November 2010 - Chimera-users - RBVI Mailing Lists

Fwd: Trojan alert Chimera 1.5
by Elaine Meng 15 Nov '10

15 Nov '10

Begin forwarded message: From: "Prof. Dirk Volkmer" <dirk.volkmer(a)physik.uni-augsburg.de> Date: November 15, 2010 4:11:32 AM PST To: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: Fwd: [Chimera-users] Trojan alert Chimera 1.5 Thank you for the quick response. I am wondering though, if you could change your code such that the similarity to some kind of Trojan programs might be reduced. The previous Chimera version did not show this problem and I am hesitating to de-activate my virus scanners for the purposed of installing your software, especially since it sends these alerts. With kind regards, dv Am 14.11.2010 18:18, schrieb Elaine Meng: > I didn't know if you already got this (you might not be subscribed to the chimera-users list) so am forwarding. Apologies if you already got the message, > Elaine > > Begin forwarded message: > >> From: Tom Ferrin <tef(a)cgl.ucsf.edu> >> Date: November 13, 2010 6:00:21 PM PST >> To: chimera-users(a)cgl.ucsf.edu >> Subject: Re: [Chimera-users] Trojan alert Chimera 1.5 >> >> It's a false positive, caused by a digital signature match between the >> trojan you cite and an icon within the Chimera executable. We've >> notified the 2 or 3 antivirus s/w vendors who are reporting the warning >> message, and we're looking at other ways to deal with the problem. >> >> >> >> On 11/13/10 4:46 AM, Prof. Dirk Volkmer wrote: >>> To whom it may concern: >>> >>> Dear developers of Chimera. >>> I am facing a problem with the currently distrbuted version (1.5 rc) of >>> Chimera. >>> When I am trying to install the program I receive a warning message from my >>> antivirus program (Avira Antivir with VDF Version: 7.10.13.235) that the >>> chimera.exe >>> windows installer is trying to install the following malware /Trojan >>> software: >>> >>> TR/Crypt.ZPACK.Gen2 >>> TR/Crypt.ZPACK.Gen >>> >>> Could you please be so kind to check if this alert is serious and >>> whether or not >>> your program might be infected ? >>> >>> Many thanks in advance sincerely >>> >>> dv >>> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -- ++++++++++++++++++++++++++++++++++++++++++++ Prof. Dr. Dirk Volkmer Chair of Solid State and Materials Chemistry Institute of Physics Augsburg University Universitaetsstrasse 1 D-86159 Augsburg (Germany) Office Room 4.34 Phone: +49 (0)821 598-3006 Secretary: +49 (0)821 598-3032 FAX: +49 (0)821 598-5955 Mobile-Phone: 0176/24872988 Home-Phone: +49(0)7303/929742 E-mail: dirk.volkmer(a)physik.uni-augsburg.de http://www.physik.uni-augsburg.de/chemie/ under construction http://www.uni-ulm.de/nawi/nawi-anorg2.html ++++++++++++++++++++++++++++++++++++++++++++

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Trojan alert Chimera 1.5
by Prof. Dirk Volkmer 15 Nov '10

15 Nov '10

To whom it may concern: Dear developers of Chimera. I am facing a problem with the currently distrbuted version (1.5 rc) of Chimera. When I am trying to install the program I receive a warning message from my antivirus program (Avira Antivir with VDF Version: 7.10.13.235) that the chimera.exe windows installer is trying to install the following malware /Trojan software: TR/Crypt.ZPACK.Gen2 TR/Crypt.ZPACK.Gen Could you please be so kind to check if this alert is serious and whether or not your program might be infected ? Many thanks in advance sincerely dv -- ++++++++++++++++++++++++++++++++++++++++++++ Prof. Dr. Dirk Volkmer Chair of Solid State and Materials Chemistry Institute of Physics Augsburg University Universitaetsstrasse 1 D-86159 Augsburg (Germany) Office Room 4.34 Phone: +49 (0)821 598-3006 Secretary: +49 (0)821 598-3032 FAX: +49 (0)821 598-5955 Mobile-Phone: 0176/24872988 Home-Phone: +49(0)7303/929742 E-mail: dirk.volkmer(a)physik.uni-augsburg.de http://www.physik.uni-augsburg.de/chemie/ under construction http://www.uni-ulm.de/nawi/nawi-anorg2.html ++++++++++++++++++++++++++++++++++++++++++++

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tuning transparency of VDW spheres
by Boaz Shaanan 15 Nov '10

15 Nov '10

Hi Elaine, Thanks for suggestions. I'll try them and see how it looks. Ribbons won't do here since I want to show a w.t. protein and mutants with substrate analogues in the active site and how they fit (or clash) so I'm only showing a few residues. Thanks again. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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tuning transparency of VDW spheres
by Boaz Shaanan 15 Nov '10

15 Nov '10

Hi, Is it possible to tune the transparency of the VDW spheres (as with surfaces for example) if I choose to render some atoms as spheres and still would like to see the bonds (rendered as sticks)? Just wondering. I'm working with the 1.4 official release. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Consurf
by Sosnovtsev, Stanislav (NIH/NIAID) [E] 10 Nov '10

10 Nov '10

I wonder if there is a short way to introduce consurf output colors to multiscale models. My virus particle has 60 trimers (three chains of the same protein). Thank you in advance, Stanislav

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loading pdb files
by Beale, John 10 Nov '10

10 Nov '10

I have a series of pdb files that I am loading into Chimera. How can I get each file to load as a backbone structure with a different color for each? I used to be able to do this, but when I loaded a newer version of Chimera it no longer works. I am sure that this must be a preferences issue, but I can't figure it out. Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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Write out frames, but the complete movie
by Leiman Petr 04 Nov '10

04 Nov '10

Hi, A backward question: Is it possible to write out a movie as a set of frames? I would like to show several structures rotating side by side and the simplest way I can think of is to collage frames using imagemagick and create a new video stream with mencoder. Many thanks, Petr

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Chimera production release candidate
by Elaine Meng 04 Nov '10

04 Nov '10

A Chimera production release candidate (version 1.5) is now available: <http://www.cgl.ucsf.edu/chimera/download.html> As described in the release notes, many new features have been added since the previous production release: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.5.html> Please try the candidate release and report any problems (Help... Report a Bug in the Chimera menu). Note Chimera 1.5 will be the last release for the X11 version on Mac. On behalf of the Chimera team, 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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Query regarding solvent accessible surface area of protein
by Aditya Padhi 03 Nov '10

03 Nov '10

Hi all, I have carried out molecular dynamics simulation of my protein of interest using AMBER 10. I need to calculate the "solvent accessible surface area (SASA)" of 6 amino acid residues in wild type and certain mutants. My query is regarding can I use chimera for the same. Is it possible to both visualize and get analytical data for the differences in solvent accessible surface area for wild type and mutants? Another query is, in chimera can I get the SASA for each and every trajectories or I have to generate average PDB (Is it correct)? Kindly help me sir. Any other suggestions will be highly grateful. Thanks and regards Aditya.

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Color sub-region with marker
by Xiaofeng Fu 03 Nov '10

03 Nov '10

Dear Chimera users, I always have problems when I color a sub-region of density map by markers. Rather than a zigzag, boundary, I try to create a smooth curve boundary of sub-region from a whole density 3D volume. In this case, if I just put one marker and select a big coloring radius, the boundary in cross-view will show a circle curve at the boundary, however if I use a very small coloring radius and put more and closer markers on the boundary, the boundary shows a sawtooth in cross-view, even I choose 4 times for subdividing surface. Or is there any other way to do this instead of markers? And I have several other questions: (1) Is that possible to have different coloring radius in one Chimera session? (2) except for ball shape, can we have more options on the coloring object with markers? For example rectangular, ellipse and so on. (3) Is that possible to put markers directly on the clip planes? Thanks in advance, Xiaofeng

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Chimera-users November 2010