Dear all,
Thank you very much for all your messages. Unfortunately, I'm still on
the same place, as yesterday...
First of all, I prepared a pdb/cif file of the ligand based on CCDC
entry 1176355 containing FESAN molecule. Also, I prepared SMILES file
based on SMILES of CB5 ligand (COSAN) available on PDB, where I simply
switched Co into Fe atom.
-> When I tried use acedrg with SMILES, I received an error info:
Input file: FSM.smi
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
workMode : 12
Can not generate a molecule from the input SMILES string!
Check your SMILES or report the bug
Can not get the element symbols of atoms. Check input file format
Error : The job stops because of errors
-> When I tried use acedrg with *pdb/*cif files I received no output
files:
Input file: fsm.cif
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
workMode : 11
Number of atoms in the cif file 0
-> When I tried use acedrg with *.mol file I received no output files:
Input file: fsm.mol
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
workMode : 13
The system contains atoms of the following elements
C B Fe H
The input ligands/molecules contains metal or other heavier atoms
Acedrg currently deals with ligands/molecules with following elements
only
C, N, O, S, P, B, F, Cl, Br, I, H
The job finishes succesfully
-> When I tried use prodrg, the program has been crashed:
The program run with command: cprodrg XYZIN
"C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"
has failed with error message
forrtl: severe (157): Program Exception - access violation
Image PC Routine Line
Source
cprodrg.exe 00007FF623CB058F Unknown Unknown
Unknown
cprodrg.exe 00007FF623CB05E0 Unknown Unknown
Unknown
cprodrg.exe 00007FF623CAFB4F Unknown Unknown
Unknown
cprodrg.exe 00007FF623CB008E Unknown Unknown
Unknown
cprodrg.exe 00007FF623C5BDA8 Unknown Unknown
Unknown
cprodrg.exe 00007FF623C3204E Unknown Unknown
Unknown
cprodrg.exe 00007FF623CAA81E Unknown Unknown
Unknown
cprodrg.exe 00007FF623CB3144 Unknown Unknown
Unknown
KERNEL32.DLL 00007FFEB3447034 Unknown Unknown
Unknown
ntdll.dll 00007FFEB4A22651 Unknown Unknown
Unknown
***************************************************************************
-> I am still waiting for tokens from the prodrg web page ;) To be sure,
I used two emails, but with no response...
-> Ok, then I back to way I used years ago... JLigand was a good
solution, but... actually it is not working at all. I'm working under
Windows 10 / CCP4i, and I remember, there was the same issue in previous
version of CCP4.
-> Ok, then I back to the oldest solution -> using Sketcher. The program
is reading my PDB/CIF, but gave a warning when preparing a library, and
of course, no output _mon_lib.cif:
WARNING : monomer:FSM - has a minimal description.
WARNING: there is no metal chirality for:Fe1
WARNING: coords are not good enough to create Chirality
WARNING : /subroutine CALC_VOBSN/
I attached the PDB file containing the ligand of interest. From my
knowledge, it looks correct, but maybe I'm wrong. Have you any idea,
where is a problem?
Best,
Rafal
---
|----------------------------------------------|
|Rafal Dolot, Ph.D. |
| |
|Polish Academy of Sciences |
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112 |
|90-363 Lodz, Poland |
|Phone: +48(42)6803325 |
|Cell: +48 502897781 |
|----------------------------------------------|
W dniu 2022-06-06 14:52, Paul Emsley napisał(a):
Although it may not be apparent, there has been a lot of work going on
in Acedrg development regarding Boron.
One cannot say the same for Coot though and I can reproduce the
behaviour reported by Rafa Dolot. If/when I can fix it, it will be
available in 0.9.8.4.
Paul.
On 06/06/2022 13:24, Boaz Shaanan wrote:
Hi,
In case you don't have a cif file for the ligand, I would load the
SMILES expression into acedrg (or use any other input option) to
create a cif file which you can then read into Coot.
Cheers,
Boaz
On Jun 6, 2022 15:06, Rafal Dolot <rdo...@cbmm.lodz.pl> wrote:
Dear CCP4 Users,
I am working with data containing a possible complex of protein with
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge,
this
ligand is not available in PDB. The closest molecule is COSAN
(cobalt
bis(1,2-dicarbollide)), which is labelled as CB5 and is available in
two
PDB entries. I can load this molecule into Coot, but attempts at
ligand
search or refinement of the manually matched molecule result in
freezing
of the Coot window. FESAN is not present in CCDC as a single
molecule,
but only in some complexes. Could you give me some advice on how to
prepare a new ligand like this one, for incorporation into the
protein
and further refinement?
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CRYST1 10.882 9.982 11.836 90.00 113.42 90.00 C 2/m 1
HETATM 19 Fe1 FSM A 1 0.000 0.000 0.000 1.00 20.00 Fe
HETATM 20 C1 FSM A 1 1.824 0.811 0.584 1.00 20.00 C
HETATM 21 B1 FSM A 1 0.527 1.423 1.490 1.00 20.00 B
HETATM 22 B2 FSM A 1 -0.336 0.000 2.129 1.00 20.00 B
HETATM 23 B3 FSM A 1 3.019 0.000 1.521 1.00 20.00 B
HETATM 24 B4 FSM A 1 2.182 1.426 2.141 1.00 20.00 B
HETATM 25 B5 FSM A 1 0.836 0.881 3.152 1.00 20.00 B
HETATM 26 B6 FSM A 1 2.380 0.000 3.164 1.00 20.00 B
HETATM 27 H1 FSM A 1 2.197 1.386 -0.276 1.00 20.00 H
HETATM 28 H2 FSM A 1 0.015 2.379 1.300 1.00 20.00 H
HETATM 29 H3 FSM A 1 -1.408 0.000 2.374 1.00 20.00 H
HETATM 30 H4 FSM A 1 4.097 0.000 1.303 1.00 20.00 H
HETATM 31 H5 FSM A 1 2.722 2.365 2.336 1.00 20.00 H
HETATM 32 H6 FSM A 1 0.500 1.460 4.025 1.00 20.00 H
HETATM 33 H7 FSM A 1 3.045 0.000 4.040 1.00 20.00 H
HETATM 34 C1E FSM A 1 1.824 -0.811 0.584 1.00 20.00 C
HETATM 35 C1A FSM A 1 -1.824 0.811 -0.584 1.00 20.00 C
HETATM 36 C1D FSM A 1 -1.824 -0.811 -0.584 1.00 20.00 C
HETATM 37 B1A FSM A 1 -0.527 1.423 -1.490 1.00 20.00 B
HETATM 38 B1D FSM A 1 -0.527 -1.423 -1.490 1.00 20.00 B
HETATM 39 B1E FSM A 1 0.527 -1.423 1.490 1.00 20.00 B
HETATM 40 B4E FSM A 1 2.182 -1.426 2.141 1.00 20.00 B
HETATM 41 H1E FSM A 1 2.197 -1.386 -0.276 1.00 20.00 H
HETATM 42 B5E FSM A 1 0.836 -0.881 3.152 1.00 20.00 B
HETATM 43 H2E FSM A 1 0.015 -2.379 1.300 1.00 20.00 H
HETATM 44 H6E FSM A 1 0.500 -1.460 4.025 1.00 20.00 H
HETATM 45 H5E FSM A 1 2.722 -2.365 2.336 1.00 20.00 H
HETATM 46 B2A FSM A 1 0.336 -0.000 -2.129 1.00 20.00 B
HETATM 47 B4A FSM A 1 -2.182 1.426 -2.141 1.00 20.00 B
HETATM 48 B3A FSM A 1 -3.019 -0.000 -1.521 1.00 20.00 B
HETATM 49 B4D FSM A 1 -2.182 -1.426 -2.141 1.00 20.00 B
HETATM 50 B5A FSM A 1 -0.836 0.881 -3.152 1.00 20.00 B
HETATM 51 H2A FSM A 1 -0.015 2.379 -1.300 1.00 20.00 H
HETATM 52 B5D FSM A 1 -0.836 -0.881 -3.152 1.00 20.00 B
HETATM 53 H2D FSM A 1 -0.015 -2.379 -1.300 1.00 20.00 H
HETATM 54 H3A FSM A 1 1.408 -0.000 -2.374 1.00 20.00 H
HETATM 55 B6D FSM A 1 -2.380 -0.000 -3.164 1.00 20.00 B
HETATM 56 H4A FSM A 1 -4.097 -0.000 -1.303 1.00 20.00 H
HETATM 57 H5D FSM A 1 -2.722 -2.365 -2.336 1.00 20.00 H
HETATM 58 H5A FSM A 1 -2.722 2.365 -2.336 1.00 20.00 H
HETATM 59 H6A FSM A 1 -0.500 1.460 -4.025 1.00 20.00 H
HETATM 60 H7D FSM A 1 -3.045 -0.000 -4.040 1.00 20.00 H
HETATM 61 H6D FSM A 1 -0.500 -1.460 -4.025 1.00 20.00 H
HETATM 62 H1D FSM A 1 -2.197 -1.386 0.276 1.00 20.00 H
HETATM 63 H1A FSM A 1 -2.197 1.386 0.276 1.00 20.00 H
CONECT 19 20 21 22 34
CONECT 19 35 36 37 38
CONECT 19 39 46
CONECT 20 19 21 23 24
CONECT 20 27 34
CONECT 21 19 20 22 24
CONECT 21 25 28
CONECT 22 19 21 25 29
CONECT 22 39 42
CONECT 23 20 24 26 30
CONECT 23 34 40
CONECT 24 20 21 23 25
CONECT 24 26 31
CONECT 25 21 22 24 26
CONECT 25 32 42
CONECT 26 23 24 25 33
CONECT 26 40 42
CONECT 27 20
CONECT 28 21
CONECT 29 22
CONECT 30 23
CONECT 31 24
CONECT 32 25
CONECT 33 26
CONECT 34 19 20 23 39
CONECT 34 40 41
CONECT 35 19 36 37 47
CONECT 35 48 63
CONECT 36 19 35 38 48
CONECT 36 49 62
CONECT 37 19 35 46 47
CONECT 37 50 51
CONECT 38 19 36 46 49
CONECT 38 52 53
CONECT 39 19 22 34 40
CONECT 39 42 43
CONECT 40 23 26 34 39
CONECT 40 42 45
CONECT 41 34
CONECT 42 22 25 26 39
CONECT 42 40 44
CONECT 43 39
CONECT 44 42
CONECT 45 40
CONECT 46 19 37 38 50
CONECT 46 52 54
CONECT 47 35 37 48 50
CONECT 47 55 58
CONECT 48 35 36 47 49
CONECT 48 55 56
CONECT 49 36 38 48 52
CONECT 49 55 57
CONECT 50 37 46 47 52
CONECT 50 55 59
CONECT 51 37
CONECT 52 38 46 49 50
CONECT 52 55 61
CONECT 53 38
CONECT 54 46
CONECT 55 47 48 49 50
CONECT 55 52 60
CONECT 56 48
CONECT 57 49
CONECT 58 47
CONECT 59 50
CONECT 60 55
CONECT 61 52
CONECT 62 36
CONECT 63 35
END
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