August 2017 - Chimera-users - RBVI Mailing Lists

Regarding getting the .pdb file of glutamine
by Dilip H N 26 Aug '17

26 Aug '17

Hello, 1] I am having difficulties in getting the Glutamine.pdb file in chimera. I tried in Build Structure - Peptide and in peptide sequence if i type GLN, i am getting peptide of glutamine...., but what i want is just glutamine molecule, and not a peptide.. So how can i generate a glutamine molecule in chimera.... 2] Another question in Diglycine peptide, i want to insert CH2 in between the molecule (say in between C=O and CA), How can i insert the methyl group there.. Any suggestions are highly appreciated -- 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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Molecule Display
by 李艺宣 25 Aug '17

25 Aug '17

Dear professor: In the process of using chimera, I encountered some problems. I found Gly residues can not be shown in stick, wire, ball-and-stick and sphere presentation. Can you help me Looking for your reply All the best.

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duplicate a EM map in window by command line
by C.J. 25 Aug '17

25 Aug '17

Dear specialists, Is there a command line to creat a model copy of a opened EM map in the window? Thank you! Best regards! Jianhao

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sent to a different url
by Arthur Szabo 24 Aug '17

24 Aug '17

I am interested in a structure 1GSG deposited in 1990. The PDB index for this file shows the enzyme Gln tRNA synthetase with the usual ribbon structure, bound to tRNA(Gln). When I fetch 1GSG using either the PDB file number only, or that file number input into PDB biounit, the structure that comes up does not have the helical or β-sheet secondary structures shown as ribbons. Rather the entire protein backbone is shown without any secondary structure definition. One can see the helical segments in the worm like structure, but not in the form of the usual helical secondary structure. How can I retrieve a structure that is similar to that in the PDB index list. I have enclosed the following: [cid:image001.png@01D31C42.7C7B48F0] This is what comes up when I fetch the PDB file. [cid:image002.png@01D31C42.7C7B48F0] Thanks Arthur G. Szabo Professor Emeritus

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setting surface color of EM map in command-line
by C.J. 23 Aug '17

23 Aug '17

Dear specialists, I want to color spherical slices of different radius of my EM map in command line/script. How to set the "surface color" dialog in command-line? If anyone could give me a example? Thank you! Best regards! Jianhao

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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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