May 2014 - Chimera-users - RBVI Mailing Lists

part-time job for Chimera professionals
by Andrew Voronkov 30 May '14

30 May '14

Dear Chimera users, if anyone may be interested in part-time job and additional income through Chimera usage, please let me know. I am looking for someone, who can regularly make nice-looking Chimera pictures. It can be 2-3 hours per week for example. Best regards, Andrew

1 0

Save to a file
by sette＠uniroma2.it 29 May '14

29 May '14

Dear all, I created a simple text file with a list of distances to be measured How to save in a file the measured distances? The saveFile options does not seems to be the solution. I use 1.7 version of Chimera on Windows 7. Thanks, Marco ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

2 5

merging 2 pdb files
by Adrian Javaherian 28 May '14

28 May '14

Hi, My name is Adrian. I am a graduate student at Bar Ilan University in Israel. I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits. I download the Chimera program. Is it possible to do this on your program and if so, can you please tell me how? Thank you so much, Adrian

3 3

mmCIF support
by Greg Couch 28 May '14

28 May '14

Hello, I'm working on improving Chimera's mmCIF support. So if anyone has a mmCIF file that is not from the PDB and that they are willing to share, please send it to me. Many thanks, Greg

2 1

domain colouring
by ce 28 May '14

28 May '14

Hi, Could You send me instruction about domain colouring (the quickest way if possible) ? Cheers, J.

2 5

After fitting a PDB into a cryo-EM density, is it possible to color the PDB atoms by the local EM density in the cryo-EM map?
by Lai, Jonathan 27 May '14

27 May '14

Dear Chimera-users, I have several cryo-EM maps of an assembly process and a PDB of the final product; what I want to do is to have a visual depiction of how the local EM density around structural elements in the final product changes over time. After fitting the PDB into the cryo-EM density, I am wondering if it is possible to color the PDB atoms by a reference EM density at each point. For example, I want to color every residue that intersects isosurface == 0 blue, every residue that intersects isosurface == 1 red, and have a continuous color scheme for all intermediate values from (0 to 1). I already have fitted the PDBs into the cryo-EM maps. Is there any easy way to do this? Cheers, Jonathan Lai University of Illinois at Urbana-Champaign

3 2

problem in picking
by Uzma Saqib 27 May '14

27 May '14

Hi , I am not able to pick atoms in Chimera from the graphics window (*picking*). pls help. FYI, snapshot attached. thanks

2 1

script
by Schulz-Gasch, Tanja 22 May '14

22 May '14

Hi there, I hope you could help me with a little script. I am pretty sure, that something must exists already;-) I need to rotate around the y-axis in 2 degree steps for a total of 44 degree and at each step export a high res graphic. Rotation of the camera/view (keeping the look-at point) would be preferable compared to rotation of the object. Anything out there like this??? Thanks for your help, Tanja -- *Dr. Tanja Schulz-Gasch *Head of Communications & Operations, pRED Basel Bldg 69, 308 Grenzacherstrasse 124 4070 Basel Switzerland Mobile: +41 (0) 79 578 4672 Work: +41 (0) 61 688 8309 Email: tanja.schulz-gasch <http://goog_20899098>@roche.com Web: www.roche.com *Confidentiality note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.*

3 5

show path in Volume Viewer or Model Panel
by Dieter Blaas 21 May '14

21 May '14

Hi, I am often looking at a number of structures with the same file name but in different directories by using e.g: chimera ./dir*/struct.mrc to look at structures ./dir1/struct.mrc ./dir2/struct.mrc ./dir3/struct.mrc and so on... since all have the same name, it is difficult to identify them in chimera. Is there a way as to let chimera display the path in addition to the file name or any other way of finding out what is what? 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 ------------------------------------------------------------------------

2 1

Custom presets
by Oliver Clarke 20 May '14

20 May '14

Hi all, I posted this last week, but it didn’t appear in the archives, so I guess it didn’t go through - if that is not the case, my apologies for the double post. I notice in the presets menu that there is the option to add custom presets, but I couldn’t find much documentation on this feature. Is it possible to save the current display options as a preset, similar to saving individual preference combinations but as a preset that can be quickly loaded? For example, displaying X-ray maps in a way that looks similar to how they are represented in Coot is a little complicated - I usually turn off “Mesh lighting”, “Cap high values at box faces”, and “Square mesh”, turn off ribbons, display all atoms and set the stick scale to 0.5, change the background to black, and alter the depth cueing - it would be very handy indeed to be able to apply all these settings at once. Also with regards to X-ray maps, I usually normalize (using vop scale #map, factor 1/SD) both the 2fo-fc and fo-fc, and then split the fo-fc into separate +ve and -ve maps, using vop threshold #map minimum 0 and vop threshold #map maximum 0. Would it be possible to assign these steps to macros or commands, and if so how would I go about doing that? Many thanks for your help, Oliver.

3 17

Chimera-users May 2014