I just tried your suggestion, and it seems to work satisfactorily.
Great. Many thanks.
best,
reyhan
From: Paul Emsley
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 21 October 2011, 18:10
Subject: Re: [ccp4bb] Sketcher problem
On 21/10/11 05:31, Debreczeni
On 21/10/11 05:31, Debreczeni, Judit wrote:
IIUC, you would like to keep the distance between the ring plane and
the Ru fixed and allow the ring to rotate freely.
I would define bond length restraints between each of the ring atoms
and Ru (I suspect that these distances will be the same for
restraints file by hand, but you might wish to try
JLigand -- the tool of choice for metal containing ligands.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of reyhan
muhammad
Sent: 21 October 2011 02:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Sketcher problem
Greetings
You can change the target torsion angle for the double bond in the .cif file
that is created when your molecule is created.
--Subhangi
On Fri, Apr 22, 2011 at 3:11 PM, Jim Fairman wrote:
> I am attempting to create a monomer with a cis-double bond using Sketcher,
> but every time I tell sketch
I am attempting to create a monomer with a cis-double bond using Sketcher,
but every time I tell sketcher to create the library files it makes the
double bond a trans-double bond. Can anyone assist me with information on
how to force it to remain cis?
--
Jim Fairman, Ph D.
Post-Doctoral Fellow
N
Dear All
can people confirm that the failing cif files only have one monomer description
in them. I have one example, but that contains two monomer descriptions.
Remove one of the and coot successfully reads the file.
Charles Ballard
CCP4
On 9 Jun 2010, at 14:34, Yahui Yan wrote:
> Hello Ga
Hello Garib,
I just tried JLigand. It's amazing. I opened the pdb file which was made by
sketcher and save lib file and coordinate file. Then load these files to
coot. Everything works fine now. I think I need to double check the ligand
as you advised.
Thanks a lot to you all.
Regards,
Yahui
Perhaps you could try to use JLigand. It may do a better job. it is
available from:
www.ysbl.york.ac.uk/mxstat/
In the jligand session there are two tutorials also. they may help you
to run and generate your ligand description.
If any problem please let me know.
In general refmac is not th
Hi Yahui!
I am having this problem as well again and agin. Most problematic is it,
if you have non-standard atoms in your compound.
I don't really know whrere the problem lies, but here is what I do:
Do not use sketcher!
Simply generate your ligand using coot by placing atoms into the density
Can you send your fragment of the pdb containing the ligand, and the cif
file?
Eleanor
Yahui Yan wrote:
Hello,
Could you please help me with the sketcher?
I'm trying to use ccp4 sketcher to generate a new ligand and then complex it
with a protein in coot. I've drawn the ligand, numbered each
Hello,
Could you please help me with the sketcher?
I'm trying to use ccp4 sketcher to generate a new ligand and then complex it
with a protein in coot. I've drawn the ligand, numbered each atom and
defined each bond type. Then I ran save file, create library description.
The pdb file was loaded
Dear CCP4s,
Apologize if this was answered before.
We are using the latest version of CCP4 and have a problem running
sketcher. When creating the library description from a displayed
structure we are getting an error when using the option regularise the
structure with Refmac. The program cre
Hi Jon,
Recently, I had the same problem:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11138.html
I suspect that Sketcher will always give you the trans isomer. Therefore,
you have to edit the torsion angle in _mon_lib.cif manually as indicated
by Liz Potterton in the previous post. T
Hi,
I'm using Sketcher to create the following:
C=C C=C
/ \ / \
C CC
The problem is that I can't figure out how to keep the carbons cis. I see
the "Add Row" button in Sketcher and I can specify the "Sign." There are
also spaces to fill in "B/3" F/4" "1/5
CCP4bbers,
I am trying to do a restrained refinement in refmac using a rhenium
tricarbonyl (RTC) fragment similar to the one in PDB 1I53. My
understanding of how to proceed is to take the PDB description of the
file, read it into sketcher, and then run libcheck to create the
various cif and li
Hi experts,
whenever create a ligand description with the sketcher that contains a
saturated ring with nitrogens (piperidine, piperazine, etc) it flattens the
nitrogens a la sp2 and consequently does weird things to the ring puckering.
One can artificially protonate the nitrogen to get a sp3 geomet
Whatever you do it is good practice to do your first run of refinement as
Review Restraints"
Under the Monitoring folder set the level to many (default medium)
and set the sigma cut off for chirals to 3.00 say to get a god list
Then run the job and you will get a list of violations of restraints
Chiralities in refmac dictionaries are local just like in smile
strings. You can of course put atoms by their priorities then
you will have correspondence to R/S assignments. However you do not
have to do it.
In many case I find it useful to put chirality 'both' and then refine
against this d
thanks for the link. I had already seen it and was using it to assign my
chirality. I guess I should clarify my question. In sketcher, does one
input the highest priority neighbor first, then the second, and finally the
third? The sketcher GUI has three columns list: B/3, F/4, & 1/5. Do these
Garib has documentation on his website that I presume matches what is
required by sketcher. It can be found at
http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html
(I did a Google of "ccp4 chiral" to find it.)
Dale Tronrud
Vu Thai wrote:
Hi All,
I was wondering how to prop
Hi All,
I was wondering how to properly define the stereochemistry for a new ligand
in sketcher. In the sketcher interface there are three columns after the
stereochem sign option. I would assume that the order in which you enter
the chiral neighbors would effect the sign that you choose for you
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