November 2018 - Chimera-users - RBVI Mailing Lists

Matching of small molecules
by Cassandra Ceccopieri 28 Nov '18

28 Nov '18

Dear Sir/Madam, I would like to ask how to overcome the following problem that I faced trying to perform an alignment of small molecules. Writing in the command line section the following instruction: match #0 at c5,c4,n7,c8,c9,s10 #1 at c9,c8,n11,c12,c13,s14 I obtain, as output, an error message saying: Error in "#0 at c5,c4,n7,c8,c9,s10" must be an integer. I checked the tutorial but the instruction for the command line seemed in the same format as mine. Therefore, I would like to ask assistance to be able to perform my analysis. Kind Regards, C.

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Using Per-Frame commands to recolor structures with attribute data is very slow
by David Slochower 27 Nov '18

27 Nov '18

Hi, As a follow up to this thread (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html>) from 2009, I’d like to color a model by a custom attribute that changes from frame to frame. Using the workaround mentioned in that thread, we are able to use Per-Frame commands to load a new attribute file each frame, and then color the structure by the attribute, but this awfully slow (probably over 1 second per frame). Is there a way to cache the attribute data? Or a way to improve the performance of defining the attributes and re-coloring the structure? I know that I could use a Python script to load each coordinate frame with its associated attribute data, save images, and then stitch them together for a movie, but the current goal is for data exploration.

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Announcement: Release of DOCK 6.9
by Scott Brozell 27 Nov '18

27 Nov '18

We are pleased to announce the release of DOCK 6.9. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.9 is available for download and free for academic users at http://dock.compbio.ucsf.edu/. This is a release of the new ligand searching method DOCK_DN: De Novo design using fragment-based assembly. De novo design can be used to explore vast areas of chemical space in computational lead discovery. DOCK_DN is an iterative fragment growth method, in which new molecules are built using rules for allowable connections based on known molecules. For full information on what is new in DOCK 6.9, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.9.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

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chimera --nogui --script option not doing anything!
by Ahir Pushpanath 27 Nov '18

27 Nov '18

Dear Chimera crew, I am having serious trouble running my script using chimera --nogui --script option. I tried running a simple script that just prints a comment, and i dont get anything returned on the cmd, let alone the actual script. The cmd does not flag up any errors , it just does nothing and return back to the prompt. I have chimera 1.13.1 and its added to the system path - "C:\Program Files\Chimera 1.13.1rc\bin\". I can launch chimera fine from the command line showing its added to path fine. I am completely stumped! Also, the script works fine within the IDLE of the GUI. See code below: import os > print "Script is running" > from chimera import runCommand as rc # use 'rc' as shorthand for runCommand > from chimera import replyobj # for emitting status messages > # change to folder with data files > os.chdir("C:/Users/JM/Documents/Public Qsync/Jenny > Taylor/IREDs/Structures/") > # gather the names of .pdb files in the folder > file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] > # loop through the files, opening, processing, and closing each in turn > for fn in file_names: > res = "tyr" > if fn == ""2NAD.pdb": > print fn > replyobj.status("Processing " + fn) # show what file we're > working on > rc("open " + fn) > for b in range(1,300): > rc("sel #0" + ":"+str(b)) > rc ("swapaa "+res + " sel criteria p") > rc ('write format pdb #0'+ " " + fn > +"_"+res+'mutated.pdb') > rc("close all") > # uncommenting the line below will cause Chimera to exit when the script > is done > rc("stop now") -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

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dsv to Chimera format
by Tavangari, Simin 27 Nov '18

27 Nov '18

Hello, I do not know how to open a discovery studio visualizer (.dsv) file in Chimera. Can you please help me with that? Thank you. Best regards, Simin

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needing help for separating structures
by Elaine Meng 26 Nov '18

26 Nov '18

P.S. I recommend you do not use that PDB file because it is missing much of the information that is in the original mmCIF file Elaine

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Basic question re: nucleotide sequence
by Pecot, Chad V. 26 Nov '18

26 Nov '18

Hello, I am trying to use Chimera to predict the structure of a nucleotide sequence that does not have a PDB ID. This is an unstudied protein, and I’m hoping to get some structure information and to visualize it using the software. I tried using the tutorials, but the best I can tell it appears to work off of already available PDB IDs. Is there a way I can enter the nucleotide sequences as a starting point? If so I’d really appreciate a few step/steps on how to do this. Best, Chad _______________________________________ Chad V. Pecot, M.D. Assistant Professor UNC Lineberger Comprehensive Cancer Center Thoracic Medical Oncology 450 West Drive, Office 32.048 Chapel Hill, NC 27599 Office: 919-966-4779 Cell: 615-305-3955 Fax: (919) 966-6735 pecot(a)email.unc.edu

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A script for deleting discontinuous/disconnected parts of a map, similar to the hide dust function in Chimera
by CHI-MIN HO 24 Nov '18

24 Nov '18

Hello Chimera Team, I would like to write a script that can automatically remove smaller blobs (disconnected parts) of a volume, exactly likely how the hide dust function works in chimera, except I want it to be automated. I would like a script that can automatically determine a good threshold, then rank the parts/volumes in the box by size, and then remove all but the largest volume, and save the result as a new volume. Do you have any existing code or sample code that accomplishes anything like this that you could point me toward? Or if not, would you be able to advise me as to the best way to achieve this? Thank you in advance! Best wishes, ~Mimi

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Running AddCharge from the command line
by Samuel FreemanFox 21 Nov '18

21 Nov '18

Hi, I am attempting to automate Vina with a python script and want to use addH and addCharge before running Vina, however I cannot run addcharge without the window opening asking me to specify net charges. I was wondering if you could advise on the correct way of writing this command Many thanks, Samuel Freeman-Fox ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Porton Biopharma Ltd, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. *******************************************

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Dual transparency in chimerax
by Yehuda Halfon 21 Nov '18

21 Nov '18

Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon

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