VMD-L Mailing List
From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Wed Apr 06 2022 - 08:04:56 CDT
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Via evaltcl, almost certainly. I don't think I've seen a change in CVS to reflect fromsels existing explicitly in molecule or Molecule on the python side.
-Josh
On 4/6/22, 8:58 AM, "Dominique Mias-Lucquin" <dominique.mias-lucquin_at_loria.fr> wrote:
Hi,
does the FROMSELS command is availlable from the python binding ?
DML.
----- Mail original -----
> De: "John Stone" <johns_at_ks.uiuc.edu>
> À: "yjcoshc" <yjcoshc_at_gmail.com>
> Cc: "Josh Vermaas" <vermaasj_at_msu.edu>, "vmd-l" <vmd-l_at_ks.uiuc.edu>, "Haochuan Chen" <haochuan.chen_at_univ-lorraine.fr>
> Envoyé: Lundi 4 Avril 2022 18:30:35
> Objet: Re: vmd-l: VMD 1.9.4 crashes after running the "Merge Structures" plugin (with psfgen 2.0)
> Hi,
> I should also point out that there's another new way of merging molecules in
> VMD 1.9.4 that people probably aren't aware of yet:
> mol fromsels $selectionlist
>
> e.g.:
> set sellist {}
> lappend sellist [atomselect 2 "index 11 to 18"]
> lappend sellist [atomselect 3 "index 20 to 30"]
> llength $sellist
> mol fromsels $sellist
>
> This bypasses any disk I/O and builds a new VMD molecule from a list of
> VMD atom selections from existing molecule(s). It can be substantially
> faster than other methods if the structures you've got loaded in VMD
> contain everything you want and you just need to put them together
> in a single molecule.
>
> You can of course then write the new molecule to a file if you like.
>
> Best,
> John
>
> On Mon, Apr 04, 2022 at 11:18:41AM -0500, yjcoshc wrote:
>> Hi Josh,
>>
>> Thanks for your information. I have tried VMD 1.9.3 with psfgen 1.6,
>> which works without the segfault. The generated files look correct,
>> so I have used them. I will try topotools if I have time.
>>
>> Thanks,
>>
>> Haochuan Chen
>>
>>
>> On 4/4/22 11:15, Josh Vermaas wrote:
>> >Hi Haochuan,
>> >
>> >If you are just trying to merge together two structures in a way
>> >that doesn't segfault, I think the "mergemols" command in
>> >topotools gives you a way around this problem. Admittedly, this is
>> >now my default approach, so I don't know how widespread this
>> >problem is with psfgen 2.0.
>> >
>> >-Josh
>> >
>> >On 4/4/22 11:06, yjcoshc wrote:
>> >>Dear VMD developers,
>> >>
>> >>I am using the "Merge Structures" plugin in VMD 1.9.4a51, and
>> >>after setting all the options and clicking the "Merge" button,
>> >>VMD encounters a segmentation fault. The VMD binary is download
>> >>from the official website. I have also tried to compile VMD from
>> >>source with debug options, and the backtrace is attached as
>> >>following:
>> >>
>> >>Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation fault.
>> >>0x00007fc70f04aded in __GI__IO_fflush (fp=0x46ac450) at iofflush.c:39
>> >>39 _IO_acquire_lock (fp);
>> >>(gdb) bt
>> >>#0 0x00007fc70f04aded in __GI__IO_fflush (fp=0x46ac450) at
>> >>iofflush.c:39
>> >>#1 0x00007fc6f4ef6c82 in newhandle_msg_text
>> >>(psfcontext=0x516c090, interp=interp_at_entry=0x4158b60,
>> >>msg=msg_at_entry=0x7ffef16f7590 "reading topology file
>> >>/home/hanatok/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all27_prot_lipid_na.inp\n")
>> >>at src/tcl_psfgen.c:71
>> >>#2 0x00007fc6f4ef6d35 in newhandle_msg
>> >>(vdata=vdata_at_entry=0x4be8230, v=v_at_entry=0x4158b60,
>> >>msg=msg_at_entry=0x7ffef16f7590 "reading topology file
>> >>/home/hanatok/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all27_prot_lipid_na.inp\n")
>> >>at src/tcl_psfgen.c:95
>> >>#3 0x00007fc6f4ef7183 in tcl_topology (data=0x4be8230,
>> >>interp=0x4158b60, argc=<optimized out>, argv=<optimized out>) at
>> >>src/tcl_psfgen.c:736
>> >>#4 0x00007fc70f8da815 in TclInvokeStringCommand () from
>> >>/lib64/libtcl8.6.so
>> >>#5 0x00007fc70f8dbad2 in TclNRRunCallbacks () from /lib64/libtcl8.6.so
>> >>#6 0x00007fc70f8e200a in ?? () from /lib64/libtcl8.6.so
>> >>#7 0x00007fc70f8e2833 in Tcl_EvalEx () from /lib64/libtcl8.6.so
>> >>#8 0x00007fc70f8e2856 in Tcl_Eval () from /lib64/libtcl8.6.so
>> >>#9 0x00007fc6f4ef98fd in tcl_psfcontext (data=0x4be8230,
>> >>interp=0x4158b60, argc=<optimized out>, argv=0x415cf90) at
>> >>src/tcl_psfgen.c:560
>> >>#10 0x00007fc70f8da815 in TclInvokeStringCommand () from
>> >>/lib64/libtcl8.6.so
>> >>#11 0x00007fc70f8dbad2 in TclNRRunCallbacks () from /lib64/libtcl8.6.so
>> >>#12 0x00007fc70f9aa1ac in ?? () from /lib64/libtcl8.6.so
>> >>#13 0x00007fc70f9a9d97 in TclServiceIdle () from /lib64/libtcl8.6.so
>> >>#14 0x00007fc70f98ce9c in Tcl_DoOneEvent () from /lib64/libtcl8.6.so
>> >>#15 0x0000000000a30f09 in TclTextInterp::doTkUpdate
>> >>(this=0x4158ac0) at TclTextInterp.C:543
>> >>#16 0x00000000009aaecb in UIText::check_event (this=0x4156990)
>> >>at UIText.C:186
>> >>#17 0x0000000000894ee3 in CommandQueue::check_events
>> >>(this=0x3a677f0) at CommandQueue.C:92
>> >>#18 0x00000000009af65a in VMDApp::VMDupdate (this=0x3a3f030,
>> >>check_for_events=1) at VMDApp.C:915
>> >>#19 0x0000000000a045ef in main (argc=1, argv=0x7ffef16f8468) at
>> >>vmdmain.C:93
>> >>
>> >>I suspect it may be caused by incorrect file descriptor
>> >>psfcontext->PSFGENLOGFILE (or wild pointer) in the new psfgen
>> >>2.0. The crash does not happen in VMD 1.9.3, which uses psfgen
>> >>1.6. Any ideas?
>> >>
>> >>Thanks,
>> >>
>> >>Haochuan Chen
>> >>
>> >>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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