- Chimera-users - RBVI Mailing Lists

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

Visualizing major and minor axes of inertia
by Felipe Vasquez 05 Sep '18

05 Sep '18

Dear all, I am interested in visualizing the major and minor axes of inertia of a ligand in a PDB structure by using UCSF Chimera. Once I calculate the axis of inertia by entering in command line: measure inertia sel I obtained the following info (in reply log): v1 = 0.985 -0.173 -0.013 a = 6.079 r1 = 2.103 v2 = -0.086 -0.553 0.829 b = 4.564 r2 = 2.765 v3 = -0.150 -0.815 -0.559 c = 1.127 r3 = 3.400 center = 38.682 56.595 62.547 However, I do not still know: 1- What are the major and minor axes of inertia? This info is given by the "a/b/c" or "r1/r2/r3" values? 2-How can I visualize the major and minor axes of inertia as planes (or arrows)? Thanks in advances for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* PhD candidate in Chemical Engineering Universidad de los Andes Bogotá, D.C., Colombia Carrera 1 #18A-12, Of. ML-754(26) +57 1 3394949 Ext. 1747

2 3

ChimeraX and crosslinks visualization
by Pascal Albanese 04 Sep '18

04 Sep '18

Dear Support Staff, first of all many thanks for developing Chimera! I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): - Is it possible to load different sets of distances/crosslinks (like with different IDs)? - is it possible to color code the distances with a cutoff (like red if >30 for instance)? - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) that's it, maybe something can be done writing the code but unfortunately it's not my job. Thanks a lot and looking forward to hear from you, Cheers, Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

3 2

Re: [Chimera-users] Mirror image proteins
by Chu Ji 04 Sep '18

04 Sep '18

Hi Eric, I was trying to get a mirror image of a PDB model and came across your thread. I know that you are typing in m = chimera.openModels.list()[0] for a in m.atoms: crd = a.coord() crd.z = 0 - crd.z a.setCoord(crd) in the Gen Control>IDLE section, but I also read on GitHub that I should change the [0] in openModels.list()[0]to the model specifier. What does that mean exactly? I tried to type in the PDB ID to replace the 0 but nothing happened…Could you show me an example? What if I want to flip Chain B of a certain model or just the entire model? Thank you so much for your help! Looking forward to hearing from you. Best, Nancy Sent from Mail for Windows 10

2 1

Chimera: Amber to PDB
by Boris TOUZEAU 04 Sep '18

04 Sep '18

Hi, I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei. I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues. Best wishes, Boris TOUZEAU

2 4

chimera error during AddCharge for MD preparation
by Waterbury, Amanda 04 Sep '18

04 Sep '18

Hi, I am attempting to perform MD stimulations with a protein containing an FAD cofactor, however, I keep receiving the following error message: Charge model: AMBER ff14SB Assigning partial charges to residue FAD (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.in.mol2 -fi mol2 -o /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 (FAD) (FAD) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (FAD) Referenced from: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (FAD) Reason: image not found (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (FAD) (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (FAD) Total number of electrons: 408; net charge: -2 (FAD) (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (FAD) Error: cannot run "/Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue FAD Check reply log for details Any help/suggestions would be much appreciate! Best, Amanda

2 1