From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Thu Apr 11 2013 - 12:24:41 CDT

I have 2x8 Gigs macbook pro. I can align to the first PDB. Thanks for your
help.

-Yarrow

> Yes the commandline would work just fine for loading the reduced set of
> coordinates. How much memory do you have on this system?
>
> regardless, of memory size, you can use catdcd to cut the dcd in as many
> pieces as you want.
> You would use separate catdcd commands to read in the first half of the
> full dcd file and then the second half.
>
> The alignment would require one extra step and that is you would need a
> pdb file of the very first structure to align the 2nd, 3rd, ... DCD files
> to.
>
>
> brian
>
>
> ________________________________________
> From: Yarrow Madrona [amadrona_at_uci.edu]
> Sent: Thursday, April 11, 2013 6:33 AM
> To: Bennion, Brian
> Cc: Yarrow Madrona; vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: how to convert dcd AND ALIGN molecules then to pdbs in
> command line
>
> Thanks Brian,
>
> When you say, "load smaller psf and dcd files into vmd" you mean in the
> command line right? After I used catdcd and removed the waters the DCD
> file was still to large (about 5 GIGS) to load into the GUI. I guess then
> you would put everything into one script and run in from the command line?
>
> -Yarrow
>
>> Hello,
>> These are the steps that will get you the quickest results until the
>> caver
>> folks have native DCD import functionality (which they said might come
>> this year).
>>
>> First, use catdcd to remove the water molecules from the original DCD
>> files. You will need to make an index file and new psf file for the
>> reduced number of atoms. Just load the original psf, and one frame from
>> the original DCD file.
>>
>> Second, load the new smaller psf and dcd files into vmd all at once.
>>
>> Third align the molecule with the attached script
>>
>> Fourth, write out individual pdbs from this realigned trajectory that is
>> already loaded into the vmd session.
>>
>>
>> Usage:
>> align 0 0 "name CA"
>> This will align all the frames to the first structure of the first
>> trajectory.
>>
>> No need for the gui interface.
>>
>> proc align { rmolid smolid2 seltext } {
>> set ref [atomselect $rmolid $seltext frame 0]
>> set sel [atomselect $smolid2 $seltext]
>> set all [atomselect $smolid2 all]
>> set n [molinfo $smolid2 get numframes]
>>
>> for { set i 1 } { $i < $n } { incr i } {
>> $sel frame $i
>> $all frame $i
>> $all move [measure fit $sel $ref]
>> }
>> $ref delete
>> $all delete
>> $sel delete
>> return
>> }
>> -----Original Message-----
>> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
>> Of Yarrow Madrona
>> Sent: Wednesday, April 10, 2013 8:41 AM
>> To: Josh Vermaas
>> Cc: Yarrow Madrona; vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: how to convert dcd AND ALIGN molecules then to pdbs
>> in
>> command line
>>
>> Thank you Josh,
>>
>> I have also realized that I really need to align all molecules before
>> converting to PDBs however, I cannot find a command for doing this. I
>> wrote a log file "log align.log" while I aligned the molecules over the
>> trajectory for a smaller dcd file. However when I look in the log file
>> it
>> only says:
>>
>> menu rmsdtt off
>> menu rmsdtt on
>>
>> followed by a buch of rotate commands.
>>
>> There is nothing referencing my selection (resname HEME). Do you know
>> how
>> to do the alignment in a script?
>>
>> I'm sorry for asking so many questinos. I know some python scripting but
>> tcl is new to me.
>>
>> -Yarrow
>>
>>
>>> I was writing by memory and didn't actually test the code first
>>> (whoops). The reason my implementation only writes one frame is
>>> because I goofed the syntax for the animate delete call, and it dies
>>> after writing the first pdb. The script should read:
>>>
>>> mol new test.psf
>>> set nowater [atomselect top "not water"] for {set i 0} {$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
>>
>>
>>
>>
>
>
> --
> 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