behaves like a mask made with e.g. xmipp_transform_mask or with spider MA SOFT. I'd like to make an arbitrary mask (level 0 - 1) from a molecular volume which has a raised_cosine falloff. When comparing a spherical mask made with chimera (as given below) and with xmipp their histograms look quite different (probably also a question of the choice of parameters). The difference becomes much more striking when using a more irregular shaped molecular assembly. I found the Chimera procedure when looking for a method to make such masks as this is not provided in xmipp (only a sphere or a crown with raised-cosine but not an irregularly shaped mask). I want to use it in 3D-reconstructions...... > > Best, Dieter > > > > > > > > Am 25.11.2013 21:25, schrieb Tom Goddard: >> Hi Dieter, >> >> You should be able to generate a smooth volume mask using "mask ones" and "vop falloff" in Chimera. Here's an example making a smooth cylinder mask >> >> shape cylinder radius 100 height 100 caps true >> mask ones #0 border 10 >> vop falloff #1 iter 100 >> >> The boundary smoothing "vop falloff" is described on this web page >> >> http://www.cgl.ucsf.edu/chimera/data/falloff-sep2012/falloff.html >> >> Maybe you saw that page and got tripped up because it gave the wrong option name "step" instead of "iterations" in the vop falloff command -- I've fixed the web page. >> >> Tom >> >> >> >> On Nov 24, 2013, at 12:41 AM, Dieter Blaas wrote: >> >>> Hi, >>> I was wondering whether it is possible to generate binary raised cosine smooth masks with 'masked ones' followed by 'vop falloff' or anything alike. I'd like to generate an arbitrary mask (from a volume) with a smooth transition (over some few pixels) to 0 but I did not really find adequate parameters. Is this possible? >>> Thanks, D. >>> >>> -- >>> ------------------------------------------------------------------------ >>> Dieter Blaas, >>> Max F. Perutz Laboratories >>> Medical University of Vienna, >>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>> Dr. Bohr Gasse 9/3, >>> A-1030 Vienna, Austria, >> > > > -- > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > ------------------------------

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generate raised cosine smoothed mask with "mask ones" and "vop falloff"
by Dieter Blaas 25 Nov '13

25 Nov '13

Hi, I was wondering whether it is possible to generate binary raised cosine smooth masks with 'masked ones' followed by 'vop falloff' or anything alike. I'd like to generate an arbitrary mask (from a volume) with a smooth transition (over some few pixels) to 0 but I did not really find adequate parameters. Is this possible? Thanks, D. -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Re: [Chimera-users] Chimera-users Digest, Vol 127, Issue 22
by Boaz Shaanan 23 Nov '13

23 Nov '13

Hi Ahir, On my Dell & Nvidia dual boot (W7/linux) laptop there is the optimus feature which if it's on decides which graphics driver to use (on-board or Nvidia). You probably have a similar feature. In the system menu I switched the optimus off completely so I work only with the Nvidia driver. I did it mostly because of the linux side but keep this mode even when I'm under W7. My 2p advice. 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: Friday, November 22, 2013 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 127, Issue 22 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. Graphics Driver not switching to Nvidia (a.pushpanath(a)mail.cryst.bbk.ac.uk) 2. Re: Graphics Driver not switching to Nvidia (Tom Goddard) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Nov 2013 09:54:51 +0000 From: a.pushpanath(a)mail.cryst.bbk.ac.uk To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Graphics Driver not switching to Nvidia Message-ID: <20131122095451.15962g65x3dljxno(a)webmail.cryst.bbk.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Dear Chimera Users/Admins, I am having a sudden issue with Chimera, which refuses to pick the Nvidia GT 540M gfx card as my primary card whenever I start the program. I always get the Debug Graphics card, regardless of whether I have told the Nvidia Optimus technology to use the Nvidia card for chimera.exe. I am not entirely sure why this is happening, any help would be recommended! The intel HD graphics card is not good enough for my needs. Ahir ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ------------------------------ Message: 2 Date: Fri, 22 Nov 2013 10:07:27 -0800 From: Tom Goddard <goddard(a)sonic.net> To: a.pushpanath(a)mail.cryst.bbk.ac.uk Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Graphics Driver not switching to Nvidia Message-ID: <98429CC0-4EEE-4FB8-90D5-B67D0E27B913(a)sonic.net> Content-Type: text/plain; charset=windows-1252 Hi Ahir, Chimera does not decide which graphics card to use, your operating system decides that. The Chimera graphics debug dialog comes up every time because you set the Chimera preference "Debug OpenGL on Startup" and saved that preference setting. To turn that off use Chimera menu Favorites / Preferences?, turn the setting off and press the Save button at the bottom of the Preferences dialog. Tom On Nov 22, 2013, at 1:54 AM, wrote: > Dear Chimera Users/Admins, > I am having a sudden issue with Chimera, which refuses to pick the Nvidia GT 540M gfx card as my primary card whenever I start the program. I always get the Debug Graphics card, regardless of whether I have told the Nvidia Optimus technology to use the Nvidia card for chimera.exe. I am not entirely sure why this is happening, any help would be recommended! > > The intel HD graphics card is not good enough for my needs. > > Ahir > ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 127, Issue 22 **********************************************

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