VMD-L Mailing List

From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Thu Apr 11 2013 - 08:25:43 CDT

Thanks, this is working!

> Yup. Aligning can be done a number of ways, but the easiest to
> understand is the measure fit command, which gives you a 4x4 move matrix
> that when applied will minimize the RMSD between two selections. A
> minimal set of commands to try in the tkconsole to show you how it works
> would be:
>
> mol new 1D1H ; # This is a NMR structure of hanatoxin if people are
> curious
> #Pick an arbitrary reference point
> set ref [atomselect top "resid 34" frame 0]
> set all [atomselect top "all"]
> for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
> $all frame $i
> set sel [atomselect top "resid 34" frame $i]
> set movematrix [measure fit $sel $ref]
> $all move $movematrix
> $sel delete
> }
>
> Note that this aligns the structure to a particular residue (in my case
> 34). From there you can adapt the idea to your own script, taking
> particular care to delete atomselections made inside a loop.
>
> -Josh
>
> On 04/10/2013 10:41 AM, Yarrow Madrona wrote:
>> Thank you Josh,
>>
>> I have also realized that I really need to align all molecules before
>> converting to PDBs however, I cannot find a command for doing this. I
>> wrote a log file "log align.log" while I aligned the molecules over the
>> trajectory for a smaller dcd file. However when I look in the log file
>> it
>> only says:
>>
>> menu rmsdtt off
>> menu rmsdtt on
>>
>> followed by a buch of rotate commands.
>>
>> There is nothing referencing my selection (resname HEME). Do you know
>> how
>> to do the alignment in a script?
>>
>> I'm sorry for asking so many questinos. I know some python scripting but
>> tcl is new to me.
>>
>> -Yarrow
>>
>>
>>> I was writing by memory and didn't actually test the code first
>>> (whoops). The reason my implementation only writes one frame is because
>>> I goofed the syntax for the animate delete call, and it dies after
>>> writing the first pdb. The script should read:
>>>
>>> mol new test.psf
>>> set nowater [atomselect top "not water"]
>>> for {set i 0} {$i < 10} {incr i} {
>>> animate read dcd CIN-SUM-every10.dcd beg $i end $i waitfor all
>>> $nowater writepdb WT_$i.pdb
>>> animate delete *all*
>>> }
>>> exit
>>>
>>> That'll teach me from not looking up syntax first. :(
>>> -Josh
>>>
>>> On 04/09/2013 07:50 PM, Yarrow Madrona wrote:
>>>> Hi Josh,
>>>>
>>>> Thanks for your help. For some reason your script only writes out the
>>>> first pdb and not the rest. This is what I am using:
>>>>
>>>> mol new test.psf
>>>> set nowater [atomselect top "not water"]
>>>> set nf [molinfo top get numframes]
>>>> for {set i 0} {$i < 10} {incr i} {
>>>> animate read dcd CIN-SUM-every10.dcd beg $i end $i waitfor all
>>>> $nowater writepdb WT_$i.pdb
>>>> animate delete
>>>> }
>>>> exit
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> Another option is to run VMD in text mode. Make a simple script
>>>>> (script.tcl) like this:
>>>>>
>>>>> mol new psffile.psf
>>>>> set nowater [atomselect top "not water"]
>>>>> for { set i 0 } { $i < 70000 } { incr i } {
>>>>> animate read dcd dcdfile.dcd beg $i end $i waitfor all
>>>>> $sel writepdb $i.pdb
>>>>> animate delete
>>>>> }
>>>>> exit
>>>>>
>>>>> This will go through each frame one by one and write it to its own
>>>>> pdb,
>>>>> while never keeping more than 1 frame in memory. You can then run it
>>>>> from the command line with something like:
>>>>>
>>>>> vmd -dispdev text -e script.tcl (see
>>>>> http://www.ks.uiuc.edu/Research/vmd/current/ug/node207.html for more
>>>>> on
>>>>> using the command line to start vmd, including the extra step
>>>>> required
>>>>> on windows)
>>>>>
>>>>> -Josh
>>>>>
>>>>> On 04/09/2013 01:12 AM, peter.schmidtke_at_fr.netgrs.com wrote:
>>>>>> Hey,
>>>>>>
>>>>>> Consider using ambertools ptraj for instance, which could do the pdb
>>>>>> export.
>>>>>>
>>>>>> Best regards.
>>>>>>
>>>>>> Peter
>>>>>>
>>>>>> -----Message d'origine-----
>>>>>> De : owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] De la
>>>>>> part
>>>>>> de Yarrow Madrona
>>>>>> Envoyé : mardi 9 avril 2013 01:43
>>>>>> À : VMD mailing list
>>>>>> Objet : Re: vmd-l: how to convert dcd to pdbs in command line
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I am trying to convert a dcd to a series of pdb's without opening
>>>>>> the
>>>>>> VMD GUI. The reason is that I don't have enough ram to store the DCD
>>>>>> (70,000
>>>>>> frames) into memory. VMD always crashes unless I use a truncated
>>>>>> DCD.
>>>>>> I
>>>>>> would like to use all frames since the frames will be analyzed by
>>>>>> another software (Caver3.0). Is there a way to tell vmd to write out
>>>>>> all
>>>>>> PDBs in the command line (preferably without water although I can
>>>>>> remove
>>>>>> those later)?
>>>>>>
>>>>>> Thank you
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Yarrow Madrona
>>>>>>
>>>>>> Graduate Student
>>>>>> Molecular Biology and Biochemistry Dept.
>>>>>> University of California, Irvine
>>>>>> Natural Sciences I, Rm 2403
>>>>>> Irvine, CA 92697
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>
>>
>
> 

-- 
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697