[ccp4bb] Methods to calculate the importance of mutated residue on the stability of protein
Dear all, Do anyone know the way to estimate the importance of mutation contributing to the stability of protein? Thanks for the help. Heng-Keat
[ccp4bb] Couldn't access the log graph in Aimless
Dear all,
I have a problem with opening the log graph in the log file in Aimless with
CCP4 suite 6.3.0 (perhaps all the log graphs in all the software). Is anybody
know why?
Then I try to access the log graph with terminal by typing:
loggraph name_aimless.log
and the error message pop up:
Error in startup script: couldn't load file
"/home/mauricetam/Documents/Software/ccp4/tcltkplusplus/lib/libBLT24.so":
/home/mauricetam/Documents/Software/ccp4/tcltkplusplus/lib/libBLT24.so: wrong
ELF class: ELFCLASS32
while executing
"load $library BLT"
(procedure "LoadBLT" line 30)
invoked from within
"LoadBLT 2.4 /home/mauricetam/Documents/Software/ccp4/tcltkplusplus/lib/blt2.4"
("package ifneeded" script)
invoked from within
"package require BLT"
(file
"/home/mauricetam/Documents/Software/ccp4/ccp4-6.3.0/share/ccp4i/bin/loggraph.tcl"
line 47)
invoked from within
"source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
(file
"/home/mauricetam/Documents/Software/ccp4/ccp4-6.3.0/share/ccp4i/bin/loggraph"
line 5)
Regards
Heng-Keat
[ccp4bb] Problem with Crank2 via ccp4i2
Hi everyone,
I have a problem with Crank2 via ccp4i2. The program went through SHELXC/D but
it failed in Bp3 with error message as shown below. May I know what is the
problem?
Thanks for the help.
Best regards
HK
-ERROR- CTaskCrank2:0 Error in wrapper crank2 0.02::
The input objects for target MAD of Bp3 could not be retrieved
Traceback (most recent call last):
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/script/crank2_script.py",
line 439, in process
crank2 = ccp4i2crank.CallCrankFromCCP4i2(self, inpfile=inpfile,
defaults=defaults, rvapi_style=rvapi_style)
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
line 28, in CallCrankFromCCP4i2
crank = parser.ParseAndRun(ccp4i2crank,defaults,rvapi_style=rvapi_style)
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/parse.py",
line 56, in ParseAndRun
crank_prep.Run()
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/process.py",
line 939, in Run
self.RunBody(*args,**kwargs)
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/manager.py",
line 140, in RunBody
self.RunSubProcess(p_run,ip)
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/manager.py",
line 716, in RunSubProcess
ccp4i2crank.RegisterOutputToCCP4i2(p_run,error,nosuccess)
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/manager.py",
line 705, in RunSubProcess
p_run.Run(from_ccp4i2=self.run.ccp4i2)
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/process.py",
line 939, in Run
self.RunBody(*args,**kwargs)
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/processes/phas.py",
line 80, in RunBody
self.GetProg().Run()
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/program.py",
line 366, in Run
self.MergeMTZ( *self.CatchMTZObjects() )
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/program.py",
line 349, in CatchMTZObjects
self.TreatInput()
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/programs/bp3.py",
line 27, in TreatInput
common.Error('The input objects for target {0} of {1} could not be
retrieved'.format(exper,self.name))
File
"/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i2/pipelines/crank2/crank2/common.py",
line 34, in Error
raise CrankError(message)
CrankError: The input objects for target MAD of Bp3 could not be retrieved
Re: [ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand
Hi Nestor, I think the reason for Arg side chain to curl up is because I refined ligand and Arg side chain with occupancy refinement, and the Arg moved away from the density, most likely due to 'repulsion' from ligand. The other question is: Is it possible that the H-bonds stay very close? As I tried to 'real space refine' in coot, and the Arg side chain flipped away from the density. Thanks for the suggestion. Best HK Quoting Nestor Concha : Hi Tam, The density looks very strong and therefore I'm going to guess that the Arg guanidimium stays in contact/interacts with the ligand and with the phosphate/sulfate next to it. Perhaps it is one of those close interactions with shorter H-bonds that usual given the arrangement of ligand-phosphate/sulfate-Arg. I'd try to find a rotamer for the Arg that leaves the interactions intact rather than refine occupancies. Seems that the Arg side chain is curled up Nestor -Original Message- From: CCP4 bulletin board On Behalf Of Heng-Keat Tam Sent: Tuesday, November 5, 2019 10:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand EXTERNAL Dear Rob, I would like to model the alternative position for the side chain of R120 but I don't really know whether the alternative conformation exist as shown in the attached figure - density without the ligand and R120 overlaid with the refined structures of modeled ligand and R120. The ligand was modeled in two different conformations. From the density, it seems to me that the density is connected or overlapped. It should not be a post-translation modification as it is well-known that there is no post-translation modification for this protein. Furthermore, the crystal was obtained by co-crystallization of protein with the ligand itself. The density seems to be the expected ligand. Thanks for the advice. Best regards HK Quoting Robert Nicholls : Dear HK, No that's not quite correct - 'occupancy group alts complete' means that both R120 and the ligand are constrained so that their occupancies sum to unity. In contrast, 'occupancy group alts incomplete' means that the occupancies of R120 and the ligand will not be constrained to sum to unity (but the sum of their occupancies must be less than one). In both cases, R120 and the ligand will "see" each other in a certain sense. But, because they are assigned to different groups, it is assumed that they are present in different parts of the crystal. This means that they can overlap. Assuming that the ligand is in the correct conformation, I suspect the source of your problem is that you are modelling the side chain of R120 as only one conformation. And I would also include the other atoms in the side chain - CB and CG. If you are modelling the sidechain of R120 with partial occupancies, then you should model those side chain atoms in two alternative positions (i.e. representing the portions of the crystal that do/don't have the ligand bound). This will help to ensure that your model makes physical sense. So the ligand plus the alt of R120 in the portion of the crystal that contains the ligand would be assigned to one occupancy group, and the alt of R120 in the portion of the crystal that does not contain the ligand would be assigned to the second group. In this case it would be appropriate to specify 'occupancy group alts complete', because the occupancies for the two alternative conformers of R120 should sum to unity. Although no doubt the estimation of the occupancies would be dominated by the ligand in this case. Be sure to check your B-factors after occupancy refinement to make sure the whole picture makes sense. Assuming your current model is essentially correct, from visual inspection it looks like R120 will have low occupancy and low B-factors when the ligand is not present (or at least B-factors consistent with the environment), but will have high occupancy and high B-factors when the ligand is present. On another note, have you considered whether that part of the ligand could be modelled in a slightly different conformation, or whether there could be a post-translation modification? I hope that helps, Rob Dr Rob Nicholls Senior Investigator Scientist MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH On 5 Nov 2019, at 13:36, HK wrote: Dear all, I have problem with occupancy refinement by Refmac5 for an overlapping electron density of part of residue (an arginine) and part of ligand (tetracyclic compound) (attached figures in Dropbox with a link as shown below). https://www.dropbox.com/sh/ppmfp5dnpy1b9e9/AAAV79bOzPHQUrVYp9loMwyha? dl=0 I refined part of the side chain of residue 120 and ligand (chain J residue 1105) with Refmac keyword as shown below. Unfortunately, the side chain of
