January 2017 - Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] dipoles
by Sagar, Vatsala (NIH/NEI) [E] 12 Jan '17

12 Jan '17

Hi Tom, So if you align the pdb files of the rotated proteins, they have an exact match. But when you make the PQR files, it adds hydrogens differently to the rotated proteins, resulting in a charge difference in the said histidine. Should the program be adding hydrogens differently to the rotated proteins, and is there a way to remedy this> Thanks a lot, Vatsala Sagar From: "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> Date: Friday, January 6, 2017 at 10:27 AM To: "chimera-bugs(a)cgl.ucsf.edu <mailto:chimera-bugs@cgl.ucsf.edu>" <chimera-bugs(a)cgl.ucsf.edu <mailto:chimera-bugs@cgl.ucsf.edu>> Subject: FW: [Chimera-users] dipoles Hi Tom, I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, Thanks, Vatsala From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> Date: Thursday, January 5, 2017 at 7:07 PM To: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> Subject: Re: [Chimera-users] dipoles Hi Vatsala, I guess you are refering to the dipole.py script on the Chimera Python scripts web page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. Tom > On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: > > Hi, > Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? > Thanks, > Vatsala Sagar > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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Re: [Chimera-users] dipoles
by Tom Goddard 10 Jan '17

10 Jan '17

Hi Vatsala, If you run the Chimera pdb2pqr command or graphical interface on a molecule and a rotated copy of the same molecule and it gives different protonation states for histidine that seems like a bug. As described in the Chimera documentation this uses the PDB2PQR web service provided by the National Biomedical Computation Resource (NBCR). https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html> You might want to contact the developers of PDB2PQR to pursue this matter further http://www.poissonboltzmann.org/support/home/ <http://www.poissonboltzmann.org/support/home/> Chimera can also add hydrogens and compute charges using the Chimera DockPrep tool so maybe that is an option for you to avoid this problem in pdb2pqr. Tom > On Jan 10, 2017, at 7:35 AM, Sagar, Vatsala (NIH/NEI) [E] <vatsala.sagar(a)nih.gov> wrote: > > Hi Tom, > So if you align the pdb files of the rotated proteins, they have an exact match. But when you make the PQR files, it adds hydrogens differently to the rotated proteins, resulting in a charge difference in the said histidine. Should the program be adding hydrogens differently to the rotated proteins, and is there a way to remedy this> > Thanks a lot, > Vatsala Sagar > > From: "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Date: Friday, January 6, 2017 at 10:09 AM > To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>, "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Subject: Re: [Chimera-users] dipoles > > Hi Tom, > I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, > Thanks, > Vatsala > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Date: Thursday, January 5, 2017 at 7:07 PM > To: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Subject: Re: [Chimera-users] dipoles > > Hi Vatsala, > > I guess you are refering to the dipole.py script on the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. > > Tom > > >> On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: >> >> Hi, >> Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? >> Thanks, >> Vatsala Sagar >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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Map conservation of my sequence compared to sequence alignment
by mfellner＠msu.edu 09 Jan '17

09 Jan '17

Good day I like the mapping sequence conservation tool in chimera, however I ran into a problem that IÂ could not overcome with anything IÂ found online. I have the consensus mapped onto my protein but that is not what IÂ want. IÂ want to show how the residues of my protein are conserved. For example at a particular residue the consensus is a C but in my structure its a W. at the moment the W is colored to be highly conserved based on the consenus of the C. The W is maybe 15% conserved, how can IÂ map the conservation of my sequence compared to all the other sequences. IÂ hope IÂ explained what my issue is Thank you for this great tool Matthias Fellner

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dipoles
by Sagar, Vatsala (NIH/NEI) [F] 06 Jan '17

06 Jan '17

Hi, Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? Thanks, Vatsala Sagar

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Mutation in Chimera
by Islam, Tanzila 06 Jan '17

06 Jan '17

Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time. I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University

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