- Chimera-users - RBVI Mailing Lists

Deterministic traversal of a chemical graph
by Jaime Rodríguez-Guerra Pedregal 08 Mar '19

08 Mar '19

Dear Chimera team, I have two questions regarding the same idea. I am trying to develop a script to find topologically equivalent residues in a structure (e.g. MOF, cages, and so on). To do this, I am using SplitMolecule.split.split_connected and then comparing the resulting pieces by number of atoms, empirical formula and, ultimately, I would like to compare the chemical graph (i.e. test for graph isomorphism). Is there any built-in function/object for that in Chimera? Since I didn't want to overcomplicate the algorithm, for now I am trusting that there won't be isomers in the structure and the empirical formula (actually a collections.Counter applied to atom.element.name<http://atom.element.name>) is enough of a test.This is working ok but, in some cases, the resulting pieces have totally different atom names because they come from a unified generic residue that encompasses all the pieces. As a result, I want to rename them in the same way consistently. My first attempt at this consists of finding the chimera.Root atom of each piece and then using chimera.Molecule.traverseAtoms to iterate over the piece. However, I've found that the Root is not always the same (topologically speaking) atom, so the naming scheme differs from piece to piece. Is there anyway to guarantee topologically equivalent traversals? I guess that both questions would lead to the same result, because it seems that I will need a chemical graph anyway. Thank you in advance, Jaime.

2 3

Saving files from MD Movie
by Divjak Maja 06 Mar '19

06 Mar '19

Hello! I have been using Chimera for analysis of H-Ras morphing from its GDP-bound inactive state to the GTP-bound active state. It works very nicely and a lovely movie is produced. What I am having difficulty with however, is saving the output of the morph as a series of PDB files that I can import to Autodesk Maya with the molecular Maya plugin. When I try to save from the movie window ie using file >save PDB, all I get is one PDB file containing a single structure. I also tried to save using the main window file > save PDB > save all frames and the same thing happens. I then tried selecting each frame individually and saving with unique numbered file names, but again, when trying to import into Maya, all I get is one structure, not a changing structure. Even the first and last frame PDBs are the same. Could you please advise as to how to save the morph output as a useful PDB series, I must be missing something? Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60] Phone +61 3 8559 5961 Email maja.divjak(a)petermac.org<mailto:maja.divjak@petermac.org> 305 Grattan Street Melbourne Victoria 3000 www.petermac.org<http://www.petermac.org/> Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

2 2

Re: [Chimera-users] Chimera installation on Windows Sub System Ubuntu
by Tom Goddard 04 Mar '19

04 Mar '19

The OpenGL graphics library is an operating system library. If you install it then Chimera should find it. There is nothing more you would have to do. Tom > On Mar 4, 2019, at 1:00 PM, Rosenberg, Mark F <mark.rosenberg(a)imperial.ac.uk> wrote: > > Hi Tom > Sorry to bother you again. > I have found installed/ the library. How do I tell Chimera where to look for it please when building ? > Thank you again. > Mark > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, March 4, 2019 6:54:44 PM > To: Rosenberg, Mark F > Cc: Rosenberg, Mark F; chimera-users(a)cgl.ucsf.edu BB > Subject: Re: Chimera installation on Windows Sub System Ubuntu > > The error installing on the Ubuntu virtual machine means that the opengl graphics library libGL.so.1 was not found. Probably you need to install a graphics driver for the Ubuntu virtual machine in order for Chimera to start. > > Tom > > >> On Mar 4, 2019, at 9:40 AM, Rosenberg, Mark F wrote: >> >> >> Dear Tom >> Hope you are well. I think I have been at this for days. I am trying to install Chimera on a Windows installation but I have had a few bugs which I have submitted to Bugs. >> >> I thought in the meantime , I could try and install Chimera in the Windows Subsystem with Ubuntu. >> >> I have got so far but I keep on getting the below error. >> >> I have tried to see if I am missing any libraries to no avail. >> >> Do you have any suggestions please ? >> >> Thank you very much. >> >> Kind Regards >> >> Mark >> >> Traceback (most recent call last): >> File "/opt/Chimera/share/__main__.py", line 73, in <module> >> value = chimeraInit.init(sys.argv) >> File "/opt/Chimera/share/chimeraInit.py", line 666, in init >> import chimera >> File "/opt/Chimera/share/chimera/__init__.py", line 16, in <module> >> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform >> ImportError: libGL.so.1: cannot open shared object file: No such file or directory >> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

1 0

Re: [Chimera-users] Chimera installation on Windows Sub System Ubuntu
by Tom Goddard 04 Mar '19

04 Mar '19

The error installing on the Ubuntu virtual machine means that the opengl graphics library libGL.so.1 was not found. Probably you need to install a graphics driver for the Ubuntu virtual machine in order for Chimera to start. Tom > On Mar 4, 2019, at 9:40 AM, Rosenberg, Mark F wrote: > > > Dear Tom > Hope you are well. I think I have been at this for days. I am trying to install Chimera on a Windows installation but I have had a few bugs which I have submitted to Bugs. > > I thought in the meantime , I could try and install Chimera in the Windows Subsystem with Ubuntu. > > I have got so far but I keep on getting the below error. > > I have tried to see if I am missing any libraries to no avail. > > Do you have any suggestions please ? > > Thank you very much. > > Kind Regards > > Mark > > Traceback (most recent call last): > File "/opt/Chimera/share/__main__.py", line 73, in <module> > value = chimeraInit.init(sys.argv) > File "/opt/Chimera/share/chimeraInit.py", line 666, in init > import chimera > File "/opt/Chimera/share/chimera/__init__.py", line 16, in <module> > from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform > ImportError: libGL.so.1: cannot open shared object file: No such file or directory > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

1 0

How to setup appropriate parameters during auto dock vina
by temban billyhp 02 Mar '19

02 Mar '19

Hi, How should I vary docking parameters when carrying out ligand/receptor docking in order to obtain correct results. Is there any logical trend to follow. I have always used the default mode. Best regards Sent from Yahoo Mail on Android

2 1

Re: [Chimera-users] Morph Help
by Elaine Meng 01 Mar '19

01 Mar '19

Hi Debamita (Paul), You may not always be able to get the trajectory you want. All I can suggest is to try: (1) changing morph parameters. You did not say whether you were using Chimera or ChimeraX. Both allow changing method and core fraction, or forcing Cartesian intermediates (the latter has not been useful in the cases I’ve worked on, however). ChimeraX also allows changing hinge spacing. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> (1b) Chimera has an option to minimize each frame, but it also has limited ability to “rescue” bad conformations, and it will take a lot longer to calculate your morph trajectory. (2) more difficult, if (1) does not solve your problem: manually create intermediate states to “guide” the overall trajectory and then morph in more stages involving these intermediates. I.e instead of morphing 1->2, create 1a and possibly 1b etc. then morph 1->1a->1b->2. I hope this helps. For future reference, to make it more likely you get your questions answered, please send to chimera-users(a)cgl.ucsf.edu or chimerax-users(a)cgl.ucsf.edu (depending on which program you’re asking about). Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 25, 2019, at 12:30 PM, Paul, Debamita <Debamita_Paul(a)baylor.edu> wrote: > > Hi, > > I am trying to morph two structures having a DNA lesion (6-4 Photoproduct). However the movie is showing weird geometry in the intermediate steps. Is there a way I can provide the parameter file for the 6-4 so that the geometry is not messed up. > > Thanks > Debamita

2 4

Chimera using question
by Khải Trần Gia 28 Feb '19

28 Feb '19

Dear Mr/Mrs, I am a person using Chimera to adding missing residues to a protein from Protein Data Bank. My protein has 2 chains: A and B which both have missing residues. I have used Chimera tools compliment with Modeller to adding missing residues in both chain. The problem is I want to save the whole protein which consists of 2 fixed chains, however when I saved with PDB it only show 1 chain. How can I do that? I am looking forward for your replying. Thank you. Best regards, Khai.

2 2

Chimera Help
by Debamita Paul 28 Feb '19

28 Feb '19

morphg5-xtal_0222_new.pdb <https://drive.google.com/a/cornell.edu/file/d/1t0Up4tsMWqLe7ipmUEfRzth0OFNN…> morphg5-xtal_0222_new.pdb <https://drive.google.com/a/cornell.edu/file/d/1C_cQTG9d5k10rKOQnW_XayfDGZt1…> Hi Dr. Meng, I emailed you earlier about having trouble in morphing two structures of a DNA bound protein. The DNA has 6-4 photo lesion. I am attaching the pdb files and the morph results (64_IB to 6cfi). You can see in the morph

2 1

Can Chimera read electron density difference map files from RIDL?
by Murpholino Peligro 28 Feb '19

28 Feb '19

Here is what RIDL is https://github.com/GarmanGroup/RIDL I can open the map in coot specifying is a difference map and it opens nicely over the protein. In chimera I can open the map but .....all my clicks won't reproduce the coot behavior :P ... Thanks

2 1

Seeking for help
by temban billyhp 27 Feb '19

27 Feb '19

SirI prepared the DNA molecule using the dock prep with its default options but when I lunched auto dock vina alongside with my ligand, I received a message that auto dock vina cannot prepare the receptor due to an error. How can I solve this problem. I will be greatful listening from you. Best wishes. Sent from Yahoo Mail on Android

2 1

Installation problem on Fedora 29
by Murpholino Peligro 26 Feb '19

26 Feb '19

[murphy@eva02 Downloads]$ ./chimera.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/murphy/Downloads' inflating: chimera_install_6JK7q6/installer inflating: chimera_install_6JK7q6/chimera.bin Enter install location: ~/.local/UCSF-Chimera64-1.13.1 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/murphy/.local/UCSF-Chimera64-1.13.1' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu and icon? yes Traceback (most recent call last): File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimeraInit.py", line 666, in init import chimera File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/__init__.py", line 2777, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/murphy/.local/UCSF-Chimera64-1.13.1/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_6JK7q6' Installation is done; press return. Help please.

2 1

how to hide just H-bonds between water molecules with themselves?
by masoud aliyar 22 Feb '19

22 Feb '19

Hello I want to find H-bonds between 3 residues and the ligand and the water molecules around the ligand in 3 angstrom, but I don’t want H-bonds between water molecules. I Just want h-bonds between residues together and residues with ligand and residues and ligand with water. I have used Per-Frame script system. But I have two problems. First, if I set selection mode on replace mode and write this script: ********************* ~display :SOL zonesel :279 3 :SOL select up display sel select :38:53:147:279 findhbond linewidth 3 color blue selRestrict :SOL:38:53:147:279 ********************* The result is fine and H-bonds that I want were display. But if I apply this script, the system searches every water residues for find H-bond and take a lot of time per frame. second, if I set selection mode on append and write this script: ********************* ~display :SOL zonesel :279 3 :SOL select up display sel select :38:53:147:279 findhbond linewidth 3 color blue selRestrict both ********************* The calculations are going faster, but also, show H-bonds between water molecules with themselves that I don’t want it. How can I hide H-bonds between water molecule with themselves but H-bonds between selected residues and ligand and water retain? Thank you, everyone,

2 1

Defining CMYK color scheme for color actions
by Boaz Shaanan 22 Feb '19

22 Feb '19

Hi, Some journals require usage of CMYK color scheme. I see that the CMYK option exists in the color editor but is it possible to define CMYK for all the color actions (actions --> color) without having to go through the color editor for each color? Or am I missing something altogether? Thanks for you advice, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

3 3

Measure angle and effect length
by Shishir Adhikari 21 Feb '19

21 Feb '19

Hi, What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? Thanks

2 2

ViewDock tool not showing PDBQT vina output file
by Walker, Kevin 21 Feb '19

21 Feb '19

The subject line summarizes the challenge. I can open all other file types of interest (pdb, pyc, py) for viewing. However, I am unable to open a pdbqt vinaout file within Chimera 1.13. The result: Chimera session freezes and can only be shut down through the Windows 10 task manager. Have uninstall and reinstalled Chimera, cycled computer off and back on, and updated graphic driver and rolled by graphic driver to previous version, all to no avail. Windows 10 64-bit Chimera 1.13 Graphics Card: AMD Radeon 480 Memory: 11 GB

3 3

Chimera PDB2PQR
by Sowmya Indrakumar 21 Feb '19

21 Feb '19

Dear Developers, I am try to use Chmiera for electrostatic calculations. I first make the PQR file using the PDB2PQR at different pH, however I do not see a change in the total charge, the REMARK section shows that total charge is 1 always. I'm using the default setting as shown in the attached screenshot. Please let me know what might be going wrong? I installed the new version twice. Thanks a lot for your help! Regards Sowmya [cid:cdf013bd-01d5-4d3d-9dd2-554c27674417]

3 2

Chimera
by Giovanny Rincon S 21 Feb '19

21 Feb '19

Hello, I am a graduate student in Balearic Islands, I am doing a protein study with Chimera, I wanted to ask if it is possible to change the background color to White. Thank you so Much

3 2

Broad selection with command
by masoud aliyar 21 Feb '19

21 Feb '19

I use "zonesel" command to select SOL residues around ligand. but this command did not select entire residue and just select atoms that are the given zone.how can I use command-line to broaden residue selection and select entire residue atoms?. I know I can use the keyboard to broaden selection, but I want to use the command-line

2 2

STL/OBJ 3D models exported by Chimera cannot be read in Office 2019
by Jaime Rodríguez-Guerra Pedregal 20 Feb '19

20 Feb '19

Hi, Chimera team! I have recently discovered that Office 2019 has support for 3D objects that can be rotated, animated, zoomed... So I was curious about the possibilities for our molecular presentations. I knew Chimera allows to export molecules to several 3D formats and crossed my fingers so there was at least one format supported by Office. - Good news: there are two! STL and OBJ are both exported by Chimera and supported by Office. - Bad news: while the files can be correctly "loaded" in Office, they are not displayed at all! "Image could not be shown". Is this something that must be addressed in Chimera or is Microsoft's fault? The error message is very succinct and does not provide more details. I have attached the files I created with Chimera just in case. Thank you very much! Jaime.

2 2

Chimera laptop features required
by p.tapi＠alice.it 20 Feb '19

20 Feb '19

Sir, I'm going to use USFC Chimera program working for La Sapienza University in Rome Italy ... before to get the program, I would like to understand the best recommended laptop features to easy run the program under Microsoft Windows WIN 10 platform .. May you answer me regarding the main laptop features ( CPU type, speed, RAM, SSD, screen resolution, etc ) you recommended ? What you suggestions ? Thanks in advance Regards Silvia Taglieri Rome Italy

2 1

linking plane slider among between volume models
by Michael Elbaum 19 Feb '19

19 Feb '19

Hi. I'm looking at volume and surface data simultaneously. I'd like to select a range of planes, and then when I change the selection to have it apply to both datasets. For example I'm looking at density in "solid" mode together with a smoothed isosurface. To keep them in step I should change the setting manually (in the gui) for each dataset individually. It's surprisingly easy to lose the precise overlap. It would be helpful to choose the datasets to which the planes parameters apply. Perhaps there's a non-gui way to do this? If not possible in Classic Chimera, then please just consider as a suggestion for ChimeraX. thanks, Michael

2 2

Re: [Chimera-users] [chimerax-users] Can ChimeraX morph between two surfaces?
by Steve Chou 19 Feb '19

19 Feb '19

Hi Elaine, Thanks for your detailed explanation! What's the format of the pseudobond file? Should it look like this? =============================== #1/A:13@NE2 #1/A:502@MG =============================== All the best, Steve On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Steve, > Actually I’m surprised the Mg and water were included (even if present at > both ends) because I thought they had to be tethered by a bond or > pseudobond (like a distance measurement) to the biopolymer chain, as > described here under “Atoms in Common”: > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > > For the case where composition changes, you could add in a fake Mg ion and > water to the structure that’s missing them, but you’d have to decide where > to put them. Also it was my understanding that they had to be tethered to > the biopolymer chain (e.g. add distance measurement, which can then be > hidden), but maybe that requirement has changed, or the Mg does already > have a metal-coordination pseudobond to the biopolymer. > > Or if you don’t care if the Mg or water move during the morph, you could > just display those atoms from the original model (that was input to > morphing) even though they are not present in the trajectory. > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou(a)gmail.com> wrote: > > > > Thanks, Elaine! > > You command "rainbow structures" works beautifully. > > There is "a Mg ion" and "a water molecule" in the two conformations. > > (1) If the two conformations have exactly the same compositions (by > shifting the structure), the "Mg ion" and the "water molecule" do not > follow the same path as the protein. They move but separate from the > protein. > > (2) If the two conformations have slightly different compositions, the > "Mg ion" and the "water molecule" do not show up in the morphed pdb > ensemble. > > Is there a way to morph the specific components properly? > > Steve > > > >

2 3

Error while doing autodock vina via chimera
by Sourav Mondal 19 Feb '19

19 Feb '19

I was tring to dock the phytochemical (cid-3114) with protein (pdb id -5YFN) , this is the error I am getting. What is the reason for the error? How to overcome this error? Model 0 (human isocitrate dehydrogenase.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. No SEQRES records for human isocitrate dehydrogenase.pdb (#0) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: #0 LYS 1.C Chain-final residues that are actual C terminii: #0 MG 410.C Chain-final residues that are not actual C terminii: 396 hydrogen bonds Hydrogens added Wrote E:\Sem 1\BIOINFO\human_isd_3114.receptor.pdb Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2B Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2D Unable to assign MAP type to atom Mg Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:MG 410:MG Wrote E:\Sem 1\BIOINFO\human_isd_3114.ligand.pdb Autodock Vina ligand docking initiated for human isocitrate dehydrogenase.pdb Status file contents: 1 1550389354.82 1550389354.92 Running AutoDock Vina for human isocitrate dehydrogenase.pdb failed; see Reply Log for more information Application stderr ----- Parse error on line 4016 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. ----- Application stdout ----- ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # ################################################################# WARNING: The search space volume > 27000 Angstrom^3 (See FAQ) Detected 8 CPUs WARNING: at low exhaustiveness, it may be impossible to utilize all CPUs Reading input ... ----- Sent from Mail for Windows 10

2 1

rmf3 control in Chimera
by Daniel Ziemianowicz 15 Feb '19

15 Feb '19

Hello, I can't find anything about this online, but I was told that there should be some control on the components of rmf3 files. Specifically, I would like to map my data onto an rmf structure from IMP. Normally I would use render/define attribute for some types of data and xlinkanalyzer plugin for crosslink data. However, I can't quite figure out how to control rmf structures in this same manner. I am hoping I could do something like this: given a bead with residue x and another bead containing residue y, I can map a crosslink to those beads. Likewise, with render by attribute, I can color the beads containing the relevant residues. The farthest I was able to get was reading the rmfalias documentation but that is also a bit confusing and I was not able to perform the aliasing - specifically it says rmfalias [ depth N ] [ skip_prefix M ] [ rmf filename ] as the command but then it gives an example filename/nodename1/nodename2/nodename3 which seems to contradict the "usage" format. Either way I was not able to select or alias-name the beads I would like. Below I attached an example of the hierarchy in my file, how can I select e.g. "13-22_bead" of "EED"? I hope this was not a confusing question, let me know if I need to clarify. I can also email Ben Webb from the Sali lab if this is more relevant for them. Thank you, Dan [cid:image001.png@01D4C486.CABA8470]

2 1

Question about AutoDock
by Cassidy Terrell 13 Feb '19

13 Feb '19

Hello, I am using the AutoDock feature in UCSF Chimera and after clicking "Apply" everything appears to work normally and then program says: E*xecution complete - check outputs to verify successful execution* In the past a ViewDock window with the results would automatically pop-up after the execution completed - however this is no longer happening and I do not know how to access the output files. The program did not write a *name.pdbqt *file - all other files are there though. Any suggestions for accessing the output file would be much appreciated!! -- Cassidy R. Terrell, Ph.D. Assistant Professor, Biochemistry University of Minnesota, Rochester 111 South Broadway Rochester, MN 55904 *Always believe something wonderful is about to happen*

2 2