- Chimera-users - RBVI Mailing Lists

model panel: long 'clicking time'
by Julian von der Ecken 17 Jan '17

17 Jan '17

Dear Chimera Team, there is a long delay between on and off of the ’S’-checkbox (show button) in the model panel. I mean the model it self vanished instantly but the ckeckbox takes much longer to be set to on/off. Mac OS X 64-bit Version tested (1.11 2016-06-30, 1.11.2 2016-12-02; ): very slow. In older versions (1.10.2 2015-07-23) it was much faster. It is kind unfortunate when you click very fast through all models manually or you just want to alternatively show and hide one model very fast to see differences. Is it possible to set the speed somewhere/somehow? Thanks a lot for your advise Julian ————————————————————————————————— Julian von der Ecken, Ph.D. Max-Planck-Institute of Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund, Germany room: B2.27 tel: (+49) (0)231 133-2306 e-mail: julian.von-der-ecken(a)mpi-dortmund.mpg.de<mailto:julian.von-der-ecken@mpi-dortmund.mpg.de> institute: http://www.mpi-dortmund.mpg.de group: http://www.mpi-dortmund.mpg.de/forschungsgruppen/raunser

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Transparency of surface colored with electrostatic potential file
by Sarah Piper 17 Jan '17

17 Jan '17

Hi, I was wondering if you can make a surface transparent, which contains an electrostatic potential file (.dx), calculated with APBS? It would be nice to be able to see the ribbon structure of my .pdb file within the coloured surface. I’m using mol maps or SES to create the surface (my surface calculations (MSMS) usually fails, probably because of too large .pdb files) and then color this surface (Surface Color) with the submitted potential file from APBS. If I then want to make the surface with the potential colouring transparent, it doesn’t work. It just works to make the ’normal’ surface color itself transparent (e.g. transp 70,s #1). Does anyone have an idea if I can make the potential file or surface with electrostatic potential transparent as well? Many thanks for your help. Best regards, Sarah

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Visualization Martini coarse grained model in Chimera
by MOHD HOMAIDUR RAHMAN 17 Jan '17

17 Jan '17

Dear All It is possible to visualize martini coarse grained bead of proteins and lipid in Chimera? if yes please guide me for same. Thanks & regards Rahman ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' *M*d* H*omaidur* R**ahman *( Research Scholar ) Lab No. 510, Computational Biophysics Lab. Department of Biotechnology Indian Institute of Technology-Madras Chennai-600 036, India *Mobile No = +91- 7845991785* '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

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on Unit Cell function
by Smith Liu 17 Jan '17

17 Jan '17

Dear All, Once we load a PDB in chimera, in Tools-Higher order structure-Unit Cell, if we click "Make copies", the copies of the PDB would be created based on space group, with each copy has a specific # (0,1,2,3..., for example). Will you please let me know is any rule available for how the number of # for each copy of PDB was defined? It seems the PDB copies with consecutive specific # were not most closely related in the Chimera display. I am looking forward to getting a reply from you. Smith

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Fixing the Frame size
by chemocev marker 17 Jan '17

17 Jan '17

Hi I am making some images and I would like to know how to fix the zoom size so that in all the images size of the secondary structure should be similar. best Jiri

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Preference/default for H-bond representation
by Markus Heller 16 Jan '17

16 Jan '17

Hello, Is there a way to set the preference for H-bonds to be represented as dashed lines, not as solid lines? I don't seem to be able to find anything in the Preferences or the documentation. Thanks and Cheers Markus

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virtualization project - UCSF
by Scholz, Sebastian 16 Jan '17

16 Jan '17

Dear Sir or Madam, we, the COMPAREX AG, are a German Reseller. For one of our clients we conduct an evaluation license and have a list of questions provided, in the answer we need your help. This involves essentially the question whether the software can be virtualized and, if so, on what terms. These are crucial questions for the future orientation of its IT strategy for our customer. The Software: (for every Software is one questionnaire) Chimera 1.x Please note, that our questions refer to the latest software version. I therefore kindly ask for a timely response to the questionnaire, which you can found in the appendix (in German and English), but not later than January 23rd 2017. Kindly forward our request to whom it may concern, if you are not the responsible contact person. Thank you for your support. I look forward hearing from you soon. Kind regards / Mit freundlichen Grüßen Sebastian Scholz International Sales Team ______________________________________ COMPAREX AG Software Inside Sales Blochstraße 1 04329 Leipzig Direct contact: Sebastian Scholz mobile: +49 341 2568 6643 email: Sebastian.Scholz(a)comparex.de<mailto:Sebastian.Scholz@comparex.de> COMPAREX AG | Blochstraße 1 | 04329 Leipzig | Amtsgericht Leipzig | HRB: 15064 | USt-ID: DE 141626867 | Vorstand: Mag. Wilfried Pruschak (Vorstandsvorsitzender, CEO) | Marc Betgem (CSO) | Dr. Thomas Reich (CFO) | Aufsichtsratsvorsitzender: Mag. Wilhelm Doupnik | phone: +49 341 2568 000 | fax: +49 341 2568 999 | email: info(a)comparex.de<mailto:info@comparex.de> | web: www.comparex.de<http://www.comparex.de/>

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Docking license
by Farah Yousef 13 Jan '17

13 Jan '17

Hello, I need an assisdtance in what I faced in submitting after I filled the required info for DOCK 6. Pages cannot be opened though I checked my net connection and I know DOCK program is free of charge and available for academic projects. Hope I get help in obtaining the license for DOCK 6, please. Best wishes,Farah Yousef

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Web services (Modeller, Blast, etc.) running
by Elaine Meng 13 Jan '17

13 Jan '17

Hello users, I believe the RBVI web services called from Chimera are now running, thanks to the efforts of my coworkers. I just now verified running Modeller, Blast (requires Chimera 1.11.2 or later), and sequence realignment with Clustal Omega or Muscle. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Deleting a surface on command line, not just hiding it
by Rebecca Swett 12 Jan '17

12 Jan '17

Hi all, I'm working on an animation, and I'd like to know if there's a way I can delete or close a calculated surface from the command line. For my purposes, I'd like to show the surface representation of the protein, remove it, then show a dynamics trajectory, and show the surface again at a separate point (while the trajectory is stopped). Currently, without being able to close the surface, it tries to recalculate the surface at each trajectory frame, which doesn't work for my purposes. Let me know if this is possible. Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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