Re: Harmonic restrains

From: Miro Astore (miro.astore_at_gmail.com)
Date: Sun Nov 10 2019 - 22:07:15 CST

No problem, the learning curve on this stuff is high. What you want to do
is extract the protein you want to fit to. So in vmd run

mol new pdbid.pdb # the file you downloaded from the pdb databank
set sel [atomselect top "atomselection text"] # here you need to figure out
what atoms exactly correspond to your reference protein. It might only be
chain A in which case you would write
#set sel [atomselect top "chain A"]
$sel writepdb reference.pdb

#this will create your reference pdb file.

Let me know if you have more questions.

On Mon., 11 Nov. 2019, 13:43 Zhang Yan, <yanzhang_at_moon.ibp.ac.cn> wrote:

> Hi Miro,
> Many thanks for your help!
> Actually, I don’t know how can I have the reference.pdb? I just have a pdb
> downloaded from PDB data bank, and what I did is flexible fitting this
> downloaded pdb to my cryo-EM density map. So what is the reference.pdb, how
> can I get it? Sorry for this naive question.
> Best
> Yan
>
> 在 2019年11月9日,下午5:08,Miro Astore <miro.astore_at_gmail.com> 写道:
>
> This is a little tricky. What you will need to do is make your system as
> normal. And then move the CA atoms into the shape of the reference
> structure .
>
> This will look something like
>
> mol new ionised.psf
> mol addfile ionised.pdb
>
> set selall [atomselct 0 "all"]
> $selall set beta 0
> set sel1 [atomselect 0 "structure selection make sure its CAs for
> simplicity"]
> $sel1 set beta 1
>
> mol new reference.psf
> mol addfile reference.pdb
>
> set sel2 [atomselect 1 "the corresponding residues you want to align"]
> set M [measure fit $sel2 $sel1]
> $sel2 move $M
> #this will align through rigid body motion the two molecules
> #Then you need to loop over the CAs in the ionised (system you want to
> simulate ) structure and move them each of them to the corresponding CA of
> the reference structure. This syntax may not be exactly right. I've assumed
> the previous selection is CAs only
>
>
> set reslist1 [ $sel1 get residue]
> set reslist2 [$sel2 get residue]
> set listlength [llength $reslist2]
> for {set i 0} {$i < $listlength} {incr i} {
> set curres1 [lindex $reslist1 $I ]
> set curres2 [lindex $reslist2 $i]
> set tempsel1 [atomselect 0 "CA and residue $curres1]
> set tempsel2 [atomselect 1 "CA and residue $curres2]
> set xcoors [$curres2 get x]
>
> set ycoors [$curres2 get y]
> set zcoors [$curres2 get z]
> $curres1 moveto [$xcoors, $ycoors, $zcoors]
> }
> $selall writepdb atoms.pdb #this is your reference positions file
>
> #this will move all CAs onto the reference structure. If you open the file
> it will look weird and scary but so long as you tell colvars to look at the
> beta column the simulation will do what you want. There may be syntax
> errors. Let me know if this doesn't work.
>
> Good luck!
>
>
>
> On Sat., 9 Nov. 2019, 19:22 Zhang Yan, <yanzhang_at_moon.ibp.ac.cn> wrote:
>
>> Hi,
>> How can I run namd with harmonic restraints? I saw from the manual that
>> harmonic restrains needs the PDB file containing constraint reference
>> positions, but how can I get this PDB file with constraint reference
>> positions?
>> Many thanks!
>> Yan
>>
>> 在 2019年11月7日,上午11:24,Zhang Yan <yanzhang_at_moon.ibp.ac.cn> 写道:
>>
>> Hi all,
>> I’m trying to do flexible fitting the crystallography structure to a
>> cryo-electron microscopy density map. I get some errors which I attached in
>> the attachment. I’m not sure which parameter is needed to be changed to
>> avoid these errors. Any suggestions or help are appreciated.
>> Best!
>> 张艳
>> Yan Zhang,
>> Associate Professor,
>> Institute of Biophysics,
>> Chinese Academy of Sciences
>>
>>
>> <屏幕快照 2019-11-07 上午10.10.09.png>
>>
>>
>> 张艳
>> Yan Zhang,
>> Associate Professor,
>> Institute of Biophysics,
>> Chinese Academy of Sciences
>>
>>
>>
>>
>>
> 张艳
> Yan Zhang,
> Associate Professor,
> Institute of Biophysics,
> Chinese Academy of Sciences
>
>
>
>
>
On Mon., 11 Nov. 2019, 13:43 Zhang Yan, <yanzhang_at_moon.ibp.ac.cn> wrote:

> Hi Miro,
> Many thanks for your help!
> Actually, I don’t know how can I have the reference.pdb? I just have a pdb
> downloaded from PDB data bank, and what I did is flexible fitting this
> downloaded pdb to my cryo-EM density map. So what is the reference.pdb, how
> can I get it? Sorry for this naive question.
> Best
> Yan
>
> 在 2019年11月9日,下午5:08,Miro Astore <miro.astore_at_gmail.com> 写道:
>
> This is a little tricky. What you will need to do is make your system as
> normal. And then move the CA atoms into the shape of the reference
> structure .
>
> This will look something like
>
> mol new ionised.psf
> mol addfile ionised.pdb
>
> set selall [atomselct 0 "all"]
> $selall set beta 0
> set sel1 [atomselect 0 "structure selection make sure its CAs for
> simplicity"]
> $sel1 set beta 1
>
> mol new reference.psf
> mol addfile reference.pdb
>
> set sel2 [atomselect 1 "the corresponding residues you want to align"]
> set M [measure fit $sel2 $sel1]
> $sel2 move $M
> #this will align through rigid body motion the two molecules
> #Then you need to loop over the CAs in the ionised (system you want to
> simulate ) structure and move them each of them to the corresponding CA of
> the reference structure. This syntax may not be exactly right. I've assumed
> the previous selection is CAs only
>
>
> set reslist1 [ $sel1 get residue]
> set reslist2 [$sel2 get residue]
> set listlength [llength $reslist2]
> for {set i 0} {$i < $listlength} {incr i} {
> set curres1 [lindex $reslist1 $I ]
> set curres2 [lindex $reslist2 $i]
> set tempsel1 [atomselect 0 "CA and residue $curres1]
> set tempsel2 [atomselect 1 "CA and residue $curres2]
> set xcoors [$curres2 get x]
>
> set ycoors [$curres2 get y]
> set zcoors [$curres2 get z]
> $curres1 moveto [$xcoors, $ycoors, $zcoors]
> }
> $selall writepdb atoms.pdb #this is your reference positions file
>
> #this will move all CAs onto the reference structure. If you open the file
> it will look weird and scary but so long as you tell colvars to look at the
> beta column the simulation will do what you want. There may be syntax
> errors. Let me know if this doesn't work.
>
> Good luck!
>
>
>
> On Sat., 9 Nov. 2019, 19:22 Zhang Yan, <yanzhang_at_moon.ibp.ac.cn> wrote:
>
>> Hi,
>> How can I run namd with harmonic restraints? I saw from the manual that
>> harmonic restrains needs the PDB file containing constraint reference
>> positions, but how can I get this PDB file with constraint reference
>> positions?
>> Many thanks!
>> Yan
>>
>> 在 2019年11月7日,上午11:24,Zhang Yan <yanzhang_at_moon.ibp.ac.cn> 写道:
>>
>> Hi all,
>> I’m trying to do flexible fitting the crystallography structure to a
>> cryo-electron microscopy density map. I get some errors which I attached in
>> the attachment. I’m not sure which parameter is needed to be changed to
>> avoid these errors. Any suggestions or help are appreciated.
>> Best!
>> 张艳
>> Yan Zhang,
>> Associate Professor,
>> Institute of Biophysics,
>> Chinese Academy of Sciences
>>
>>
>> <屏幕快照 2019-11-07 上午10.10.09.png>
>>
>>
>> 张艳
>> Yan Zhang,
>> Associate Professor,
>> Institute of Biophysics,
>> Chinese Academy of Sciences
>>
>>
>>
>>
>>
> 张艳
> Yan Zhang,
> Associate Professor,
> Institute of Biophysics,
> Chinese Academy of Sciences
>
>
>
>
>

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