- Chimera-dev - RBVI Mailing Lists

Release note suggestions
by Thomas Goddard 06 Nov '02

06 Nov '02

Hi Greg, I looked at the release notes again. Under performance optimizations it says "... is much faster ...". It would be helpful if this was more precise, like "... is approximately 2 times faster..." Some times "much faster" means 10% faster, and sometimes it means 10 times faster. I'm sure the speed up depends on the particular case but I like to give a number for a common case when I make optimization claims. Maybe move "Side View no longer drawn if containing dialog is closed" to be one of the perfomance optimization sub-points. Maybe put "splash screen shows up faster" under the performance optimizations item, and make "Chimera window pops up at splash screen position" a separate point. Benchmark extension description says "on chimera on chimera". To the Volume Viewer extension description you can add: "Subregion history and named subregions were added." I found the following hard to understand quickly. "Menu Functions tutorial expanded and changed to Getting Started -- Menu Version. Getting Started tutorial changed to Getting Started -- Command Version." Maybe something like "Getting Started tutorial now comes in a menu version and a command version." Tom

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release notes comments
by Elaine Meng 06 Nov '02

06 Nov '02

Hello, here's my 2 cents worth on the Release Notes: (1) I don't like "- -"...would make them all " - ", at least the ones embedded in the tutorial names. (2) I would change the wording describing the Select menu changes, since Chemistry contains other options besides the new one for residue type, and Structure contains sidechain/mainchain along with the automatic categories. The description is just a jumble as it is. I would just say: Select menu reorganization - new entries for sidechain/mainchain, residue type, automatic categories (ligand, main, solvent, ions) or if you prefer to mention the new headings under Select: Select menu reorganization - Chemistry section including new residue type item, Structure section including new entries for sidechain/mainchain and automatic categories (ligand, main solvent, ions) (3) "More flexible reading of MSF files" is kind of vague...what does that mean?? (4) New Extension: "Benchmark" should be in bold. I would change the description, because even though volumes are shown the performance indicates performance in molecular display tasks, and because speed (not "how well") is the quantity being assessed. Maybe something like: "measures hardware performance on graphical display tasks" Thanks, Elaine

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release notes for next release
by Greg Couch 06 Nov '02

06 Nov '02

Please review http://www.cgl.ucsf.edu/home/gregc/relnotes.html for inaccuracies and omissions and please let me know if you find any! Thanks, Greg

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Re: linux/371
by David E. Konerding 08 Oct '02

08 Oct '02

pett(a)cgl.ucsf.EDU wrote: >Synopsis: problem with chimera on redhat 8.0 > >Responsible-Changed-From-To: gnats-admin->pett >Responsible-Changed-By: pett >Responsible-Changed-When: Thu Oct 3 15:20:14 2002 >Responsible-Changed-Why: > transferred from pending > >http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=371&database=chimera > I have a VMware Red Hat 8.0 image with chimera installed that I can send you guys- that would make it trivial for you guys to test/reproduce/inspect this in the lab... Why does _chimera.so link against both the libstdc++.so that comes with chimera and the libstdc++.so that comes with Red Hat 8.0? _imaging.so => /home/dek/chimera-1516/lib/_imaging.so (0x403e0000) libtr.so => /home/dek/chimera-1516/lib/libtr.so (0x4040f000) libwrappy.so => /home/dek/chimera-1516/lib/libwrappy.so (0x40413000) libtogl.so => /home/dek/chimera-1516/lib/libtogl.so (0x40418000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0x4042e000) libGL.so.1 => /usr/lib/libGL.so.1 (0x404aa000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x4051d000) libstdc++.so.4 => /home/dek/chimera-1516/lib/libstdc++.so.4 (0x405fc000) libm.so.6 => /lib/i686/libm.so.6 (0x4066b000) libgcc_s.so.1 => /home/dek/chimera-1516/lib/libgcc_s.so.1 (0x4068d000) libc.so.6 => /lib/i686/libc.so.6 (0x42000000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x40695000) libz.so.1 => /usr/lib/libz.so.1 (0x406b3000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x406c2000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x406d8000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x406e6000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x40738000) libpthread.so.0 => /lib/i686/libpthread.so.0 (0x407ea000) libdl.so.2 => /lib/libdl.so.2 (0x4081a000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x80000000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x4081e000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x40827000) I wonder if that's not the problem as the backtrace is within some libstdc++ code: (gdb) #0 0x4206fdd5 in _IO_sgetn_internal () from /lib/i686/libc.so.6 #1 0x420633e9 in fread () from /lib/i686/libc.so.6 #2 0x40698d57 in std::__basic_file<char>::xsgetn(char*, int) (this=0x2000, __s=0x2000 <Address 0x2000 out of bounds>, __n=8192) at basic_file.cc:163 #3 0x407f370f in std::basic_filebuf<char, std::char_traits<char> >::_M_underflow_common(bool) (this=0x0, __bump=true) at ../../../../libstdc++-v3/src/fstream.cc:76 #4 0x406bc0b7 in std::basic_filebuf<char, std::char_traits<char> >::uflow() (this=0x2000) at fstream:147 #5 0x406b9f4d in std::basic_streambuf<char, std::char_traits<char> >::sbumpc() (this=0x6bd68040) at streambuf.tcc:59 #6 0x406c5405 in std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char) ( __in=@0x8708130, __str=@0xbfffdf40, __delim=10 '\n') at istream.tcc:1187 #7 0x4034a557 in (anonymous namespace)::read_gfxinfo(std::istream&, std::string const&, std::string const&, std::string const&, std::string const&, std::string const&) () from /home/dek/chimera-1516/lib/_chimera.so #8 0x4034c662 in (anonymous namespace)::initialize() () from /home/dek/chimera-1516/lib/_chimera.so #9 0x4034d375 in GfxInfo::makeCurrent() () from /home/dek/chimera-1516/lib/_chimera.so #10 0x401a89cf in chimera::GfxState::initialize() () from /home/dek/chimera-1516/lib/_chimera.so

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segfault chimera
by David E. Konerding 08 Oct '02

08 Oct '02

On Red Hat 7.3, chimera-1516 will segfault running the following: Midas.open("1oct") chimera.openModels.openState(0,0).xform = None

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[Fwd: [omniORB] ANN: omniORB 4.0.0 and omniORBpy 2.0]
by David Konerding 25 Sep '02

25 Sep '02

Hi, OmniORB 4.0 and OmniORBpy 2.0 have been officially released. They add a number of really nice features of OmniORB and fixed many bugs, (see attachment) and I think the next release of Chimera would benefit from moving to this new version. Dave

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Re: [chimera-dev] duping status in replies
by Eric Pettersen 17 Sep '02

17 Sep '02

On Tuesday, September 17, 2002, at 11:26 AM, Thomas Goddard wrote: > How about log? 'log' seems okay by me. I'll change it this afternoon unless someone objects. --Eric

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duping status in replies
by Eric Pettersen 17 Sep '02

17 Sep '02

Once I had implemented an 'echoToReplies' keyword in ModelessDialog status lines, I immediately became too lazy to not have the same keyword available to replyobj.status(). So now the latter has the keyword also (default false). --Eric

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question about AddH
by Euna Jeong 12 Sep '02

12 Sep '02

Dear Chimera developer, I am looking for a program to add hydrogen atoms to a pdb file. Chimera is a good tool to do it. After adding hydrogen atoms to a PDB file, I'd like to save the result file to a PDB file, not tiff image . Chimera can do that now? Thanks. Euna Jeong School of Computer Science and Engineering Inha University Inchon 402-751, South Korea 82-32-860-7388 (phone) 82-32-863-4386 (fax)

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Re: bad PDB
by David E. Konerding 12 Sep '02

12 Sep '02

Elaine Meng wrote: > Hi Dave, >When I opened it (it did open on the SGI), I got the usual >bad PDB record warnings, plus: >warning: duplicate atom serial number found: 1 >warning: duplicate atom serial number found: 2 >warning: duplicate atom serial number found: 3 >warning: duplicate atom serial number found: 4 >warning: duplicate atom serial number found: 5 >warning: duplicate atom serial number found: 6 >(etc. on up to 141) >Perhaps this is the problem. I deleted the first 141 atoms with 0.0 >coords and did not get those messages; that still leaves plenty of >0.0 coord atoms at the end, which are not complained about. You might >want to try this. >Elaine > > By the way, I fixed the atom serial numbers so they are numbered sequentially from 1, and chimera still crashes, showing it's not related to the serial number warning. Dave

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GUI design
by Greg Couch 11 Sep '02

11 Sep '02

Apple has released its "Aqua Human Interface Guidelines" in both html and pdf formats at: <http://developer.apple.com/techpubs/macosx/Essentials/AquaHIGuidelines/>. Chapter 2 "Human Interface Design Principles" looks good. And the section on "Using Ellipses in Menus and Buttons" might still be useful :-). There is also a short guide for Windows programmers at: <http://developer.apple.com/ue/switch/windows.html>. Greg

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Feature request
by David E. Konerding 10 Sep '02

10 Sep '02

I would like the "sequence panel" to be on the "Controllers menu". Since the sequence panel normally requires a model to be selected first (since it only displays the sequence of 1 model at a time), it should be updated to show sequences for all models. It's very clunky to have to go Controllers->Model Panel->select model->scroll to sequence->click sequence given that dealing with the protein sequence is such a common operation. Dave

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new PC version available internally
by Greg Couch 04 Sep '02

04 Sep '02

on socrates in /usr/tmp/gregc/chimera1.1549.exe. Enjoy. It is already installed on ryle :-) Greg

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ryle
by Greg Couch 28 Aug '02

28 Aug '02

It appears that someone reinstalled chimera on ryle and that blew away all of the development only stuff in the Chimera installation tree. Please don't ever do that again. Thanks, Greg

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a reminder about arnauld
by Greg Couch 23 Aug '02

23 Aug '02

Please keep the arnauld console logged in as administrator so bilbo, the linux development host, can continue to run. If for some reason you do log out as administrator, you need to first go to the vmware bilbo window and shutdown bilbo by logging into bilbo as root and running shutdown. The problem when someone logs out the administrator is that there is a chance that bilbo's disks will get trashed unless it is brought down cleanly first. (FYI, the fsck was successful, and I don't need to know who logged out without bringing bilbo down first.) This problem is getting worse where someone wants to use arnauld to demo/debug and someone needs arnauld/bilbo to build the Linux distribution, so I'd like to get bilbo moved to another computer, preferably a linux server in the machine room running linux natively (ASAP). Greg

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congratulations to the new beta release
by C. Klein 22 Aug '02

22 Aug '02

Hello, I have been writing to you before and you may remember that we communicated a bit about chimera. Now I have found the improved version on your www pages and would like to congratulate you on that. I especially like the new columns in the "model panel" with those checkboxes. What I still find missing is the option to display atom numbers (as taken from the input file) as labels. This can often be handy, for example when defining rotatable bonds in small molecules for docking studies, or when editing pdb files by hand. Best regards, Chris Klein -- Dr. C. Klein; cklein(at)pharma.anbi.ethz.ch Dept. of Applied Biosciences, Pharmaceutical Chemistry Swiss Federal Institute of Technology / ETH Zuerich Winterthurerstr. 190 CH-8057 Zuerich Phone: +41 1 6356062 FAX : +41 1 6356884

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Re: [chimera-dev] congratulations to the new beta release
by Elaine Meng 15 Aug '02

15 Aug '02

Hi Chris, The "write file" capability is actually already implemented in our working version and will be available in the next release (likely in the neighborhood of Oct/Nov). The man page for that command is http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html Basically, you will be able to write a PDB file of a model in transformed or untransformed coordinates. Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, R.Ph., Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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hydrogen optimization
by Terry Downing 14 Aug '02

14 Aug '02

Hi, I am attempting to add hydrogens to proteins with ligands bound...I am using the AddH extension, which appears to add hydrogens with reasonable bond lengths and bond angles...However, I notice that because default torsion angles are being used, there are situations in which the cartesian coordinates of the hydrogens are not optimized and result in clashes...This is particularly a problem with hydrogens that are attached to heavy atoms that are free to rotate (ie methyl and amide groups)...Are there any torsion minimization protocols available where I can optimize the torsional angle of just the newly added hydrogens without changing the cartesian coordinates of the heavy atoms (allow them to rotate to optimize the hydrogen placement but not move away from the experimental coordinates)?...I just spoke with Tom Ferrin and he said that Eric was the person most experienced with the AddH extension, and he recommended that I look at the documentation from both him and Elaine...Anything you can recommend on this would be greatly appreciated... Sincerely, P. Therese Downing Kuntz Lab

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Re: [chimera-dev] hydrogen optimization
by Elaine Meng 14 Aug '02

14 Aug '02

Hello, Currently there is no "force field" functionality within Chimera, and thus no minimization/dynamics. At this point you would need to use AMBER or SYBYL to perform those types of calculations. We plan to have such capability in the future, but it is a nontrivial operation. Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, R.Ph., Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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meeting reminder
by Conrad Huang 08 Aug '02

08 Aug '02

There will be a Chimera meeting at 1:30 in S922 today. The agenda is at https://wwwtest.cgl.ucsf.edu/intranet/chimeradevelopment/agenda.html Conrad

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Re: [chimera-dev] writing pdb files
by Elaine Meng 02 Aug '02

02 Aug '02

Dear Jim, If you have a UNIX system, the "pdbrun" command may be able to do what you want. Only the transformed coordinates are written out. I recommend the "nouser" keyword to avoid getting a lot of extra information in USER records. If there are multiple models, they all get sent to one file with END records in between (some postprocessing may be required). example usage: pdbrun all nouser cat >file.pdb See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdbrun.html The "write" command is much better for this purpose (and works for all of the platforms) but is not in the current release. It has been implemented in our working version and will be available in the next release. See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html I am not sure when the next release will come out, however. Finally, I believe there is a way to get the transformation matrices but I must defer to the programmers on the team to address this point. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, R.Ph., Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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writing pdb files
by J. H. Prestegard 02 Aug '02

02 Aug '02

I hope commands to write out pdb files for trandformed molecules (or the transformation matrices) will be implemented soon. Since we do additional calculations on files transformed by commands such as match, these are very important tools for us. Jim Prestegard

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Mouse Trigger
by Mike Liang 01 Aug '02

01 Aug '02

Hello! Is there a way to register a trigger for the mouse? I want the user to be able to rotate the molecules all they want, but perform my (slow) computation when their done moving the models. So it'll be nice to have a MouseUp-like handler (or maybe you have an alternative method). Thanks! Mike

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Fwd: cancel vs. close
by Eric Pettersen 31 Jul '02

31 Jul '02

Can we put this on the discussion agenda for the next Chimera meeting? --Eric Begin forwarded message: > From: "David E. Konerding" <dakone(a)uclink.berkeley.edu> > Date: Wed Jul 31, 2002 10:11:47 AM US/Pacific > To: pett(a)cgl.ucsf.edu > Subject: cancel vs. close > > Why do you guys use the button named 'cancel' where it you should be using > 'close'? I think we had this > discussion at a chimera group meeting before. But normally, I think of > "cancel" in the literal sense- cancel > the change I made (not that the Windows desktop uses it to mean that) > rather than "close the dialog window" > (which isn't a cancellation). > > Dave

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request for feature
by David E. Konerding 31 Jul '02

31 Jul '02

Hi, I would like the following feature: I can currently load a pdb file from the command line using: pdb:1oct which is very convenient. Now, I would love to have a feature where I could load a scop PDB file using: scop:d1octc1 I am currently using the following code fragment to load scop PDB files, which are all available on the web: PDBSTYLE_ADDRESS = "http://astral.stanford.edu/pdbstyle-1.59" domainfile = "%s/%s/%s.ent" % (PDBSTYLE_ADDRESS, self.domainName.get()[2:4], self.domainName.get()) print domainfile f = urllib.urlopen(domainfile) pdb = f.read() f.close() t = tempfile.mktemp() f = open(t, "w") f.write(pdb) f.close() mols = chimera.openModels.open(t, type="PDB") A glance at the pdbstyle-1.59 page, http://astral.stanford.edu/pdbstyle-1.59.html also suggests that rather than retrieving by filename, this CGI script will retrieve the PDB file directly, without the need for knowing the directory structure schema: <form method="get" action="pdbstyle.cgi"> <input type=submit value="Retrieve"> the PDB-style file for <b><font size=-1>SCOP</font></b> domain <input type ="text" maxlength=7 size=7 name=id> (i.e. "d1dlwa_") I'm fairly confident the url won't change; I can check with the astral/scop developers to get an idea if this service will be consistent and that the interface is relatively stable. Thanks, Dave

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