- Chimera-users - RBVI Mailing Lists

Parse error Chimera
by Dorfner, Maja 15 Jul '19

15 Jul '19

To whom it may concern, Using Swissmodel, I have constructed a model based on an original PDB file. NAP is part of this model. The docking works when the option of either "Ignore chains of non-standart residues" or "Ignore all non-standart residues" is chosen as false. The Problem is that in the PDBQT file of the receptor shows that NAP was not considered during the docking, making the Substrate float either within the NAP or to far from it. The docking worked fine with the original PDB file but not with the newly modeled one. Could the problem be that the NAP is a separate chain? I have already tried to erase the H before using AutoDock Vina. Here is the Reply log: Running AutoDock Vina for PmWT.pdb failed; see Reply Log for more information Application stderr ----- Parse error on line 3578 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. # ################################################################# Detected 4 CPUs Reading input ... ----- Thank you for your patience. Sincerely, Maja Dorfner

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Surface render error in MD movie for morph conformation
by Edel Fenix 15 Jul '19

15 Jul '19

Everything works at the basic level and has produced very useful data and animations. I am most grateful for these tools and your help. The BIG problem I have is that for some frames no surface is rendered at all. Other parts "magically" disappear and reappear during the transformation. *What I would want to do:* 1. There are missing structures/regions in need of repairs in the PDB files I work with (see attached screenshot example). The files are for the same protein but different regions missing in different models and they differ some, ideally they shouldn't. I am using Chimera and Modeller to repair these with loops/refinement. Ideally I would want to match/alter the proteins so the gaps connect correctly and their amino acid structure is the same for all models. I feel like this may be the/one cause for the surface errors when rendering? I've tried using modeller both locally and the web service so I have verified installation, integration and function. Must I generate multiple drafts and manually review and select the one best corresponding or is there a way to get it performed for all models loaded of the same protein? Further, if I want them to have the same genetic makeup, can I somehow use one as reference to alter the others? 2. Align the protein snapshots from the configurational change using matchmaker (works great!). 3. Use morph conformation to generate an animation of the configurational change with surface rendered. Works sort of, with errors for some frames where no surface is rendered at all or regions magically appearing/disappearing. 4. Solve the surface error I get, see attached error message :( If I use split copying from the example page, the model looks nothing like it should look like and more like boiling gruel. I am not experienced with Chimera but I feel like if I ensure the files have no gaps and are structurally identical with the same amino acid makeup it may work as is? *The problems with existing suggested solutions:* The link below present 4 possible solutions linked from the error message. Solution 1 looks nothing like what I want when rendered in my test. Solution 2 does not solve the issue of disappearing structures magically appearing again. I am not sure of the cause but could be because the models have different structure/missing parts. If repaired and matched across all protein models in the animation might work? If so, might not even give an error message? Looks viable but does not solve the problem. Solution 3 is not viable as I am looking to render the surface in details, not "overall" look for large structures. Solution 4 is not applicable as I do not want CPK. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Any help would be greatly appreciated, Edel [image: Screenshot 2019-07-15 at 12.05.12.png] [image: Screenshot 2019-07-15 at 14.30.00.png] )

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Integer Values instead of Floats in Render by Attribute
by Daniil Prigozhin 11 Jul '19

11 Jul '19

Hello, I am using the latest nightly build and in the Render/Select by attribute window the values in the Value box (defining the color scheme) are reported as integers and accept only integer input, when in fact the Attribute that I defined is a float, and shows up as a float. This does not happen with "native" attributes, only with the newly defined one. Is it a problem with the defattr function not determining/passing the data type correctly? I am pasting the top of the attribute deffinition file below. Many thanks, - Daniil attribute: shannonEntropy match mode: 1-to-1 recipient: residues #0:1.L 0.865 #0:2.L 0.743

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Issue regarding Chimera-Vina
by Prabuddha Bhattacharya 11 Jul '19

11 Jul '19

Dear Sir, I am a beginner in the field of molecular docking. However, I started doing it using Chimera Vina. UCSF Chimera 1.13rc provides the interface while AutoDock Vina does the docking part. For a couple of cases I have found that inspite of keeping all the parameters same, the best obtained dock scores are coming different for each individual job-run. Is it so because it is a stocastic method? With such different dock scores, what should I do? I will be extremely grateful of you can kindly address this issue. Thanking you in advance, Best regards -- *Prabuddha Bhattacharya *

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Structure overlay
by Chakraborty, Joydeep 10 Jul '19

10 Jul '19

Dear all, I am trying to overlay two structures. 1. Wild type enzyme and 2. A mutant, with a single point mutation on the wild type. However, somehow when I am opening the structures, both are overlapping automatically and showing as one structure. I need to have two separate strands overlay, so I can show the change in the active site pocket. I was hoping if anyone could shed some light on this issue. Thanks, Joydeep.

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Volumes comparison
by Dmitry A. Semchonok 09 Jul '19

09 Jul '19

Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry

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Associate Scientist/Scientist Position in Protein Engineering
by Andrew Waight 07 Jul '19

07 Jul '19

Dear Chimera Users We are seeking a fresh phD graduate or postdoc with a structural, biophysics or computational background to join our group. This is an excellent opportunity for anyone looking to break into the extremely desirable field of antibody engineering for immuno-oncology. The position entails the design, cloning, purification and in vitro testing of multispecific antibody type molecules. The training involves in silico design (including MD analysis) molecular biology, HEK and CHO expression, Antibody purification and biophysical analysis including SEC, MALS, DLS, RP, Mass Spec, Kinetic analysis (Octet) Binning, Humanization, and *in vitro* validation including FACs analysis, immune cell activation and cancer cell line killing assays. Although experience is not necessary, we expect interview candidates to have researched the above topics thoroughly and to express and explicit interest in the field of protein engineering for immuno-oncology. If interested, please see the link below and feel free to contact me personally with any questions. So sorry to the rest of Chimera-users for the spam. https://www.linkedin.com/jobs/view/1358848339/

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Question regarding RR Distance Maps
by Meysam T. Chorsi 03 Jul '19

03 Jul '19

Hello, I need to use Chimera to determine the distance map, but for some reason the output matrix is not symmetric. I used other software as well, they all giving a symmetric matrix which makes sense to me. Could you please let me know how can I fix this? Thank you Sincerely, Meysam -- *Meysam T. Chorsi* *University of Connecticut * *191 Auditorium Road, Storrs, CT 06269, USA*

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Cylinder coloring extension
by Thomas Marcellino 03 Jul '19

03 Jul '19

Dear Chimera Team, I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? Looking forward to an answer, Thank you for your time reading my suggestion. Thomas M

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Creating a smooth disk
by Henrique C. S. Junior 02 Jul '19

02 Jul '19

Dear list, I'd like to create a disk that didn't show lines in the surface depending on the orientation angle (see the image attached). Right now I can clearly see that the circle is formed by several triangles, so I'd like to smooth things up. I can actually get rid of the triangles by disabling the silhouette of the plane, but I'd like to keep it to show where the plane ends. Thanks in advance -- *Henrique C. S. Junior*

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