- Chimera-users - RBVI Mailing Lists

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]

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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

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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

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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.

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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

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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

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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 > > > >

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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

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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]

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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*

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