- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] HBONDS comparing GROMACS and CHIMERA
by Elaine Meng 31 May '22

31 May '22

----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco Forwarding to the list so that somebody who knows more about the code can answer... > On May 30, 2022, at 1:23 AM, Sourpis, Anastasios <asourpis(a)uni-mainz.de> wrote: > > Dear Elaine, > > I would like to ask you if > CHIMERA is openned source. > > And if yes how can I have access to the Hbonds > class/funtion to understand better how it works? > > Kind regards, > Tasos > > > > On May 25, 2022, at 11:32 AM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > > > > > Dear Tasos Sourpis, > > > It is not surprising that different programs give (partially) different results, because each program uses somewhat different methods and/or parameters to identify H-bonds. There is no universally accepted exact method. However, my guess is that they would agree in the majority of cases. > > > > > > The method used by Chimera is described in the help page: > > > <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhb…> > > > > > > To summarize, there are several different distance and angle cutoffs depending on the atom types (element and hybridization state) of both the donor and acceptor. The diagram of how the angle is defined would also depend on both of those types. > > > > > > So probably what you are interested in are the exact diagrams for the different donor-acceptor pair types and the cutoff values for distances and angles. These are in the figures and tables of the paper cited in the link above, namely > > > > > > Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22. > > > > > > Then Chimera allows adding tolerance values to the cutoffs of distances and angles from the paper, because they were defined on very high-resolution crystal structures, but used on structures that may not be so precise. > > > > > > I hope this helps, > > > Elaine > > > ----- > > > Elaine C. Meng, Ph.D. > > > UCSF Chimera(X) team > > > Department of Pharmaceutical Chemistry > > > University of California, San Francisco > > > > > > > > >> On May 25, 2022, at 2:57 AM, Sourpis, Anastasios via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > >> > > >> Dear All, > > >> > > >> I would like to ask about the hydrogen bonds' built-in configuration > > >> of CHIMERA. > > >> > > >> Can I possibly have some insight into how it works? > > >> > > >> Regarding the distance and angle constraints do you have any > > >> graphical representation of the conditions. > > >> > > >> I would like to attach a figure and ask if this is the correct > > >> applying configuration regarding the distance and the angle > > >> (hbonds_lst.pdf). > > >> > > >> > > >> Also, I would like to share with you the output > > >> when I compare gmx hbond using GROMACS and > > >> chimera. > > >> > > >> ATTENTION: using gmx hbond I have the connected atoms > > >> via hydrogen, but the two configurations are essentially > > >> different (chimera_(molecules).tga and gromacs_atomonly.tga). > > >> > > >> Thank you in advance. > > >> Kind regards, > > >> Tasos Sourpis > > > > > > > > > _______________________________________________ > > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

3 2

how to solve the problem of topology
by Kenji MATSUI 31 May '22

31 May '22

Dear Chimera Thank you for your support the other day. I also apologize for contacting you outside of business hours due to the time difference. Excuse me, I have a question about the issue of ligand topology for the docking study. ligand: 25-hydroxy cholesterol The topology did not match when I used this ligand for the docking study. Could you tell me how to solve this problem? The thing I tried 1. I tried to add hydrogen atoms on UCSF Chimera by following the URL below, but it did not work Reference: https://www.swissparam.ch/SwissParam_gromacs_tutorial.html 2. I tried to change the conformation of the C23-24 part, but the situation won't be changed. Reference:< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.… > --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

2 2

Drawing a set of spheres describing a pocket in a protein
by svle＠tiscali.it 30 May '22

30 May '22

Hi all, I would like to draw a set of colored and transparent spheres that describes a pocket knowing the coordinates of the center and the radius for each of these shapes. For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on. Can you suggest me a way to do this. Thanks. Saverio Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

3 6

Fwd: [chimerax-users] relative position of a marker
by C.J. 25 May '22

25 May '22

Thank you both Tom and Elaine. I just test the command but it doesn't work. See attached picture. Elaine Meng <meng(a)cgl.ucsf.edu> 于2022年5月25日周三 11:45写道： > Hi Jianhao, > It depends what you mean by relative position. If you mean distance, one > way would be to place a marker at the map center and then measure distance > between it and the marker you already have. > > You can place a marker at map center with "measure center" and the "mark > true" option: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#center> > > ....or at specific coordinates such as 0,0,0 with "marker" and the > "position" keyword to specify a point: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html#create> > > Then you can select the two markers (same as atoms) with Ctrl-click, > Shift-Ctrl-click and then use command "distance sel": > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> > > Or regardless of whether you wanted to measure any distances, you can save > the marker(s) to file and just look at the file with a text-editor to see > what its coordinates are: > <https://rbvi.ucsf.edu/chimerax/docs/user/markers.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 May 25, 2022, at 7:54 AM, C.J. via ChimeraX-users < > chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi, > > I place a marker in a cryoEM map with "Volume Tracer" tool. How can I > know the relative position of the marker to the origin or center of the > map? Thank you! > > Best, > > Jianhao > >

2 1

HBONDS comparing GROMACS and CHIMERA
by Sourpis, Anastasios 25 May '22

25 May '22

Dear All, I would like to ask about the hydrogen bonds' built-in configuration of CHIMERA. Can I possibly have some insight into how it works? Regarding the distance and angle constraints do you have any graphical representation of the conditions. I would like to attach a figure and ask if this is the correct applying configuration regarding the distance and the angle (hbonds_lst.pdf). Also, I would like to share with you the output when I compare gmx hbond using GROMACS and chimera. ATTENTION: using gmx hbond I have the connected atoms via hydrogen, but the two configurations are essentially different (chimera_(molecules).tga and gromacs_atomonly.tga). Thank you in advance. Kind regards, Tasos Sourpis

2 1

Place Objects output to mrc
by Ricardo Righetto 20 May '22

20 May '22

Hi, Regarding https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-March/018516.html I stumbled upon this thread somewhat late, so here is my approach to do what Pranav asked, just in case: 1. Use the "Place Objects" plugin to map back your particles into the tomogram, using STL files to represent the average 2. Generate an MRC volume made up entirely of "ones", exactly the same size as your tomogram. For example, for a volume that is 928x928x464 voxels one can do this in EMAN using: $ e2proc3d.py :928:928:464:1 ones_bin4.mrc You could obviously use some other program to do the same thing, or Python, MATLAB, etc. 3. Load this "ones" volume in your Chimera session. Make sure all regions are loaded in step 1, e.g. vol #2 style surface step 1 level 0.5 region all (the volume doesn't have to be visible, though) 4. Mask your "ones" volume using the surface of the mapbacks from "Place Object", e.g.: mask #1 #2 fullmap true 5. Save the new, masked volume as an MRC file The result is essentially a binary volume (well, not exactly because of the masking interpolation) where voxels of your mapped-back particles are 1 and the rest is 0. This is quite useful to compose segmentations and mapbacks on tomograms in Chimera or ChimeraX having full control like we do with any MRC volume (unlike e.g. STL or COLLADA objects). Note you may get some artifacts on the edges, so you might have to play a bit with the thresholds both when creating the STL of your subtomogram average and when displaying your new volume "sculpted" by the mapbacks, to minimize those. The results however have been good enough in my experience, working with low-resolution averages :-) Hope this helps! Best wishes, -- Ricardo Diogo Righetto

2 1

Allocating GPUs
by Giono Matteo (PSI) 19 May '22

19 May '22

Dear all, Does anyone know if it’s possible to make Chimera use GPUs instead of CPUs? I have a 2021 Macbook Pro with 12-core GPUs and knowing that all the work is done by the CPU make all these GPUs kind of useless. Best, MG

5 5

USCF CTRL + Left Click
by Luke Kurfman-Student 19 May '22

19 May '22

Hello Sr./Ms., Most everyone in my laboratory has access to UCSF Chimera and can use it with no issues. However, one new person has had trouble selecting atoms. Specifically, neither CTRL + Left Click nor CTRL + SHIFT + Left Click appear to work on selecting atoms in a molecular geometry, even though their computer can run the program. They can translate, rotate, and zoom in-and-out of the geometry, and they can use actions such as "Select All" . However, they cannot deselect individual atoms once the entire geometry is selected, and they can only CTRL + Left Click outside the geometry to deselect the entire geometry. Additionally, drag-clicking does not appear to work. CTRL + Click is a fundamental feature that our group uses, especially since we use Chimera for journal figures. Are there any suggestions on how to troubleshoot the issue with selecting atoms? For reference, their computer runs Windows 10 and operates on a x64 bit system. Any help is appreciated, Luke

2 2

Set scale factors from displayed contours?
by Oliver Clarke 17 May '22

17 May '22

Hi, When combining maps using vop maximum (or volume maximum in chimerax), we often want to adjust the scale factors of the maps such that the overlapping bits of two aligned maps are visually on the same scale. It is possible to calculate the appropriate scale factors from the displayed thresholds, but this becomes a little time consuming when combining many maps. Would it be possible to add a flag, something like "get scalefactor from display thresholds" that would take care of this automatically? Cheers Oli

3 4

Assigning nucleotide representation to non-canonical nucleotides
by Jérôme Rihon 16 May '22

16 May '22

Dear I was wondering if there is a way to represent non-canonical (otherwise known as xenobiotic) nucleic acids through UCSF Chimera (specifically, not ChimeraX .. haven't made the jump yet). I've looked through your documentation on the `nucleotides` section but was not able to find something along those lines. My PI told me it was possible, but I can't seem to find it. My apologies if I should be looking for this function elsewhere, but I thought it'd be easier to just ask. Many thanks in advance! Kind regards, Met vriendelijke groeten, Cordialement, ______________________ Rihon Jérôme jerome.rihon(a)kuleuven.be | +32 16 32 53 57 PhD researcher @Rega Institute for Medical Research | Laboratory of Medicinal Chemistry | Computational Research Herestraat 49 - box 1041, 3000 Leuven

3 4

Making a movie from map series while keeping map's colors
by Michal Arie Shmuelov 16 May '22

16 May '22

Hi everyone, I have 20 maps (from 3D variability analysis) that I open as series in chimeraX. I'm coloring the map series using the command "color zone #X near #X distance X" (coloring the map according to pdb model). Next I'm trying to make a movie of this map series while retaining the map colors. For some reason when the morph/ vseries starts to run the colors disappear. Can someone help me to solve this problem? What are the commands that I should write? Thanks, Michal

2 1

question Help
by Firat KURT 16 May '22

16 May '22

*Hi, * *I have several problems regarding running some features of and registration of chimera. * *Firstly, I am not able to do registration. It keeps giving the error message below: * Error reading 1yti: Error during PDB fetch: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host Model 0 (AT4G26590_1_ATOPT5.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. error Exception in Tk callback Function: <bound method BugReportGUI.Submit of <BugReport.BugReportGUI.BugReportGUI object at 0x000000001A1CAFD0>> (type: <type 'instancemethod'>) Module: <module 'BugReport.BugReportGUI' from 'C:\Program Files\Chimera 1.16\share\BugReport\BugReportGUI.pyc'> (line: 348) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\BugReport\BugReportGUI.py", line 426, in Submit BUG_SELECTOR, fields) File "C:\Program Files\Chimera 1.16\share\CGLutil\multipart.py", line 33, in post_multipart_formdata retcode, retmsg, headers = h.getreply() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1196, in getreply response = self._conn.getresponse() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) error: [Errno 10054] An existing connection was forcibly closed by the remote host error: [Errno 10054] An existing connection was forcibly closed by the remote host File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) See reply log for Python traceback. IOError Exception in Tk callback Function: <function command at 0x00000000151E8898> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.16\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.16\share\chimera\register.py", line 294, in Register file = urllib.urlopen(regURL, params) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 89, in urlopen return opener.open(url, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 215, in open return getattr(self, name)(url, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 351, in open_http errcode, errmsg, headers = h.getreply() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1196, in getreply response = self._conn.getresponse() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) IOError: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host IOError: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) See reply log for Python traceback. *Secondly, when I try to model a sequence using modeller, I am having error message in first step. When I select "Tools>sequence>sequence>balst protein" and paste the sequence of interest to the respective area, I got the error message below :* Error reading 1yti: Error during PDB fetch: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host Model 0 (AT4G26590_1_ATOPT5.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. error Exception in Tk callback Function: <bound method BugReportGUI.Submit of <BugReport.BugReportGUI.BugReportGUI object at 0x000000001A1CAFD0>> (type: <type 'instancemethod'>) Module: <module 'BugReport.BugReportGUI' from 'C:\Program Files\Chimera 1.16\share\BugReport\BugReportGUI.pyc'> (line: 348) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\BugReport\BugReportGUI.py", line 426, in Submit BUG_SELECTOR, fields) File "C:\Program Files\Chimera 1.16\share\CGLutil\multipart.py", line 33, in post_multipart_formdata retcode, retmsg, headers = h.getreply() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1196, in getreply response = self._conn.getresponse() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) error: [Errno 10054] An existing connection was forcibly closed by the remote host error: [Errno 10054] An existing connection was forcibly closed by the remote host File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) See reply log for Python traceback. IOError Exception in Tk callback Function: <function command at 0x00000000151E8898> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.16\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.16\share\chimera\register.py", line 294, in Register file = urllib.urlopen(regURL, params) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 89, in urlopen return opener.open(url, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 215, in open return getattr(self, name)(url, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib.py", line 351, in open_http errcode, errmsg, headers = h.getreply() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1196, in getreply response = self._conn.getresponse() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.16\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) IOError: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host IOError: [Errno socket error] [Errno 10054] An existing connection was forcibly closed by the remote host File "C:\Program Files\Chimera 1.16\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) See reply log for Python traceback. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 100, in download return sax.parse(string=content) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\sax\parser.py", line 133, in parse sax.parse(source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\xmlreader.py", line 123, in parse self.feed(buffer) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\expatreader.py", line 224, in feed self._err_handler.fatalError(exc) File "C:\Program Files\Chimera 1.16\bin\lib\xml\sax\handler.py", line 38, in fatalError raise exception SAXParseException: <unknown>:76:2: mismatched tag Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\blastpdb\ParserBlastP.py", line 362, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. *I also attached the image of my input. Would you help me with this please? How can I fix these problems??* *My operating system is Windows 10 64X and chimera version is 1.16* *Regards, * [image: image.png] -- İyi çalışmalar dilerim, Doç. Dr. Fırat Kurt Bitkisel Üretim ve Teknolojileri Bölümü Uygulamalı Bilimler Fakültesi Muş Alparslan Üniversitesi Muş-Türkiye Tel :+90 436 249 10 83 Dahili: 2686 Fax :+90 436 231 22 01 ---------------------------------------------- Fırat Kurt, Ph. D. Associate Prof. of Plant Biotechnology Department of Plant Production and Technologies Faculty of Applied Sciences Mus Alparslan University Mus-Turkey Phone :+90 436 249 10 83 Ext. :2036 Fax :+90 436 231 22 01 www.alparslan.edu.tr

1 1

Can't open web file
by Emma Belcher 13 May '22

13 May '22

Hi there, I am a complete beginner with Chimera so apologies for the very basic question. I am trying to open a Consurf output which is a .chimerax file. I have downloaded Chimera to do this and have not changed any default settings (running MacOS Monterey 12.2.1). When I try to open the file (either by clicking “Open with Chimera” on the file or opening Chimera and going File > Open… and selecting the file), it comes up with the following error message: Error reading consurf_1652376787.chimerax: Couldn't find url 'https://consurf.tau.ac.il/results/1652376787/msa_file_fasta.aln.clustalw': [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661) I have no idea what this means or how to fix it, so would appreciate any tips! Thank you, Emma Belcher

2 3

Save reply log through chimera command line
by Reeki Emrizal 12 May '22

12 May '22

Hi I working on an automated python script to calculate the rmsd between two molecules using rmsd command. I'm using --nogui when running the script. The standard output did not show the rmsd value. When using the chimera gui, I noticed that the rmsd value is shown in the reply log. Is there a way I could save the content of the reply log through python script? I found previous post with similar issue that use: from chimera.tkgui import saveReplyLog saveReplyLog(path) The solution does not work for me though as the text file is empty even though there is content in the reply log. Kind Regards

2 2

RMSF calculations
by Reza Khayat 12 May '22

12 May '22

Hi, I'm trying to write a script to perform the procedure described here: https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-March/013247.html Can someone help with the command line syntax for associating a structure with a defined sequence? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

3 5

Re: [Chimera-users] [chimerax-users] interface plot
by Elaine Meng 12 May '22

12 May '22

Hi Pranav, If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission. In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include Select Contact Residues of B and C Select Contact Residues of B with C Select Contact Residues of C with B <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram> Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> Then use "info residues sel" and possibly "log save" as mentioned above. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> Example: measure buriedarea (/A&protein) with (/B&protein) list true I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Indeed! Although, as a suggestion, would it be possible to highlight > in the description that in order for the plot to inherit residue > colors, one needs to invoke the plot _after_ the residues have been > identified and colored? Also, could I save the output of the analysis > to a text file? > Best, > Pranav > -- > Pranav Shah > Postdoctoral Research Fellow. > > Division of Structural Biology, > Wellcome Trust Centre for Human Genetics, > University of Oxford, > Roosevelt Drive, Oxford OX3 7BN, > UK > > On Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> haha, glad you like it!! >> >> Best, >> Elaine >> >>> On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> <3 >>> <3 >>> <3 >>> <3 >>> <3 >>> >>> Best, >>> Pranav >>> -- >>> Pranav Shah >>> Postdoctoral Research Fellow. >>> >>> Division of Structural Biology, >>> Wellcome Trust Centre for Human Genetics, >>> University of Oxford, >>> Roosevelt Drive, Oxford OX3 7BN, >>> UK >>> <image.png>_______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>

1 1

use of the program UCSF Chimera
by GABRIELLE LUPETI DE CENA 12 May '22

12 May '22

Goodnight! My name is Gabrielle, I am a Master's student at UNIFESP (Federal University of São Paulo), SP, Brazil. I'm using UCSF Chimera to analyze the secondary structure of some peptides that I'm studying. When I load the .pdb file in the program, it generates a different structure than the one desired. In the examples below, we have two structures alpha helix and random coil, but the images generated are different and I don't understand why. Could you help me, explaining what is happening, or what I should do to have the image as in the first figure (NATTP_05 chimera). Thanks -- ---- A Universidade Federal de São Paulo segue a política de e-mail Institucional disponível em https://sti.unifesp.br/documentos/termos-de-uso-do-email <https://sti.unifesp.br/documentos/termos-de-uso-do-email> <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

2 2

crystal contacts
by Meital Bachar 12 May '22

12 May '22

Hello, my name is Meital and I am a Ph.D. student at the school of chemistry at Tel-Aviv university. i am trying to identify the crystal contacts of a protein that I am studying. and I was wondering if it is possible to get an output for the calculated crystal contacts in a way that the actual residues are listed. appreciate a lot your response. Meital

2 2

Get rotation between two views?
by Oliver Clarke 11 May '22

11 May '22

Hi, In either Chimera or X, is there a way to obtain the orientational relationship between two views? E.g. if I have two views saved, I would like to be able to say "view 1 is related to view 2 by a 45deg rotation about X and a 25deg rotation about Y" - this would be very useful for figure making/writing purposes. Does this exist? Cheers Oli

3 3

Re: [Chimera-users] Get rotation between two views?
by Elaine Meng 10 May '22

10 May '22

Hi Zhen, Are you using Chimera or ChimeraX? Remember they are two different programs with many differences from each other. Chimera only has a "viewdock" command (no "view" series, but I'm not sure what you mean by that anyway). Also if you are having a problem like your window freezing, instead of sending a message to me or the list, it is better to report it by using menu: Help... Report a Bug (both Chimera and ChimeraX have this) and filling out the dialog. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2022, at 10:31 AM, Gong, Zhen <zg2234(a)cumc.columbia.edu> wrote: > > Hi Elaine, > > Thank you very much for your reply. I was trying to use the “view” series command in chimera 1.13 but always get complaint like “no such file” or “unknow view Dockfile type”. Is that these commands could only be used in ChimeraX but not Chimera? > > By the way, I also had problems using chimera 1.16 on my mac (MacOs Montery version 12.2). The window will just freeze once I clicked on the “command line interface” icon and it will take about half minute to come back. Do you know how to solve this problem? > > Many thanks in advance! > > Best, > Zhen

2 1

Move model with associated map?
by Oliver Clarke 10 May '22

10 May '22

Hi all, Is there any way to apply the same transformation used by matchmaker for alignment to a map? I have two structures (map+atomic model) in different frames of reference. I would like to align one structure on the other, but also move the associated map in the same way. Is this possible? Cheers Oli

2 2

ValueError: can't normalize zero length array
by jyoti vishwakarma 04 May '22

04 May '22

ValueError Exception in Tk callback Function:<function<lambda> at 0x000000000EF38DD8> (type:<type 'function'>) Module:<module 'Tkinter' from 'C:\Program Files\Chimera 1.16\bin\lib\lib-tk\Tkinter.pyc'> (line: 590) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\bin\lib\lib-tk\Tkinter.py", line 592, in callit func(*args) File "C:\Program Files\Chimera 1.16\share\chimera\tkgui.py", line 3025, in<lambda> lambda s=self, e=event: s.showLabelBalloon(e)) File "C:\Program Files\Chimera 1.16\share\chimera\tkgui.py", line 3030, in showLabelBalloon objs = self.viewer.pick(event.x, event.y) ValueError: can't normalize zero length array ―――――――――――――――――――― -- Regards, Jyoti Vishwakarma UGC-SRF c/o Dr. R. Ravishankar Biochemistry & Structural Biology Division CSIR-Central Drug Research Institute Lucknow-226031

2 1

Web service issue?
by LaLone, Carlie 03 May '22

03 May '22

Hello, Could you provide advise on how to remedy the issue below? You are now running Chimera version 1.16 (build 42360). Your previous version was 1.15 (build 42258). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) #0, chain X: fatty acid-binding protein, liver Model 1 (m1_Fruit_fly+3stm+X.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download fp = self.options.transport.open(Request(url)) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open return HttpTransport.open(self, request) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 67, in open return self.u2open(u2request) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open return url.open(u2request, timeout=tm) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 435, in open response = meth(req, response) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 548, in http_response 'http', request, response, code, msg, hdrs) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 467, in error result = self._call_chain(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 654, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 429, in open response = self._open(req, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 447, in _open '_open', req) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1241, in https_open context=self._context) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1198, in do_open raise URLError(err) URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:ClustalOmegaService' is unavailable. See Reply Log for more details. Thank you, Carlie Carlie A. LaLone, Ph.D. Research Bioinformatician Great Lakes Toxicology and Ecology Division Office of Research and Development U.S. Environmental Protection Agency 6201 Congdon Blvd. Duluth, MN, 55804 Work: (218)529-5038 BIG NEWS…SeqAPASSv6.0 is now available!!!!! Try the Sequence Alignment to Predict Across Species Susceptibility<https://seqapass.epa.gov/seqapass/> (SeqAPASS) tool and predict chemical susceptibility to hundreds to thousands of species Publications 1. International Consortium to Advance Cross‐Species Extrapolation of the Effects of Chemicals in Regulatory Toxicology<https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.5214> 2. Integrative Computational Approaches to Inform Relative Bioaccumulation Potential of Per-and Polyfluoroalkyl Substances Across Species<https://academic.oup.com/toxsci/article-abstract/180/2/212/6112015> 3. Evidence for Cross Species Extrapolation of Mammalian-Based High-Throughput Screening Assay Results<https://pubs.acs.org/doi/abs/10.1021/acs.est.8b04587> 4. In Silico Site-Directed Mutagenesis Informs Species-Specific Predictions of Chemical Susceptibility<https://academic.oup.com/toxsci/article/166/1/131/5060571> 5. Evaluation of the scientific underpinnings for identifying estrogenic chemicals in nonmammalian taxa <https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.3456> 6. SeqAPASS: A Web-Based Tool for Addressing the Challenges of Cross-Species Extrapolation <https://academic.oup.com/toxsci/article/153/2/228/2578709> 7. Molecular target sequence similarity as a basis for species extrapolation to assess the ecological risk<https://www.sciencedirect.com/science/article/pii/S0166445X13002312>

2 1

Error in using the "align chain sequences" tool in chimera
by Chara Spanou 02 May '22

02 May '22

Dear all, After performing the structure comparison of 2 structures using the "MatchMaker" tool of the chimera software,I need to run an alignment of the structure sequences using the "align chain sequences" tool of the chimera. Unfortunately, I am getting the following error message in the reply log that persists for weeks: Traceback from web service request (connection setup):Traceback (most recent call last): File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download fp = self.options.transport.open(Request(url)) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open return HttpTransport.open(self, request) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 67, in open return self.u2open(u2request) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open return url.open(u2request, timeout=tm) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 437, in open response = meth(req, response) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 550, in http_response 'http', request, response, code, msg, hdrs) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 469, in error result = self._call_chain(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 409, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 656, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 431, in open response = self._open(req, data) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 449, in _open '_open', req) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 409, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 1240, in https_open context=self._context) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 1197, in do_open raise URLError(err)URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590)> Typically, if you get a TypeError, it's a problem on the remote serverand it should be fixed shortly. If you get a different error orget TypeError consistently for more than a day, please report theproblem using the Report a Bug... entry in the Help menu. Pleaseinclude the traceback printed above as part of the problem description.Traceback from web application request:Traceback (most recent call last): File "C:\Program Files\Chimera 1.12\share\WebServices\appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears "NonChimeraError: Web service appears to be down. See Reply Log for more details.Service 'opal:ClustalOmegaService' is unavailable. See Reply Log for more details. Can you please help? Thanks a lot for your time,Chara

2 1

Questions in ChimeraX comparing with Chimera
by Long Gui 27 Apr '22

27 Apr '22

Dear Chimera users, I have been recently transferring to ChimeraX from the conventional Chimera and I am currently struggling with two features existing in Chimera but not in ChimeraX. 1. How could I combine two or several different ChimeraX files? I have been doing in Chimera as I was opening new chimera files by "Files...Open...", this is a window pop-up as the following and if I click "No", the new Chimera will be added to the cold Chimera as the old one was not closed. However, when I performed the similar operation in ChimeraX, there is no such window and the new ChimeraX would REPLACE the old one. I wonder if there is a way (probably using command to open? but I did not find the correct open options.) to open the new ChimeraX without closing the old one? [cid:23bcde4a-3b02-4fc4-9b5e-7b034cd22a9f] 1. I am also working with tomogram slices and cellular segmentation. Previously, in Chimera I can set this Transparency value to 0 and the Plane of the tomogram will be totally opaque. Now in ChimeraX I have used the command "transparency #2 0" (#2 is the tomogram files) but it still look quite different from my previous images in Chimera. Is there a way to set it up in ChimeraX so it could look similar as before? [cid:1e2eb72a-f2e5-4c83-b4e4-81b881b9dc67] Thanks again and I am very grateful if any advice or help could be provided. Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 1