- Chimera-users - RBVI Mailing Lists

Splitting the ligand cluster file
by SAPTARSHI MUKHOPADHYAY 14BBT0011 11 Apr '18

11 Apr '18

Hello! I recently performed a ligand-protein docking job in SwissDock and downloaded the output file which contained the "clusters.dock4.pdb" file. I performed the ViewDock analysis on Chimera and now want to save a specific binding mode of a ligand from the cluster. I understand that the "Split" function is to be used in this regard, but I am not sure on how to implement this because of my limited experience with Chimera. Can I be provided with the exact steps for using this function? Thanks, Regards, Saptarshi

2 1

the .chimerax suffix was used for Chimera web data
by Elaine Meng 10 Apr '18

10 Apr '18

Hi Boaz, Long before we decided to name the next-generation package ChimeraX, we had used the .chimerax filename suffix for Chimera web data files. We decided it was obscure enough not to cause too much confusion going forward… <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.…> ChimeraX does not use “.chimerax” suffix files at present; suffix .cxc is used for ChimeraX command files and .cxs for ChimeraX session files. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#composite> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 10, 2018, at 2:19 PM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi Eric, > I'm sure this is a revelation for you but oddly enough (or maybe not) the Consurf output has .chinerax type but is easily read into good old chimera. I was puzzled the first time I noticed this but it works. Perhaps I'm off the point in this discussion. > Cheers, > Boaz

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 180, Issue 8
by Boaz Shaanan 10 Apr '18

10 Apr '18

1 0

ConSurf script on ChimeraX
by Fabian Glaser 10 Apr '18

10 Apr '18

Hi, I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX ModuleNotFoundError: No module named 'cPickle' File "consurf_final_zn.py", line 1, in See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. Is this something that can be fixed or updated? More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that? Here is the beginning of the original chimera script import cPickle, base64 try: from SimpleSession.versions.v65 import beginRestore,\ registerAfterModelsCB, reportRestoreError, checkVersion except ImportError: from chimera import UserError raise UserError('Cannot open session that was saved in a' ' newer version of Chimera; update your version') checkVersion([1, 12, 41623]) import chimera from chimera import replyobj replyobj.status('Restoring session...', \ blankAfter=0) replyobj.status('Beginning session restore...', \ blankAfter=0, secondary=True) beginRestore() def restoreCoreModels(): from SimpleSession.versions.v65 import init, restoreViewer, \ restoreMolecules, restoreColors, restoreSurfaces, \ restoreVRML, restorePseudoBondGroups, restoreModelAssociations molInfo = Thanks a lot, Best, Fabian Fabian Glaser PhD Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/> Tel +972 (0) 4 8293701

2 3

Dear team UCSF chimera, kindly help me I download and installed the UCSFf chimera but its showing short cut
by Maria Yousuf 09 Apr '18

09 Apr '18

Dear team UCSF chimera Hi I download and installed the UCSFf chimera followed the linkon windows 7 Microsoft Windows 64-bit chimera-1.12-win64.exe<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> Size: 150984696 bytes MD5: b662f97cdacb8be458662aa638dd6694 Oct 24, 2017 Instructions<https://www.cgl.ucsf.edu/chimera/data/downloads/1.12/win64.html> Documentation<https://www.cgl.ucsf.edu/chimera/data/downloads/1.12/docs/> Runs on Windows 7 or later. Initially It worked well, but after 2 days a shortcut appeared in the file and some of its features are not functional, I cant able to open a docked file in .pdb format Kindly share the functional link to download chimera on 64bit windows 7 looking forward to hear from you soon regards Dr.Maria <http://aka.ms/weboutlook>

2 1

Chimera's hydrogen bond counting tool (FindHBond) from command-line?
by Gustavo Seabra 09 Apr '18

09 Apr '18

Hi all, Is there a way to run the Chimera's hydrogen bond counting tool (FindHBond) using the command line only? Could someone post me to the best way? -- Gustavo Seabra Professor Adjunto Universidade Federal de Pernambuco Recife - PE - Brasil +55-81-2126-7450 x5023 (goo.gl/ktsXSc)

2 3

chimeraX consurf
by Fabian Glaser 08 Apr '18

08 Apr '18

Hi, I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX ModuleNotFoundError: No module named 'cPickle' File "consurf_final_zn.py", line 1, in See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu<mailto:chimerax-bugs@cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. Is this something that can be fixed or updated? Thanks a lot, Best, Fabian Fabian Glaser PhD Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ Tel +972 (0) 4 8293701

1 0

How to change 32bit map into 16bit map
by Jun Ha Song 05 Apr '18

05 Apr '18

Hello, I sometimes invert my map using Fiji, and I also convert my 32bit map into 16bit map using Fiji's "Image → Type → 16-bit" function, but the only way to retrieve the map from Fiji is to save the map as .tif stack, then use IMOD's "tif2mrc" to get it back as .mrc file. However, once I save my map as .tif, the pixel spacing information of the map is set to 1,1,1. Because of this, I always have to re-adjust the pixel spacing back to original using IMOD's "alterheader" once I use Fiji for any kind of image adjustment. I know I can invert a map in Chimera (without setting the pixel spacing to 1,1,1 like Fiji) by using "Volume Filter → Filter Type : Scale → Scale by -1", but I don't know how to turn my 32bit map into 16bit map. Although the "Value Type" of scale filter allows me to specify which bit I want the map to be in, when I filter my float32 map with value type set to either int16 or uint16, the filtered map shows histogram with only few lines. Can UCSF Chimera turn float32bit map into 16bit map? Best, Junha Song.

2 2

Hello I have a question
by Teddy Chen 05 Apr '18

05 Apr '18

Hi my name is Teddy, I used UCSF Chimera for my research, and it is a very good software! I appreciate you made it. I have a question about structure comparison, I usually use Matchmaker to overlap 2 similar protein fragment to compare the difference. I wonder if the structure is bent or twisted during the matching process, in order to fit the reference structure more? For example, the attachment is for demonstration. There is a protein A, and protein A have a short from that miss some amino acid (the green part is missed). So the result produced by the Matchmaker would be A or B? If the result is A, can I make result B by UCSF Chimera? Thank you!

2 2

Minimum system requirements for software
by Kerley, Jeremy L 04 Apr '18

04 Apr '18

I have a faculty member who uses the Chimera software. While using the software, his current computer continually freezes/locks-up and must be rebooted. Please email the minimum/recommended system requirements for the Chimera software. I’m in the process of building out a replacement system and need that information. Regards, —— Jeremy Kerley Computing Support Specialist II Emory University School of Medicine Dept of Pediatrics IT Ph: (404)727-4781 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 1