Hi Yikan,
I'm attaching a script (energyPlot.py) to plot the value of the different
energy terms throughout a run, as reported in the log file. For example, to
plot the value of the "impr" term vs. the print count (which counts the times
the energy has been printed in the log file), type the following in the command
line:
energyPlot.py IMPR < log.out &
(where log.out is the specified log file). If you omit the energy term above,
all are printed.
I hope this helps.
Guillermo
________________________________
From: ZhangYikan <[email protected]>
Sent: Monday, December 11, 2017 6:25 PM
To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling
hello Guillermo,
Thank you for your scripts, I have tried it. I found that there are still some
wrong topology structures and clahes(some overlaps):1) I will try to fix the
repel parameter and rerun the script;
2) in the outputs of the previous zp_0-3.py, I found the terms of “impr” seems
unusual(in the .viols), did you have some tools to analysis this energy term ?
Thank you!
Best,
Yikan
Ph. D candidate
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
在 2017年12月12日，上午2:00，Bermejo, Guillermo (NIH/CIT) [E]
<[email protected]<mailto:[email protected]>> 写道：
Hi Yikan,
I notice that your script seems to be more complicated than it has to be. I'm
not sure this will solve your problem, but I'm attaching a simpler script based
on eginput/rna/fold.py. It's basically the script used to fold an RNA
molecule from an extended conformation (described in the paper I mentioned
before). I modified it so that you load your input pdb structure and define
the different rigid bodies (look for the lines with an inline comment "#
COMPLETE !", where you must enter the right information). Then, it does
torsion angle dynamics using the remaining torsional degrees of freedom (i.e.,
at the linker(s)).
I commented all the experimental restraints. If you want to have the radius of
gyration term (which appears in your script), you can introduce it yourself.
Also, you might want to use it as a starting point for more complicated stuff,
like "breaking" the linkers and randomizing the position of the domains.
A suggestion to try to avoid (and detect) knotted structures is to increase the
atomic radii (see the 'repel' argument in initRepel).
Best,
Guillermo
________________________________
From: ZhangYikan <[email protected]<mailto:[email protected]>>
Sent: Monday, December 11, 2017 10:43 AM
To: Bermejo, Guillermo (NIH/CIT) [E];
[email protected]<mailto:[email protected]>
Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling
hello Guillermo,
I want these domains move (as rigid body)randomly and freely to sample all
possible conformations of the RNA.
Yikan
Ph. D candidate
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
在 2017年12月11日，下午11:27，Bermejo, Guillermo (NIH/CIT) [E]
<[email protected]<mailto:[email protected]>> 写道：
Hi Yikan,
Can you tell me what you are trying to do?
Best,
Guillermo
________________________________
From: ZhangYikan <[email protected]<mailto:[email protected]>>
Sent: Friday, December 8, 2017 6:56 PM
To: Bermejo, Guillermo (NIH/CIT) [E];
[email protected]<mailto:[email protected]>
Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling
hi Guillermo,
yes, i have received your last mails. And the attachment is my scripts.
Yikan
Ph. D candidate
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
在 2017年12月9日，上午12:43，Bermejo, Guillermo (NIH/CIT) [E]
<[email protected]<mailto:[email protected]>> 写道：
Hi Yikan,
I realized that my original response was only sent to you and not included in
the mailing list. Here it is.
One possibility is that there's something wrong with your script(s).
I recommend basing your calculations on the scripts found in eginput/rna
directory (within your Xplor-NIH directory). There you'll find:
* fold.py, for initial calculations starting from an extended conformation.
* refine.py, for subsequent refinement.
In addition, you'll find all the restraints for an example system, in case you
want to play with the scripts before venturing into your data. The scripts are
highly commented, which should help in customizing them for your needs.
There's also a paper describing them [Bermejo et al., 2016, Structure 24,
806-815].
Best,
Guillermo
________________________________
From:
[email protected]<mailto:[email protected]>
<[email protected]<mailto:[email protected]>>
on behalf of ZhangYikan <[email protected]<mailto:[email protected]>>
Sent: Friday, December 8, 2017 6:53 AM
To: [email protected]<mailto:[email protected]>
Subject: [Xplor-nih] Wrong topology structures in conformational sampling
hello all,
Recently, I am doing conformational sampling with Xplor-NIH. And I got many
pdbs, but when I check them I found that some pdbs have wrong topology
structures like the attachments(in the pink cycle ): The RNA linker did not run
with the right way and It went through the helix. I have tried to pick the
structures by the “total energy” or “repel” terms, but it make no sense. Are
there someone know how to kick out these wrong structures or to void these
errors in the sampling process? Thank you!
Yikan
Ph. D candidate
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
<fold.py>
#!/usr/bin/env pyXplor
(opts,args) = xplor.parseArguments(('noLegend:0',
'points:0',
'vsTime:0',
'printOut:0',
'reset:1')
)
plotLegend=True
plotVs='cnt'
style="-"
noMinimize=False
infilename=None
reset=None
printOut=False
for opt in opts:
if opt[0]=='noLegend':
plotLegend=False
pass
elif opt[0]=='vsTime':
plotVs='time'
noMinimize=True
pass
elif opt[0]=='points':
style='*'
pass
elif opt[0]=='reset':
reset=opt[1]
pass
elif opt[0]=='printOut':
printOut=True
pass
elif opt[0]=='help-script':
print usage
sys.exit(0)
pass
pass
included=args
if len(included)==1:
plotLegend=False
pass
if infilename==None:
from sys import stdin
else:
stdin = file(infilename)
pass
cnt=0
energyMode=False
from parseTools import readFloat
vals={}
names=set()
names.add('delta_t')
startTime=0
for line in stdin.readlines():
if line.startswith("*--- Dynamics") or line.startswith(" -- PC6 "):
if not vals.has_key(cnt): vals[cnt]={}
buf=str(line)
while "---" in buf:
buf=buf.replace("---","--")
pass
fields=buf.split("--")
step=int(fields[2].split('=')[1])
time,dummy=readFloat(fields[3].split('=')[1])
delta_t,dummy=readFloat(fields[4].split('=')[1])
vals[cnt]['step'] = step
try:
if step==0 and cnt>0:
startTime = vals[cnt-1]['time'] + vals[cnt-1]['delta_t']
pass
vals[cnt]['time'] = time+startTime
vals[cnt]['delta_t'] = delta_t
energyMode=True
except KeyError:
pass
pass
elif not noMinimize and (line.startswith("*-- POWELL") or
line.startswith(" --------------- cycle=") ):
if not vals.has_key(cnt): vals[cnt]={}
buf=str(line)
while "---" in buf:
buf=buf.replace("---","--")
pass
fields=buf.split("--")
step=int(fields[2].split('=')[1])
energyMode=True
pass
if reset and reset in line:
cnt=0
pass
if (line.startswith("*--------------") or
line.startswith(" ------------------------------")):
cnt += 1
energyMode=False
pass
if energyMode and (line.startswith("|") or
line.startswith(" |") ):
buf=str(line[1:][:-1]).strip()
if buf.startswith('|'): buf = buf[1:]
while buf:
pos=buf.find("=")
if pos<0:
break
name=buf[:pos].strip()
val,buf=readFloat(buf[pos+1:])
names.add(name)
vals[cnt][name] = val
pass
pass
pass
indices=sorted(vals.keys())
#for name in names:
# for index in indices:
# print index,name,vals[cnt][name]
# pass
# pass
excluded=['temperature','E(kin)+E(poten)','E(kin)','E(poten)','grad']
import pylab
import matplotlib
fig=pylab.figure()
ax = fig.add_axes((0.1,0.1,0.86,0.85))
legendLabels=[]
curves=[]
for name in names:
if included:
if not name in included:
continue
pass
elif name in excluded:
continue
y=[]
x=[]
for index in indices:
if name in vals[index].keys():
y.append(vals[index][name])
x.append(index)
if printOut:
print name, x[-1], y[-1]
pass
pass
if plotVs=='time':
x=[vals[index]['time'] for index in x]
pass
legendLabels.append(name)
curves.append( ax.plot(x,y,style,label=name) )
pass
if plotLegend:
ax.legend(legendLabels)
pass
if not printOut:
pylab.show()
pass
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