Hi Tom,
Something that might help in general to familiarize yourself with the Python interface is the reference below. Let me know if you can't access it so that we try something else. Best, Guillermo Bermejo & Schwieters (2018) Protein Structure Elucidation from NMR Data with the Program Xplor-NIH in Methods in Molecular Biology, vol. 1688 (link below) https://link.springer.com/protocol/10.1007/978-1-4939-7386-6_14 ________________________________ From: Thomas Pochapsky <[email protected]> Sent: Friday, August 9, 2019 7:40 AM To: List XPLOR-NIH <[email protected]> Subject: Re: re-learning XPLOR Charles, How much of an old style .inp file can be placed between the xplor.command() in .py scripts? Does each .inp command need a separate () or does the script just keep reading until the end of the parentheses? It looks like the patch files I need are all .inp. We are trying to place an Fe(II) ion ligated by His and Glu, with some added water ligands for the metal. Thanks, Tom P. On 8/7/19 4:01 PM, Charles Schwieters wrote: > Hello Tom-- > >> After a long absence, I am trying to learn how to use XPLOR with the >> python interface, instead of modifying fossil scripts from 1991. Two >> questions that have come up so far (I am sure I will have more!): >> >> 1) Is there a way of importing heavy atom coordinates from an existing >> crystal structure once a .psf file has been built from the same >> structure (I used pdb2psf)? I don't think we want to start from >> scratch with random coordinates. > Sure. If you have a PSF you can > > protocol.initStruct('file.psf') > protocol.initCoords('file.pdb') > > protocol.addUnknownAtoms() > > The last line will add any missing atoms (like protons) with correct > covalent geometry. > >> 2) Are there any tutorials on PSF and structure patching (we have a >> metal center with bond lengths and angles known)? >> > There are examples in eginput/PSF_generation in the Xplor-NIH > distribution, but these is frequently a one-off task which differs a > bit for each case. This snippet for one of the zinc finger patches > might help give you a clue as to what the topology entry should look > like: > > AUTO ANGLe=False DIHEdral=False END > > ! patch to create Zn (Cys)3 (His)1 > ! 1, 2 and 3 should be CYS > ! 4 should be HIS > > > presidue ZC3H1 > delete atom 1hg end > delete atom 2hg end > delete atom 3hg end > ! delete atom 4hd1 end > add bond 5ZN+2 1sg > add bond 5ZN+2 2sg > add bond 5ZN+2 3SG > add bond 5ZN+2 4nd1 > add angle 1SG 5ZN+2 2SG > add angle 1SG 5ZN+2 3SG > add angle 1SG 5ZN+2 4nd1 > add angle 2SG 5ZN+2 3SG > add angle 2SG 5ZN+2 4nd1 > add angle 3SG 5ZN+2 4nd1 > end > > best regards-- > Charles > > ######################################################################## > > To unsubscribe from the XPLOR-NIH list, click the following link: > http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1 ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1 ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
