Re: AW: AW: How to refer to side-chain via tcl-force scripting?

From: zeynab mohamad hoseyni (zmhoseyni_at_yahoo.com)
Date: Mon Jun 16 2014 - 11:20:46 CDT

Hi Norman, In addition to the way to suggested here, which works very well, the tcl force tutorial has provided another way (Example 3: Forcing a Subset of Atoms ,TclForces )  TclForces TclForces View on www.ks.uiuc.edu Preview by Yahoo through which you may introduce a target pdb, marking all the side-chains you are interested in and then opening the pdb, reading the lines and extracting the atoms in each side-chains in order to refer to them in the next steps. I was wondering which way is more efficient, specially in the case that you need to apply force on the side-chains of all residues containing in the protein (397 residues in my case)? I went through the way you suggested here and it works very slowly. I'm looking for a way to improve the efficiency  significantly and I wonder if you can guide me. Thanks in advance, Zeynab   On Friday, June 13, 2014 9:26 AM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote: You need to source the prepare script to VMD. Afterwards source the resulting conf file within TCL forces and work with the “sidechains” array.   Norman Geist.   Von:zeynab mohamad hoseyni [mailto:zmhoseyni_at_yahoo.com] Gesendet: Freitag, 13. Juni 2014 10:21 An: Norman Geist Cc: Namd Mailing List Betreff: Re: AW: namd-l: How to refer to side-chain via tcl-force scripting?   Hi Norman, Looks great! thanks! just one more question: sourcing the tcl through the tcl-force script is different from to write it down directly in the tcl-force script? Because when I write it down directly I receive the error from which I defer that the script can not realize the commands regarding the side chain..   All the Best, Zeynab   On Friday, June 13, 2014 8:56 AM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:   Guess no! A good way to do it, is do write a TCL script for VMD to prepare some kind of config file containing the information you need and source this configuration within your TCLForces script. Like (expects to have a molecule loaded already):   prepare.tcl:   puts “Input) Molid?” gets stdin molid puts “Input) Resids?” gets stdin resids   array unset sidechains; #save restart array set sidechains {} foreach resid $resids {                 set sel [atomselect $molid “resid $resid and sidechain”]                 set sidechains($resid) [$sel get index]                 $sel delete }   set fp [open “prepared.conf.tcl” w] puts $fp [list array set sidechains [array get sidechains]] close $fp puts “Info) Done, you’re are now prepared!”   So within your TclForces script:   source prepared.conf.tcl #loop over sidechains foreach resid [array names sidechains] {                 puts “Now doing something with sidechain of resid $resid having this atoms: $sidechains($resid)” }   Norman Geist.   Von:owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von zeynab mohamad hoseyni Gesendet: Freitag, 13. Juni 2014 07:53 An: namd-l_at_ks.uiuc.edu Betreff: namd-l: How to refer to side-chain via tcl-force scripting?   Dear all,   I need to impose force on the side-chain of some residues, using tcl-force scripting. Do you know if the tcl-force interface provides any command so that you can refer to side-chain of the desired residue?   Thanks in advance for your help, Zeynab   ________________________________ Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.     ________________________________ Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.

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