- Chimera-users - RBVI Mailing Lists

Chimera
by Arnaout, M. Amin,M.D. 18 Oct '19

18 Oct '19

I<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…>I downloaded chimera-1.14-mac64.dmg<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…> on my iMAC with Catalina OS but cannot open Chimera (see attached).

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Chimera on macOS Catalina (10.15)
by Tom Goddard 16 Oct '19

16 Oct '19

Apple released their next version of macOS, version 10.15, called Catalina, a week ago. I have tested the Chimera 1.13.1 and Chimera 1.14 release candidate with Catalina and they worked without obvious problems. macOS Catalina has introduced new security measures where you must give permission to each application to allow it to access Desktop, Downloads and Documents folders and external disk drives. So you will see those permission dialogs appearing in Chimera and will need to press Allow. You only need to grant permission once for each folder when you try to open data from that folder and those permissions will apply to all future Chimera uses, so it is not too annoying. Tom

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depict hydrophobicity surface in super large molecules in chimera
by Marta Perez Illana 15 Oct '19

15 Oct '19

Hi all I was trying to analyze the hydrophobic surface of two very large structures ( 3 chainsx 900 aa each so 2.700aa). As expected the default surface calculation has failed. Normally for electrostatic potential what works for me is making a mol map (molmap #3 4 gridSpacing 0.5) and then calling the pdb2pqr and apbs servers directly from chimera, which is very convenient. However I cannot find an analogous way to make it with hydrophobicity... Since the surface fails for such big molecules, the straight forward way (present-3interactive surface hydrophobicity) does fail as well... Then... is there any server than can be called from chimera, to get hydrophobicity as an attribute to be depicted? Or alternatively could you suggest any server that gives output hydrophobic column, compatible to get it after to chimera attributes? Reading a bit I found that, not as electric fields, that can be computed for structures, hydrophobicity comes just for the sequence, without taking into account the neighbours and context... P.D: I have managed to represent in other programs the hydrophobic surface, but I really want to make it in chimera, to make it more consistent and easy to organize myself... Thanks a lot! and sorry if the question goes beyond Chimera... Marta

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Bond-type error
by Laia Ferrer Duran 15 Oct '19

15 Oct '19

Hi, I recently started using chimera for one project from university. At first I worked in the university computer that it had the program. Today, as I have to work from home I downloaded the latest version of chimera in the web page and I tried to do a dock prep in the protein from DB 2am9. With the receptor it worked well, but when I done it with the ligand TES it seems to have a problem with the add charges fase. I searched first in all you webs and all it seems to say is that the molecular structure isn't correct but I really think there isn't a problem with the structure because with exactly the same steps it used to work in the university computer. The error says: (TES) sh: 1: C:/Program: not found (TES) /usr/bin/antechamber: Fatal Error! (TES) Cannot properly run "C:/Program Files/Chimera 1.14rc/bin/amber18/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac". Failure running ANTECHAMBER for residue TES Check reply log for details I don't know if it could be some problem with my program or if I should change the configuration of the program or what it is that isn't working. Thanks in advanced and I look forward you answer.

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surface color
by Schmid, Michael F. 14 Oct '19

14 Oct '19

I’m trying to do the same thing as Chimera’s “Surface Color”, but in ChimeraX, on the command line. After reading the docs, I tried “color height #1 (the map designation) center 0,0,0 axis z rainbow”. It gave “expected a keyword”. What did I miss? Thanks, Mike

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FAD binding site on Cryptochrome
by Margiotta, Joseph 11 Oct '19

11 Oct '19

Hi-> I am very new to molecular modeling and have a very basic novice user issue. We are studying cryptochrome proteins some of which are known to bind the chromophore Flavin adenine dinucleotide (FAD) and for this and other reasons are considered photopigments. We have looked at a cryptochrome in chicken that binds FAD and is light sensitive (GallusCRY4) and have sent the AA sequence to Zhang’s COACH site for Protein-ligand binding site prediction (https://zhanglab.ccmb.med.umich.edu/COACH/) at the University of Michigan. The results come up with a C-score confidence prediction of 0.59 with a cluster size of 63 for FAD binding to GallusCRY4. The results allow you to download the 3D model and the residue-specific binding probability, which is estimated by SVM, the predicted bound ligands and detailed prediction summary, and the templates clustering results. We’d now like to extend this modeling to GallusCRY1 and GallusCRY2 to see get a FAD binding prediction and the complex structure with the most representative ligand in the cluster. The COACH site lets you export the model and complex structure in PDB format and I downloaded Chimera to visualize and analyze the PDB results. I would like to be able to label the structures using the binding probabilities, and template clustering results to include the predicted FAD binding pocket on the three CRY proteins and also label a tetrad of Trp residues that are thought to be responsible for electron transfer. Can you give me some general guidance on how to start this analysis? -- Joseph F. Margiotta, PhD Professor of Neurosciences UT College of Medicine & Life Sciences Block HS 120A Mail Stop 1007 Toledo, OH 43614 419-383-4119

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Centroid/axis question
by Luca Pellegrini 08 Oct '19

08 Oct '19

Hello, I have generated a bunch of axes and centroids for my protein complex structure. Now I would like to change their appearance by changing their radius, to make them the size I want for a picture. Is there a way to do this for an existing axis/centroid, or do I need to create them again? I have got quite a lot of them… Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Question about electron density map
by Zhang, Bixia 04 Oct '19

04 Oct '19

Dear Developer, I want to have a figure of my ligand only and its electron density, and I used my protein mtz file to generate a CCD4 map in phenix and then open in chimera. I tried fit in map but it does not fit well. Could you please help me out? And after I have the electron density, how to hide the backbone electron density? Thanks a lot! Best, Bixia

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next/previous buttons suggestion
by Oliver Clarke 04 Oct '19

04 Oct '19

Hi, I like and frequently use the next/previous buttons (present in the daily builds) for sequential model display or activation. They are very useful for quickly comparing multiple 3D classes, or multiple aligned atomic models. One thing that would make this feature even more useful would be the capacity to lock display of a model - that is, temporarily remove it from the next/previous sequence. This would be useful, for example, when one wants to keep a single “reference” atomic model (or density map) displayed, but sequentially compare with multiple other maps/models. Would this be possible to add? Either as a command, or adding another checkbox that controls the lock/unlock status of the currently displayed model. Cheers Oli

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[ Asking how to combine loops of models after refinement ]
by Hồ Phương Dung 03 Oct '19

03 Oct '19

Dear Sir/Madam, I am Dung. I am currently using Chimera to do the refinement for my protein because it has some large missing residues segments. I use Tools/ Loops- Model refinement of Chimera software to do that task. As it was failed to generate models if I performed refinements for all missing residues segments. Thus, I decided to refine them not at once. The problem is that I could not find how to combine the separated loops from models after refinement. I am new to Chimera so I hope that my description can be useful for you to imagine my problem. I hope that you could support me to solve this problem. I really appreciate it. Thank you for spending your valuable time. Yours sincerely, Dung Hồ Ngọc Phương Dung International University - Vietnam National University Email: phuongdunghongoc(a)gmail.com

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