April 2020 - Chimera-users - RBVI Mailing Lists

Enquiry regarding electrostatics calculations of outersurface
by Jian Chen 16 Apr '20

16 Apr '20

Dear all Chimera users, Chimera has capability to color molecular surface by electrostatic potential using data calculated by apbs module, and the values could be exported into txt files using the surfval.py script. However, there are too many electrostatic potential values exported, and the number of values seems exceed that of atoms. My question is, how to define a surface point whose electrostatic potential value whoud be calculated? I want to obatain the values of outersurface, how to screen out the values of outersurface of protein from them? I would greatly appreciate your help. Best Regards, Jian Chen

2 3

Help with symmetry of fusion protein
by Hasan khan 15 Apr '20

15 Apr '20

Hi there I was hoping I could get some help with a modelling challenge that I am having as I am very new to protein modelling as a whole and Chimera. So I developed a fusion protein of a single monomer of an encapsulin structure (PDB:3DKT), I wanted to build the final icosahedral structure with the added fusion protein. So I tried to align 10 of the fusion monomers to the di-pentamer of the original PDB file and ran the sym command generating the native structure with the added fusion protein. I am unable to save this symmetry structure and I'm not sure if its due to the alignment of the 10 monomers onto the di-pentamer that I did first and then ran the sym command using coordinates of the original PDB or if Chimera is not able to produce coordinates for the structure in a new PDB. When I export it as a PDB the coordinates are not saved. So I was wondering if there is a way I could save this newly generated structure as other methods are not currently working. Thank you Kind regards HK

3 4

remove of the list
by Jose Alirio Mendoza Mesa 15 Apr '20

15 Apr '20

Please, could you remove my email from the list. *Qco. JOSE ALIRIO MENDOZA MESA* Candidato a Doctor en ciencias Universidad Nacional de Colombia. cel. 3173829637

2 1

Saving changes made in PDB files
by Liam fletcher 15 Apr '20

15 Apr '20

Good day, I am hoping you may be able to help me with an enquire I have for current work I am performing using the Chimera software for my final year project. I am attempting to save a PDB file separately following changes made e.g. Highlighted reside(s), change the background. I am having trouble in saving these files separately. More specifically, I am attempting to save different file versions where changes have been made to the protein for predicting the function. Is there a way to save these PDB files as I have been following the instruction. But, I am confusion about which of these instructions is the right instructions to use. I thank you in advance and hope to hear from you soon. Kind regards, Liam Fletcher

2 1

CSG of a kind
by Esser, Lothar (NIH/NCI) [E] 14 Apr '20

14 Apr '20

Hi, I am sure this is possible I just could not find it in the documentation: Can someone quickly remind me how to subtract density that surrounds a molecule so as to leave the extra density in the map ? Volume eraser seems to use a sphere but this is too crude. I am interested in an extra domain that is not (yet) in my model and it would help to remove the portion that I know from the density. There is probably a very simple solution that I just can't seem to find. Thanks, Lothar

2 2

Charge assignment to a ligand
by Prabuddha Bhattacharya 14 Apr '20

14 Apr '20

Dear Sir, I had a query regarding charge assignment to any ligand in chimera. While minimizing the energy of a particular ligand (Tools --> Structure Editing --> Minimize Structure) and also during Dock Prep, I found that for most of the aliphatic and alicyclic amines, they are getting protonated with a residual positive charge; while the aromatic amines remain unprotonated (and hence no residual charge). I understand that this is because of their differential pKb values (basic strengths). On the other side, deprotonation never occurs with the carboxylic acid (-COOH) group. Does the Chimera (force fields) control this issue of protonation and deprotonation considering the physiological pH ? I will be extremely grateful if some one may kindly clarify my doubts. Thanking you in advance, With Best Regards, *Dr. Prabuddha Bhattacharya * *Dept. Of Chemistry* *Adamas University* *Kolkata 700126* *India*

3 4

Re: [Chimera-users] [chimera-dev] icosahedron with a T number
by Wei Zhang 11 Apr '20

11 Apr '20

Hi Elaine, I am able to use hkcage and build a spherical sphere with pentagons and hexagons. Is there a way to color those pentagons differently? Thank you, Wei On Fri, Apr 10, 2020 at 10:41 AM Wei Zhang <zhangwei(a)umn.edu> wrote: > Hi Elaine, > > Thank you for the quick reply and the instructions. > I will use the other email address next time. > > Best regards, > > Wei > > On Fri, Apr 10, 2020 at 10:12 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > >> Hi Wei, >> >> Take a look at the "hkcage" command if you want hexagons and pentagons >> instead of triangles. You give it the h and k values which are related to >> T number by the equation shown in that page: >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html> >> >> For this kind of question (next time) you probably want the >> chimera-users(a)cgl.ucsf.edu mailing list, not chimera-dev which is more >> for programming questions. >> >> Thank you for the good wishes -- you stay safe too! >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Apr 9, 2020, at 4:21 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: >> > >> > Hello, >> > >> > I have been playing with the icosahedron utility in Chimera. I really >> like this feature, especially with the sphere factor. >> > >> > The current routine uses a subdivision factor to represent the number >> of triangles on an icosahedral surface. However this lattice is not the >> same as we see in icosahedral viruses, which use a T number to designate >> symmetry. With a subdivision number, there are always hexamers on any edge >> of the icosahedron, whereas in the virus structure this is not the case. >> > >> > I am wondering if Chimera has an utility that can use the T number as >> the basis for building an icosahedron surface. >> > >> > Thank you. >> > >> > Hope everything is going well and stay safe! >> > >> > Wei >> >>

3 4

MINIMIZATION BY CHIMERA
by Jonathan Javid 10 Apr '20

10 Apr '20

Dear Instructor Please guide meabout how minization is performed of protein Structure from chimera.Guide me step by step kindly. Waitig for your positive response. Thank you Reagrds Jonathan Javid

2 2

How to to do that in chimera?
by Krivic, Denis 09 Apr '20

09 Apr '20

To whom it may concern, I have just started working on a project which includes docking and analysis of the results several weeks ago. So figuring out software for docking and the docking procedure itself was one set of problems (solved), and now I could really use your help in order to analyze my data - docking results (output files). At the moment, I am using Windows 10 (x64), Chimera 1.14, AutoDock Vina 1.1.2 and AutoDock 4.2.6. So, I have a protein (ion-channel) and several different ligands, for which I want to see how they and if they (at all) may interact with the protein. Therefore I dock the ligand in the two mentioned programs and got different output files. Vina generates a single file with 9 different positions, and 4.2. generates 9 different files for each position. Now, the first problem I encountered was that in Chimera I can open and analyze only Vina output (single file). How do I open 4.2. output? The second problem is that I am able (know how) to analyze polar interactions (HBonds). But can I somehow check for hydrophobic or other kind of interactions? The third thing is that, for example, I have Vina output files for ligand docked in 2 different (but adjacent) places in protein (so 18 positions in total). Is there any chance to merge those files so I can see the energy differences among all of them? Fourthly, is there any way to merge vina and an other program's output (4.2 or DOCK for example) and see if there are common structures (same one generated by both) and the ones that are not common for the two? Finally, is there any graphical way of representing the docking poses and see the likeliness of the binding of a certain poses? Or some sort of clustering of poses into more probable binding candidates or something similar? Thank you in advance, Denis What kind of docking What you want to do, meaning achive Which steps have you carried out Description of the status, when you get stuck

2 1

How to split multiple ligands in mol2 files
by sunyeping 09 Apr '20

09 Apr '20

Dear all, I seem to read some posts in the chimera email-list that discuss split combined mol2 files contains many compound into single mol2 files for virtual screening, but now I cannot find them. I wish to do some virtual screening with autodock 4. I have split a sdf file contains over a thousand compounds into single mol2 file with the linux shell "csplit" command. However, I find lots of such mol2 files still contain multiple ligands （LIG1, LIG2, LIG3, etc.) whose coordinates mix together and so can not be split by shell command "csplit". Please find three such examples at: https://drive.google.com/drive/folders/1AiW00lbA4tRfLu-l47QfxWVn8PqnQ-5J?us… I can split the ligands in a mol2 file manually in Chimera GUI: first open the mol2 file, then select the ligands and save them as pdb files respectively to get separate pdb files for these ligands. After then reopen these pdb files respectively and save them as mol2 file. However, to process a large amount of mol2 files manually is impossible, so I need a command or script to do this. I hope chimera can do this. Chimera has a command "split": split [ model_number(s) ] [ chains ] [ ligands ] [ connected ] [ atoms atom-spec ]n However, it doesn't seem to be suitable for my scenario. Does anyone know whether chimera can split such mol2 files and how? I will appreciate any help of you. Best regards. Yeping Sun

2 1

Chimera-users April 2020