From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 24 2011 - 21:28:18 CST

Hi Francesco,
For what it's worth, this is a tcl error, not c++.

In any case, I haven't been able to reproduce this, so I really need a
minimal set of steps to get it (preferrably not involving typing in 20
patches -- incidentally, if you have a lot of patches you may wish to
use the command line version of autopsf to make your procedure more
repeatable and easier to edit). Can you get it with just a couple
patches? Does it happen with one in particular? What structure are you
working on? I've used autopsf before on structures requiring hundreds of
ASPP/GLUP patches, but that was the command line version, so either
there's something peculiar to your structure going on here, or there's a
bug that only shows up in the GUI.

Thanks,
Peter

On 02/23/2011 04:03 PM, Francesco Pietra wrote:
> John:
> I tried with 1.9beta1 on my old desktop Pentium with Debian GNU/Linux
> i386. All patches could now be submitted and I am pretty sure that
> there was no error in the couples within DISU patches. However, "Apply
> patches and finish PSF/PDB" led to
>
> can't read "logfileout": no such variable
> can't read "logfileout": no such variable
> while executing
> "puts $logfileout "Applying patch: [lindex $patch 0] [lindex $patch
> 1]:[lindex $patch 2] [lindex $patch 3]:[lindex $patch 4]""
> (procedure "::autopsf::makepatches_gui" line 13)
> invoked from within
> "::autopsf::makepatches_gui"
> invoked from within
> ".autopsf.patches.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autopsf.patches.finish"
> (command bound to event)
>
> Is that lack of something from my side?
>
> Incidentally, should (in autopsf) the reorganization of dihedrals etch
> follwing the application of patches occur automatically? I remember
> vaguely that time ago there was a button (may be regen?) to do that.
>
> francesco
>
>
>
> On Wed, Feb 23, 2011 at 5:47 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>> Francesco,
>> I understand. If you can test the new code by this weekend that is
>> soon enough that if there is still a bug we might be able to address it
>> before VMD 1.9 is released.
>>
>> Cheers,
>> John
>>
>> On Wed, Feb 23, 2011 at 05:42:55PM +0100, Francesco Pietra wrote:
>>> John:
>>> I forgot to mention that I was using 1.8.7 on Debian GNU/Linux. It
>>> will take some time to report on your suggestion because it deals of
>>> some forty patches
>>> francesco
>>>
>>> On Wed, Feb 23, 2011 at 5:34 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>>> Francesco,
>>>> Can you try using the new VMD 1.9beta1 version and see if you still
>>>> encounter this problem? A few changes were made to autopsf that might
>>>> relate to your problem.
>>>>
>>>> Cheers,
>>>> John
>>>>
>>>> On Wed, Feb 23, 2011 at 05:21:11PM +0100, Francesco Pietra wrote:
>>>>> Hello:
>>>>> While applying very many ASPP, GLUP, and DISU patches, at 3/4 way the
>>>>> "Autopsf - Add Patch" refuses to add further patches, reporting a
>>>>> C-typical (though for me obscure) error. Below the log:
>>>>>
>>>>> expected integer but got ""
>>>>> expected integer but got ""
>>>>> while executing
>>>>> "format $patchformat5 [lindex $patch 0] [lindex $patch 1] [lindex
>>>>> $patch 2] [lindex $patch 3] [lindex $patch 4]"
>>>>> (procedure "update_patchtexts" line 13)
>>>>> invoked from within
>>>>> "update_patchtexts"
>>>>> (procedure "::autopsf::addpatch" line 17)
>>>>> invoked from within
>>>>> "::autopsf::addpatch"
>>>>> invoked from within
>>>>> ".patchadder.buttons.addpatch invoke"
>>>>> ("uplevel" body line 1)
>>>>> invoked from within
>>>>> "uplevel #0 [list $w invoke]"
>>>>> (procedure "tk::ButtonUp" line 22)
>>>>> invoked from within
>>>>> "tk::ButtonUp .patchadder.buttons.addpatch"
>>>>> (command bound to event)
>>>>>
>>>>> Unable to find a specific precedent on the web; grateful for help.
>>>>>
>>>>> thanks
>>>>> francesco pietra
>>>>
>>>> --
>>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>>> Beckman Institute for Advanced Science and Technology
>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>>>
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>