November 2013 - Chimera-users - RBVI Mailing Lists

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.

2 2

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, > ------------------------------

1 0

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 ------------------------------------------------------------------------

2 1

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 **********************************************

1 0

Graphics Driver not switching to Nvidia
by a.pushpanath＠mail.cryst.bbk.ac.uk 22 Nov '13

22 Nov '13

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.

2 1

Re: [Chimera-users] Chimera STL files
by Tom Goddard 20 Nov '13

20 Nov '13

Hi Julian, The problem is that you create a large density map for your protein, but then Chimera doesn't display it at full resolution, because it is so large. To make Chimera display the contour surface of the full resolution map set the "Step" value in the volume viewer dialog to 1, or use the equivalent command "volume #0 step 1" after the molmap command. Making the grid spacing 0.1 (40 times smaller than the resolution of 4 Angstroms) is likely to create a huge STL file that the printer will have trouble with, and it won't give any smoother appearance than say 0.4 I think. Tom On Nov 20, 2013, at 7:54 AM, Julian Gough wrote: > Dear Tom, > > I read what you wrote here: > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008825.html > > I am really struggling to make an STL file for a coiled coil protein for 3D printing. What I see happening in Chimera does not seem to correspond to what you say, i.e. I use "molmap #0 4 grid 0.1" which according to you should be super-smooth -being far beyond what you suggest-, but the STL file that I export still has very large and obvious triangles. > > I have played with it a great deal and I cannot find any way to control the number of triangles in the STL file. Whatever parameter I use for the grid, the output file is roughly similar in size. I can certainly fill the memory and crash it by making the grid smaller, but this is not reflected in the exported STL file. > > ANy guidance much appreciated. > > Julian > > > -- > ~~~~~~~~~~~~~~~~ > Julian Gough > Professor of Bioinformatics > University of Bristol > Department of Computer Science > Merchant Venturers building > Woodland rd, Bristol, UK, BS8 1UB > Tel: +44 (0)117 3315221 > Web: http://bioinformatics.bris.ac.uk > <owen2.py><owen2.stl>

1 0

Set interatomic distances
by George Patargias 19 Nov '13

19 Nov '13

Hello Do you know if there is a way to set interatomic distances to a certain value in chimera (rather than measuring them)? Basically what I want to do is rotate/translate a peptide with respect to a protein so that a set of interatomic distances between the two are satisfied Many thanks! George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568

3 3

measuring distances
by Ryan Pavlovicz 19 Nov '13

19 Nov '13

Hi, I am trying to measure the distance between two atoms from many different PDB structures using a python script. Using a command like: chimera.runCommand('distance #0:1@C1 #0:1@C2') will correctly output the distance within a tenth of an angstrom, however, i would like to output a more accurate measurement (more decimal places). Is there a way to do this when using chimera within a python script? Thanks for your help, ryan

2 2

Commands for label formatting (font size etc)
by Andreas Göransson 18 Nov '13

18 Nov '13

Hi! How do I set font size for label / rlabel command in a command file? Can't find info in the documentation or in the mail list archive. Thanks, Andreas

2 2

WebGL
by Hansen, Bryan (NIH/NIAID) [F] 18 Nov '13

18 Nov '13

Hi, I'm trying to export a scene using the WebGL feature within Chimera, but something seems to be going wrong. I'm attaching what opens up after Chimera saves the scene. I'm not able to rotate the output at all either. Is there a setting I need to change somewhere within Chimera? Thanks for your help and input. ************************** Bryan Hansen Microbiologist Electron Microscopy Lab NIH/NIAID/Rocky Mountain Laboratory 903 S 4th St Hamilton, MT 59840 (406) 363-9202 *********************************************************** 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. ***********************************************************

2 1