August 2016 - Chimera-users - RBVI Mailing Lists

question
by A G Szabo 23 Aug '16

23 Aug '16

I recently downloaded the new version of Chimera. No issues with that so far. However, when I save a session it is still saved as a Chimera file, or a PYC file on my desktop. So when I went to my desktop file list, and tried to open one of the files I would click on "open with ." Two programs would be listed, Adobe, and Chimera. So I would select Chimera and the file would open satisfactorily. However, with the new version of Chimera, if I repeat the above, the only program that is listed is adobe. If the file type is listed as Chimera, then adobe would be listed, and there would be other programs listed but not Chimera. I can open the file in a round about way, but the former way was more efficient and user friendly. If I go to my programs list, there doesn't seem to be a way that I can conveniently open the file without first opening up Chimera. Your comments will be appreciated. Arthur G. Szabo

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Select Non-conserved residue
by Markus Heller 23 Aug '16

23 Aug '16

Hi all, I used matchmaker to align two homologues proteins, and to calculate the sequence alignment. How can I select all non-conserved residues, in one fell swoop? Thanks and Cheers Markus -- Markus Heller, Ph.D. Senior Scientist, NMR 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 | www.cdrd.ca Follow us: 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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Re: [Chimera-users] What is the default of ribbon?
by Elaine Meng 20 Aug '16

20 Aug '16

Hi Root, You cannot change this preset, but you can control what is shown “manually," for example hiding all atoms and then displaying residues within 5 angstroms of ligand and 3.2 angstroms of ions with commands: ~disp disp ligand z<5 disp ions z<3.2 To make a more simple one-step action, you can make an “alias” combining several commands, and that could be listed in an Aliases menu. This is sort of like “make your own preset”. For examples, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007230.html> I hope this helps, Elaine On Aug 19, 2016, at 1:03 AM, 郭尚哲 <b02b02049(a)ntu.edu.tw> wrote: > Dear Elaine, > I have another question. How can I change this 3.6 Å criteria, if it is possible? > Root > ________________________________________ > 從: Elaine Meng [meng(a)cgl.ucsf.edu] > 寄件日期: 2016年8月19日上午 12:54 > 至: 郭尚哲 > 副本: chimera-users(a)cgl.ucsf.edu > 主旨: Re: [Chimera-users] What is the default of ribbon? > > Hi Root, > It is described in the “preset” documentation: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets> > > … specifically, > "Interactive 1 (ribbons) - shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.” > > In other words, if the amino acid residue has any atom within 3.6 Å of what Chimera thinks is “ligand” or “ion” the whole sidechain will be shown, except any H atoms attached to C atoms. > > You do not need to search on the net, you can just look at the manual included with your download, using menu: Help… Search Documentation. For example, you could search for “presets” or “ribbon interactive preset”. The information you found is explaining something different: why the backbone atoms are not shown. > > 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 Aug 17, 2016, at 11:13 PM, 郭尚哲 <b02b02049(a)ntu.edu.tw> wrote: >> >> Hi all, >> I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below: >> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo… >> It says "By default, when ribbon is shown for a residue, the mainchain atoms of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)." >> I can't get more imformation, and still don't understand. >> What is the rule chimera follow to show the sidechain of certain residues? >> Thanks, >> Root > >

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segmenting cryoEM maps
by giulia palermo 20 Aug '16

20 Aug '16

Dear all, I am new to chimera and I am working with density maps. I have segmented my cryoEM map successfully. I want now to group some of the segmented regions in a single region and subequently save the obtained map. Is there a way of doing it? Thank you very much Best wishes Giulia Palermo

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Re: [Chimera-users] Add Hydrogens - non standard residue - protonation state
by Elaine Meng 19 Aug '16

19 Aug '16

Hi Subha, This is out of my area, since I don’t know python. (We always recommend sending questions to the chimera-users list, CC’d here, since you are more likely to get a good answer by asking multiple people!) I can only say that as far as I know if it works in the command line, then you should be able to use python to run the same command, as described in this page in the Chimera programmer’s guide: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Best, Elaine On Aug 19, 2016, at 1:57 PM, Subha Kalyaanamoorthy <kalyaana(a)ualberta.ca> wrote: > Hi Elaine, > > Just another question, > > Is there anything I need to import for using setattr in a python script. I get an error when I use it as a part of script. But, it works fine when I type it on the command-line of Chimera gui. Not sure what I am missing. > > Thanks and Best Regards, > Subha >

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Default contour level in Volume Viewer
by MICHAEL POTEAT 19 Aug '16

19 Aug '16

Hello all, How is the default contour level in the Volume Viewer calculated when you first open up a .mrc file? I've tried the average density, and the root-mean-square of all voxels, but both do not match Volume Viewer's default level. I've tried looking here [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame…] for documentation on this, but it does not mention it. Thanks, Mike

2 1

Add Hydrogens - non standard residue - protonation state
by Subha Kalyaanamoorthy 18 Aug '16

18 Aug '16

Hi There, Can anybody please suggest me how to use 'setattr' (or any other function) to assign a protonation state for an atom in a non-standard residue. I have a ligand and I am using a python script to add hydrogens and charge to the ligand molecule using chimera no-gui. I see that chimera adds an extra hydrogen to a nitrogen atom in the ligand and assigns a charge of +1 to the molecule. Removing this hydrogen using GUI is simple but not practical for large set of molecules. So, it would be helpful if somebody suggest me a command-line to set specific protonation states for atoms (in non-standard residue). Thanks and Best Regards, Subha

2 2

splitting and surfaces
by A G Szabo 18 Aug '16

18 Aug '16

I am working on a large multi subunit structure (4CR2). Originally I selected one of the subunits, and received the error message that suggested I should use the split command. Which I did and obviously I must have been successful in splitting the subunits. Each of the subunits is now labelled as being split, i.e. (#0.14) etc. I was successful in showing the surfaces of 4 subunits, and colored them differently. However, when I tried to show the surface of one of the subunits with 437 residues, (several residues cannot be resolved) I received this error message One subunit which I successfully was able to show the surface in the image had 467 residues and also had a large number of residues that were not resolvable. So I am stuck! Your help would be appreciated. AGSzabo

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further
by A G Szabo 18 Aug '16

18 Aug '16

Further to my last message regarding surfaces it would be highly convenient to have the url listed at the bottom of the error message open as a link. Secondly it is not even possible to copy it and paste it into my browser. ags

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What is the default of ribbon?
by 郭尚哲 18 Aug '16

18 Aug '16

Hi all, I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo… It says "By default, when ribbon is shown for a residue, the mainchain atoms<https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)." I can't get more imformation, and still don't understand. What is the rule chimera follow to show the sidechain of certain residues? Thanks, Root

2 1

Chimera-users August 2016