- Chimera-users - RBVI Mailing Lists

I Can't Open My ZDOCK Output File Into Chimera
by Nissa Nabila 22 Aug '17

22 Aug '17

Hello and hi! My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem? Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review. Thank you in advanced!

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Helix voxels labeling
by natan geier 22 Aug '17

22 Aug '17

Hello, I am currently studying the connection between density maps and the secondary structure elements. I have a density map file for a certain protein, giving for each voxel a density value, and what I am missing is a "helix map", giving a binary value for each voxel, representing wether it is a part of a helix or not. In order to build this "helix map", I need to use the .pdb file of that protein, but I am not really sure how to extract an appropriate 3D boolean matrix out of this file. Any suggestions would be greatly appreciated. Thanks

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Regarding generating a .pdb file of peptide (Diglycine)
by Dilip H N 22 Aug '17

22 Aug '17

Hello, I have install chimers in ubuntu 14.04.. I am finding difficult to get the .pdb format for diglyicne peptide... 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:- Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590) 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error.. So can anybody kindly help....i am a novice here.. Thank you... -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dili…>

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biounit
by Arthur Szabo 18 Aug '17

18 Aug '17

When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? Arthur G. Szabo

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move different map to the same origin of coordinate
by C.J. 18 Aug '17

18 Aug '17

Dear specialists, I open a map(#1) and make icosahedron surface(#1) using Tools-> Higher-Order structure->icosahedron surface. But the model #0 and #1 don't have the same center, how could I center them into the origin of same coordinate? Thanks! -- Best regards! Jianhao

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advanced option for WebGL?
by Albert 17 Aug '17

17 Aug '17

Hello, I noticed that Chimera can export a scene as HTML file which is based on WebGL. However, we can no longer change the displaying styles through this .html file since there is no any menu or option button in the page. Would it be good if Chimera could provide this function? As far as I know, PyMOL has similar function, but the generated .html provide a menu to change the scene styles. see here https://pymolwiki.org/index.php/Pymol2glmol Thank you very much. Albert

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Draw Line
by Catherine Jenifer Rajam Rajendran 17 Aug '17

17 Aug '17

Hi Eric, Can you please tell me what are the ways to draw an axis. I have a directional vector - x, y, z coordinates (e.g., 0.407 -0.747 0.526) and a point (14.395, 37.07, -12.029). How to draw an axis in chimera tool with these two data? Thanks, Catherine

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command line minimization
by Milo Westler 16 Aug '17

16 Aug '17

We are trying to automate the minimization of a series of compounds using the system command line. Since we have quite a few compounds, we are interested in using the Gasteiger method for assigning charges. The command line minimize includes the AM1-BCC method.. Is there a way to run an automatic minimization using the Gasteiger method? Currently we use: chimera --nogui --silent R.mol opt.cmd Where opt.cmd is: minimize write #0 R_min.pdb -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

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Match->Align commandline
by sonal rashmi 10 Aug '17

10 Aug '17

sir/mam, i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. I tried out the python codes posted on the portals but non of them are giving proper alignment. kindly advice as to what i can do? Is there any commandline available for it? Thanking You Sincere User

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Problem with added ions in Amber
by George Tzotzos 08 Aug '17

08 Aug '17

In MD movie I loaded complex.prmtop and complex.inpcrd files In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red). I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 NOTE: I unticked the Removed existing ions/solvent box I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA I generated complex_solv.prmtop and complex_solv.inpcrd files When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). > resinfo #Res Name First Last Natom #Orig #Mol 1 ASP 1 14 14 1 1 2 THR 15 28 14 2 1 ——————— 250 LEU 3988 4006 19 250 3 251 VAL 4007 4023 17 251 3 252 KBR 4024 4062 39 252 4 253 WAT 4063 4065 3 253 5 ———— 10272 WAT 34084 34086 3 10272 10024 10273 WAT 34087 34089 3 10273 10025 Is this what should be expected? Should I consider the solvated complex charge neutralised? Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions Thank you in advance for any suggestions.

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