- Chimera-users - RBVI Mailing Lists

Calculating screw transformation between two protein subunits
by Nikita Chopra 17 May '18

17 May '18

Hi I have two protein subunits, which I have aligned along the z-axis. I am considering both the subunits as rigid bodies. Is there a way I could find the screw transformation (rotation along z-axis and displacement along xy plane) between them in chimera ? Thank you for your help.

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Volume viewer levels question
by Markus Heller 15 May '18

15 May '18

Hi all, I have an issue displaying a map file that I opened using the insightgrid.py script. When displaying the grid at the highest level I can get, the levels are still too low, but when I set the levels higher by typing something into the level field (e.g. 1.2e+03 instead of the 1e+03), the levels disappear altogether as shown in the second screenshot. As soon as I adjust the slider, the levels reset to 1e+03. What am I doing wrong? Thanks Markus [cid:image001.png@01D3EC35.74E6A210] [cid:image004.png@01D3EC35.9B86A230]

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insightgrid.py
by Markus Heller 14 May '18

14 May '18

Hi all, I'm looking for a copy of Tom's insightgrid.py script, referenced here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009651.html If somebody could let me know how to get hold of a copy, that'd be great! Thanks and Cheers Markus

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query about splitting volumes using local resolution criterion
by Banavali, Nilesh K (HEALTH) 14 May '18

14 May '18

ResMap, a program that calculates local resolutions for cryoEM maps, also provides a chimera script to visualize the local resolution. This script opens Volume #0 (cryoEM map), and colors its regions using the values from Volume #1 (ResMap-generated file) as follows: open #0 example_map.mrc open #1 example_map_resmap.mrc volume #1 hide scolor #0 volume #1 cmap 3.00,blue:5.00,cyan:7.00,green:9.00,yellow:11.00,orange:13.00,red I was wondering if there is a way to generate split maps based on the resolutions stored in Volume #1 instead of just coloring the original map. Alternatively, is there way to play with the transparency of the regions with specific resolutions stored in Volume #1. The goal is to separate low resolution regions from the higher resolution regions in the original map to be able to better understand/annotate the accuracy of atomic models that are generated based on the map. I tried to look for ways to do this using 'volume', 'scolor zone', and 'vop' options, but was unable to make any progress. Any help would be greatly appreciated. Thanks, Nilesh

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Regarding saving image in chimera nogui
by NAGARAJAN 14 May '18

14 May '18

Hi all, I have to use chimera --nogui and do the following 1. load a structure 2. make Surface representation 3. Color surface of selected residues with a selected color 4. save image Any idea how to do the 4 steps in chimera --nogui? Thank you

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tiling multiple chain structures
by Healey, Joe 11 May '18

11 May '18

Hi chimera team, Sorry for pestering you again so soon! Very quick question though. If I have a couple of structures on screen which are made up of multiple PDBs, is there any way to tile them, but as groups? e.g. if I have one complex A-B-C, and another X-Y-Z, that I group into Group1 and Group2, I'd like to tile group1 and group2 next to each other. The tile command, as far as I can tell, is only capable of tiling A B C X Y Z as seperate models though (unless I went through the process of saving them all as a single PDB first). Is there any way to do this without the hassle of saving and reloading? Many thanks! Joe Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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Re: [Chimera-users] saving new position of the model (map saving)
by Elaine Meng 10 May '18

10 May '18

Hi Dmitry, You need to specify two maps, the one you are sampling and the one whose grid you are sampling on, e.g. vop resample #0 onGrid #1 This means map #1 with the desired grid must already exist. As mentioned in that link, you could create it with “vop new” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new> You can show outline boxes indicating axis orientation with the data display options in Volume Viewer or “volume” command, and move models separately by specifying model to move with the “models” option of “turn” (or “roll”) or with the mouse after freezing some models by unchecking their “A”ctive buttons in the Model Panel. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2018, at 11:56 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > Dear Elaine, > > Thank you for your answer. > > I read the last link > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting > > but I still can not save the map > > <F8EED359A67845868DD4F80A9DAF3499.png> > > If I put onGrid I get this > > <B7696E2A55B04A298BEB09E32A85BDF2.png> > > Could you please briefly tell how to make it work? > > Thank you. > > > Sincerely, > Dmitry > > > Sent from Mail for Windows 10 > > From: Elaine Meng > Sent: Thursday, May 10, 2018 5:59 PM > To: Dmitry Semchonok > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] saving new position of the model > > Dear Dmitry, > For atomic models, of course: you can just specify saving transformed coordinates in the Save PDB or Save Mol2 dialog (or “write” command). > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> > > The rotating could be done by hand with the mouse or with commands “turn” or “roll." > > However, I’m guessing you probably mean a map since that is more complicated. As explained in the “Saving Maps After Fitting” link below, you would generally have to resample the map onto a different grid that has the axes oriented how you want: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 10, 2018, at 8:34 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > > > Dear colleagues, > > Is there a way to rotate the model and than save it with a new x y z? > > Thank you > > Sincerely, > > Dmitry > > > <F8EED359A67845868DD4F80A9DAF3499.png><B7696E2A55B04A298BEB09E32A85BDF2.png>

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saving new position of the model
by Dmitry Semchonok 10 May '18

10 May '18

Dear colleagues, Is there a way to rotate the model and than save it with a new x y z? Thank you Sincerely, Dmitry Sent from Mail for Windows 10

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Setting map origin index to 0 while keeping fitted structures
by Ahmad Abdelzaher 08 May '18

08 May '18

Hello, I have spent some time fitting structures to my map. I want to set the origin to 0, however, that will lose me all the work I did. Any suggestions? Regards.

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Help
by Kimberley Perry 08 May '18

08 May '18

Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong? Kim

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