June 2017 - Chimera-users - RBVI Mailing Lists

Smooth "Rocking" Loop Movie
by Andrew Oliver, II 14 Jun '17

14 Jun '17

Dear Chimera, I am trying to create a "rocking" movie of a molecule that will continuously loop. I am using the command: movie record; rock y 10 68; wait; rock y -10 68; wait; movie stop; movie encode However, when I do this, there is always a slight pause at the end of the movie, before it starts the next loop -- which means it doesn't loop smoothly. Is there a way to create the movie so that there will be no pause before each successive loop? Many thanks, Andrew Oliver

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region bounds for pdb
by Edoardo D'Imprima 14 Jun '17

14 Jun '17

Dear Chimera users, I find very handy the function “Region bounds” to cut the EM maps in order to better visualise some part of the volume. I was wondering if there is an equivalent for PDBs. Many thanks in advance, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

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Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3
by Savriama, Yoland F 13 Jun '17

13 Jun '17

Greetings, I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message: "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'" I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera? Best wishes, Yoland Savriama, PhD P/O Jernvall Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND

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Helix represented as sheet, dispite best efforts
by Matthias Vorländer 13 Jun '17

13 Jun '17

Hi everyone, for some reason, chimera displays one helix in a structure as a messed up beta sheet. I am attaching the PDB file and an image (same structure as backbone and ribbon representation). I have tried adding HELIX records manually, ksdssp or the setattr command, but the result is always the same. I would be very grateful for suggestions what could be causing this problem, as I will have to remake all my figures in pymol otherwise (which displays the helix correctly). Many thanks Matthias Vorländer PhD student EMBL Heidelberg - Müller Lab Meyerhofstraße 1, 69126 Heidelberg

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sphere transparency
by Thomas Pochapsky 12 Jun '17

12 Jun '17

Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand? I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme. I will probably have other questions, but this seems like a good place to start... Thanks, Tom Pochapsky

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Re: [Chimera-users] Axis Of Symmetry
by Elaine Meng 09 Jun '17

09 Jun '17

Hi Catherine, Please send Chimera questions to chimera-users(a)cgl.ucsf (CC’d here) to ensure a response. This "measure rotation” command does not use any atoms, it merely reports how a model is currently rotated and translated relative to the another model. The rotating/translating is done by the matching command before that measurement. From our previous emails I see you were using the “matchmaker” command (same as “mmaker”) which, as described in the manual, uses only CA atoms: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> If you want to use other atoms in the fitting, you have to instead use the “match” command with the specific atoms given in the command. See the manual: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> See also the page on “Superimposing Structures” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> and for a specific example, the “Matching” section in the Glycoside Hydrolases tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 9, 2017, at 12:02 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hi Elaine, > > Can you tell me how Axis is configured? after using the command measure rotation, it gives me the reply log with information like axis, axis point, rotation angle etc., But I want to know specifically if Axis is calculated by just using the CA atoms of the chains or All atoms? Is there a way to find axis only using CA/All atoms. > > Thanks, > Catherine > > On Tue, Jun 6, 2017 at 4:33 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Catherine, > (Cc’ing chimera-users(a)cgl.ucsf.edu which is the recommended address for Chimera questions) > > As the message suggests, your models #0 and #1 are not rotated from each other. I’m guessing that you opened the same dimer structure twice and then matched it to itself. For example, if your structure contains chains A and B, it sounds like A was matched to A and B to B, so there was no rotation (zero degrees). You have to make sure that the matching is A to B and B to A. To do this with the “mm” command, for example, you would have to specify the chains AND use the “pair ss” option. > > There is a specific example of commands for structure 5hvp in this previous post. > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html> > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > On Jun 6, 2017, at 1:22 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > > > Hi Eric, > > I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error: > > > > <image.png> > > > > I am using chimera version 1.11.2. Can you please help me with this? > > Thanks, > > Catherine > >

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model recordings
by P. Buscemi Ph.D. 08 Jun '17

08 Jun '17

Dear Users groups. I've been struggling with this issue for some weeks. I will describe the problem and then as what information I should supply to help me solve the issue. It's a prototype adsorption experiment. Water onto polyethylene oxide. Each component, when run individually in a simulation will complete in a normal fashion with a good recorded video. All simulations were run with live presentation. However when the two models are run together, the story is different. The sequence below represents 1) the two loaded files ( water and PEO) 2) the PEO selected for later constraint ( control drag) 3) moving the water into positon. At this state the " live" simulation aappears normal. The peo does not move, and the water more or less jiggles into position on the PEO. However, in running the movie, molecules of the PEO are disrupted (4) and occupy the space in fragments originally occupied by the water molecules when it was first loaded. The same phenomenon occurs with a PE surface and with models of EtOH. The temperature is set to 0->100K, Hydrogents added Gasteiger charge calculation, 0 charge total, no periodic box. Again, I do not expect any suggestions ( although none would be refused !) only to ask the proper channels and information needed to approach the issue. Regards Paul Buscemi cid:image002.jpg@01D2DED8.C01C06501 cid:image001.jpg@01D2DED8.C01C06502 cid:image002.jpg@01D2DED8.64FCD8803 cid:image003.jpg@01D2DED8.64FCD8804

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PDB file opens from chimera GUI but not from python script ( )
by Nikolaos Bismpikos 07 Jun '17

07 Jun '17

Hello, I am having a problem with trying to open a .pdb file using a python script. The file opens and the protein structure is displayed properly when I open the file using the Chimera GUI. However, when I try to run the code from a python script, using the demo script for looping through .pdb files I get the following error: ---------------------------------------------------------------------- File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression ---------------------------------------------------------------------- This is the code I am trying to run: ---------------------------------------------------------------------- import sys import os 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("/home/nick/Python/pdb") print >> sys.stdout, retval # 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: replyobj.status("Processing " + fn) # show what file we're working on rc("open " + fn) replyobj.status("Opened " + fn) # show what file we're working on rc("align ligand ~ligand") # put ligand in front of remainder of molecule rc("focus ligand") # center/zoom ligand rc("surf") # surface receptor rc("preset apply publication 1") # make everything look nice rc("surftransp 15") # make the surface a little bit see-through # save image to a file that ends in .png rather than .pdb png_name = fn[:-3] + "png" rc("copy file " + png_name + " supersample 3") rc("close all") ---------------------------------------------------------------------- The error in more detail, including the traceback from the terminal is the following: ---------------------------------------------------------------------- Processing prediction[NoEnergy-K:0-BS:0.00]-21(20.310186).pdb Traceback (most recent call last): File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open models = func(filename, *args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython loadFunc(sandboxName, fileName, f) File "test1.py", line 23, in <module> rc("open " + fn) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 2747, in runCommand makeCommand(*args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1552, in doOpen paths = testPath(text, wildcarding) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1538, in testPath return glob(expanded) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 27, in glob return list(iglob(pathname)) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 49, in iglob for name in glob1(os.curdir, basename): File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 83, in glob1 return fnmatch.filter(names, pattern) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/fnmatch.py", line 56, in filter _cache[pat] = re_pat = re.compile(res) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 194, in compile return _compile(pattern, flags) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression error: bad character range Error while processing test1.py: error: bad character range File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression See reply log for Python traceback. ---------------------------------------------------------------------- The error obviously appears at the 2nd line of the for loop ( rc("open " + fn) ) Any tips on why this might happen? I am using Ubuntu 14.04 LTS and the Chimera version I installed is chimera-1.11.2-linux_x86_64.bin

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Axis Of Symmetry
by Catherine Jenifer Rajam Rajendran 06 Jun '17

06 Jun '17

Hi Eric, I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error: I am using chimera version 1.11.2. Can you please help me with this? Thanks, Catherine

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measure surface area
by 陈柳青 06 Jun '17

06 Jun '17

Hi! i want measure several selected residues surface area and volume, but in the reply log, it always give the total surface area and volume of the protein, how can i get only the selected residues surface area? because this residues make a cavity , which may binding substrate. in addition, the castP server can't give me the pocket i wanted, because it give a bigger pocket than i wanted. thanks in advance！ liuqing chen -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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Chimera-users June 2017