- Chimera-users - RBVI Mailing Lists

Atom specifiers for selected atoms
by BuddySphinx 16 Sep '18

16 Sep '18

Dear Chimera users, I have a simple question, if I have selected some atoms from my coordinates using mouse and draw a square. How do I know which atoms I have selected? Is there any way to show the atom specifier? Best, Yangqi Sent from Mail for Windows 10

2 1

Calculating surface area
by Yangqi Gu 14 Sep '18

14 Sep '18

Dear Chimera users, I am trying to visualize the interface surface of my two monomers. Is there anyway to show the interacting surface from Chimera by using the EM map? Or should I do it from PDB coordinates? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

2 4

Morph colors
by Rajan Prabu 14 Sep '18

14 Sep '18

Hello again, Following another old thread, http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012743.html I could morph/play the coordinates and Volume at the same time. The script is given below. ---------------------------------------------------- # Open maps and set threshold open 1.mrc open 2.mrc open start_full.pdb open end_full.pdb vol #0,1 level .025 # Create a marker for coloring measure center #2 mark true radius 20 color red ~display #4 # Create morph volume vop morph #0,1 frames 0 model #5 # Create morph models model #6 morph start #2 frames 200 morph interpolate #3 frames 200 morph movie # marker on morph measure center #6 mark true radius 20 color red # Color near marker scolor #5 zone #6 range 50 coordset #6 1,100; vop morph #0,1 start 0 playstep 0.01 frames 100 model #6 ---------------------------------------------------- Still the color is at centre of of the first Frame of morph. If I understand correct I have to measure the centre for each Frame and add marker and color it. But I still can't make it. Any help/directions in this regard would be very helpful. Thanks in advance for your time and help. best regards Rajan

3 4

Open Structural Measurement table
by Ayala Carl 13 Sep '18

13 Sep '18

Hi, I have been having difficulty opening a previously saved table of measured distances. I cannot open in as any file type listed by chimera and unfortunately I did not save the session that I measured the distances. If I open my models is there a way to impose the distances saved to the opened models? Thanks in advance

2 1

Morph colors
by Rajan Prabu 13 Sep '18

13 Sep '18

Hello all, First please accept my apologies for to open a topic which is discussed already, but I couldn't get it working. I would like to morph a volume and colour its subregions. I made the following script ( adopting old messages in this forum ) open 1.mrc open 2.mrc open start_full.pdb open end_full.pdb vol #0,1 level .025 # Create a marker for coloring measure center #2 mark true radius 20 color red ~display #4 # Create morph vop morph #0,1 frames 0 model #5 # Color near marker scolor #5 zone #4 range 50 #Play morph vop morph #0,1 model #5 frames 200 interpolateColors false In the above script everything works, but color stays at place. Unfortunately for my morphing the marker has to move along with the morph. But I dont know how to do that. Any help in this regard would be very helpful. best regards Rajan

1 0

Errors applying AddCharge to PDB files with non-Chimera protonation
by Matthias Bal 12 Sep '18

12 Sep '18

Hi, I have a large amount of PDB files which need explicit hydrogens for MD and quantum calculations. To go beyond Chimera's AddH function, I've tried using the Protoss tool among others. Trying to add charges (AMBER ff14SB) using Chimera to PDB files protonated in this way leads to errors regarding non-standard atom names in standard residues. For example, the protonated PDB case 1amw gives the following errors in the Reply Log: > Non-standard atom names: > ALA H (ALA 2.A H) > Total charge for #0: -12.939 > The following residues had non-integral charges: > ALA 2.A 0.4009 > LYS 102.A 0.66 > Correct charges are unknown for 1 non-standard atom names in otherwise standard residues > Charges of 0.0 were assigned to the unknown atoms I know the suggestion of the help page on AddCharge is to remove the hydrogens and re-add them using AddH since they are often the problem, but that's not really an option in this case. Is there an overview somewhere of all the different PDB hydrogen naming conventions (like a more recent version of https://www.ics.uci.edu/~dock/pdb2pqr/programmerguide.html) and how they relate to what Chimera/Amber is using? And is there a way to script the conversion to treat files in batches? Thanks a lot, Matthias

2 2

Unix download
by KEITH MUNSON 10 Sep '18

10 Sep '18

Hi Chimera, I downloaded chimera-1.13-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x8…> into my Dell desktop Downloads dir but there was no chimera-installer.bin included in the download. Where do I get the installer? Thanks, Keith Munson

2 2

Writing models in PDB only working via model panel, not via drop-down menu (UCSF Chimera 1.3)
by Jun Ha Song 10 Sep '18

10 Sep '18

Dear RBVI, I noticed that I could not write .cmm marker sets in UCSF Chimera as PDB file via drop down menu from main window, but that I could write it as PDB via Model Panel's side menu. Is this a bug? Best, Junha Song.

2 2

max density value using a script
by Tamas Hegedus 07 Sep '18

07 Sep '18

Hi, I subtract two electron density maps and I would like to get the min and max density values of the resulted map. I can see these values in the GUI, but I would like to get them running chimera without a gui using a python script. (Without saving the final map into an .mrc file and reading the header of that file.) Thanks for your help, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org

3 4

calculate density from an AA model
by Tamas Hegedus 06 Sep '18

06 Sep '18

Hi, Is there an option (command, tool) in Chimera to calculate the theoretical electrondensity map for an all atom protein model? Similar to the MDFF tool in VMD. https://www.ks.uiuc.edu/Training/Tutorials/science/mdff/tutorial_mdff-html/… Thanks, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org

2 2