Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed
Dear CCP4 Users, Thank you very much for all suggestions. Special thanks to Oliver for the ready-to-use files. Great job :) Hopefully it will solve my problems... Best wishes, 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 | |--| To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed
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 PCRoutineLine Source cprodrg.exe7FF623CB058F Unknown Unknown Unknown cprodrg.exe7FF623CB05E0 Unknown Unknown Unknown cprodrg.exe7FF623CAFB4F Unknown Unknown Unknown cprodrg.exe7FF623CB008E Unknown Unknown Unknown cprodrg.exe7FF623C5BDA8 Unknown Unknown Unknown cprodrg.exe7FF623C3204E Unknown Unknown Unknown cprodrg.exe7FF623CAA81E Unknown Unknown Unknown cprodrg.exe7FF623CB3144 Unknown Unknown Unknown KERNEL32.DLL 7FFEB3447034 Unknown Unknown Unknown ntdll.dll 7FFEB4A22651 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 a
[ccp4bb] Help with preparation of the ligand coordinates/restraints needed
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? Best regards, Rafal Dolot -- |--| |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 | |--| To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Problems with refinement of nucleic acid structure
Dear all, Thank you for the response. I will try to explain it more precisely. The molecule of interest is a duplex with 9 nt length, but is paired on the length of eight bases, with overhangs at ends. Molecules form a parallel strings across the crystal lattice, parallel to C-axis, because of these stacked overhangs. The structure was solved by MR using Molrep. Trials using Phaser were failed. The initial model was obtained by ZN-SAD. Refinement was dome for space group P43212, with cell parameters 31.96 31.96 95.07 90 90 90, with one duplex molecule per AU. Schreuder, Herman /DE wrote: At this resolution, one sees many amino-acid side chains with alternative conformation, so it might be a good idea to test if this is also true for nucleotides. Dear Herman, I'm working on some protein ultra-high resolution structures (around 1.0 A or higher), and alternative conformations are nicely visible on electron density maps. In this case, there is visible almost all molecule, when you switch contouring to 2 sigma or lower on Fo-Fc maps, so I think, in this case it's not the same situation. Matthew Snee wrote: Maybe test the spacegroup with Zanuda, and reprocess with the most likely lower symmetry group. I guess the stats should improve if you identify a pseudo symmetry operator that is currently being treated as a true symmetry operator? Eleanor Dodson wrote: Sometimes ghost like this mean there is a spacegroup error - absences can be the result of the non-crystallographic translation and not be truly indicitive of the spacegroup. What is the possible spacegroup and what is the NC translation vector? Dear Matthew and Eleanor, I run Zanuda on my datasets, and the output (which is below) suggested, that spacegroup is right chosen. Step 1. R-factors for the starting model. Transformation into a supergroup. - | Subgroup | Spacegroup | R.m.s.d. | Refinement in tested group | | || from the || | Ref|| starting | Rigid | Restrained | | || model, A |--|-| | || |R |R | R-free | |--||--|--|--|--| | >> 10 | P 43 21 2 | 0.0002 |--| 0.5107 | 0.4871 | | 10 | P 43 21 2 | 0.0002 |--|--|--| ^ Step 2. Refinements in subgroups. There are 8 subgroups to test. ^ | >> 10 | P 43 21 2 | 0.0002 |--| 0.5107 | 0.4871 | - | 1 | P 1| 0.0883 | 0.5252 | 0.4985 | 0.4883 | | 2 | C 1 2 1| 0.0828 | 0.5447 | 0.5006 | 0.4877 | | 3 | P 1 21 1 | 0.0824 | 0.5367 | 0.5018 | 0.4921 | | 4 | P 1 21 1 | 0.0789 | 0.5292 | 0.4971 | 0.4846 | | 6 | P 21 21 21 | 0.0956 | 0.5380 | 0.5064 | 0.4929 | | 7 | P 43 | 0.0935 | 0.5183 | 0.4952 | 0.4835 | | 9 | C 2 2 21 | 0.0908 | 0.5435 | 0.5042 | 0.4910 | | 10 | P 43 21 2 | 0.0855 | 0.5427 | 0.5097 | 0.4913 | - | << 7 | P 43 | 0.0935 | 0.5183 | 0.4952 | 0.4835 | ^ Step 3. Refinement of the best model. Candidate symmetry elements are added one by one. ^ | >> 7 | P 43 | 0.0935 | 0.5183 | 0.4952 | 0.4835 | - | 1 | P 1| 0.0927 | 0.5293 | 0.4991 | 0.4950 | | 8 | C 1 2 1| 0.0848 |--| 0.5017 | 0.4906 | | 9 | C 2 2 21 | 0.0871 |--| 0.5059 | 0.4928 | | 10 | P 43 21 2 | 0.0919 |--| 0.5180 | 0.5109 | - | << 10 | P 43 21 2 | 0.0919 |--| 0.5180 | 0.5109 | - R-factor in the original subgroup is (almost) the best. The original spacegroup assignment seems to be correct. According the non-crystallography translation vector, there is an output from xtriage: - | XYZ | height | p-value(height) | - | 0.000, 0.000, 0.334 | 53.049 | 4.456e-05 | | 0.000, 0.000, 0.167 | 28.966
Re: [ccp4bb] According correct space group assignment...
Dear all,
Thank you for your response.
I think, Phoebe is right. I should add some more information, maybe it
will be useful:
- the molecule of interest is a single DNA strand 11mer with sequence
5'-GGTGTGG-3', what theoretically can formed G-tetraplex, but this
kind of structure can be formed by one, two, or four molecules,
- crystals was obtained after long time (almost three years, now I will
try to reduce this time) from conditions contained CaCl2, PEG400, with
addition of spermine. Crystals are long, thin needles. I collected two
useful datasets:
1) 200 x 0.5 deg, above 1.00A, processed in I222/I212121 with cell
dim. (20.64, 22.95, 43.36, 90, 90, 90)
2) 720 x 0.5 deg, 1.10A, but only first 640 img are useful, the rest
are blank.
I tried reprocess data to other proposed lower symmetry SG: C2 and P1,
but I observed that Rmeas goes strongly up, with cut-off of useful
resolution and completeness,
- there is no evidence of twinning, but tNCS is present. Output from
phenix.xtriage is below:
Frac. coord. :0.0000.5000.000
Distance to origin: 11.475
Height relative to origin : 52.460 %
p_value(height) :4.848e-05
- I tried shelxt on this I222 dataset - obtained SG is Ibca as output
- I back to images. I tried to index it again under iMOSFLM. Of course,
the most probably solutions are identical with those from XDS, but
predictions don't cover all spots on images. In addition I observed two
or three spots in the line on some images, with short distances between
them, so for me it can suggests much longer cell dimension in one
direction. Maybe there is an explanation. But when I tried add some
spots manually, usually iMOSFLM couldn't estimate cell parameters...
Best regards,
Rafal
---
|--|
|Rafal Dolot, Ph.D.|
| |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Department of Bioorganic Chemistry|
|Macromolecular Crystallography Team |
|Sienkiewicza 112 |
|90-363 Lodz, Poland |
|Phone: +48(42)6803215 |
|Cell: +48 502897781 |
|--|
W dniu 2018-04-21 23:02, Phoebe A. Rice napisał(a):
Sadly Rafal is right the unit cell dimensions don't make sense -
either the space group is wrong or the contents have been digested
before crystallization.
The size of the overall unit cell is ~21 x 23 x 43. Given a
(DNA-centric but close enough) view that a duplex is ~25A wide and
there are 3.4A per bp (and 43A/3.4 gives 12bp) , if this 11mer was a
simple symmetric duplex, there could only be 2 chains, max, but I222
has 8 asymmetric units.
This handy tool gives the same answer in a more accurate manner:
http://csb.wfu.edu/tools/vmcalc/vm.html
It says that if the RNA is intact and the space group is P2, there is
about 56% solvent. If the space group is really I222, the solvent
content would be a rather fascinating negative 75%.
-Phoebe
On 4/20/18, 2:37 PM, "CCP4 bulletin board on behalf of Randy Read"
<CCP4BB@JISCMAIL.AC.UK on behalf of rj...@cam.ac.uk> wrote:
I think that starting with a direct methods program like shelxt
would be fun. If that doesn’t work, it could be interesting to try to
solve it by molecular replacement with fragments varying from a
tetraplex, a base pair or even just single bases. (Assuming that
Phoebe’s concern about twinning does not turn out to be correct…)
Best wishes,
Randy Read
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223
336827
Hills Road
E-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
> On 20 Apr 2018, at 20:09, Tim Gruene <tim.gru...@psi.ch> wrote:
>
> Dear Rafal,
>
> shelxt does not require the space group, it only needs the Laue
group. If it
> finds a decent solution, it'll find also the space group for you.
>
> Best,
> Tim
>
> On Friday, April 20, 2018 3:30:36 PM CEST Rafal Dolot wrote:
>> Dear CCP4BB,
>>
>> I've recently collected data for 11mer build of DNA (9xG, 2xT).
XDS, and
>> DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with
cell
>> dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for
this
>> size of the molecule. 11mer is rich in G, so we expect the
G-tetraplex
>> formation. Data were collected to almost 1 A, so it should be
enough for
>> trials with direct methods/ab initio solution. What I should do
f
[ccp4bb] According correct space group assignment...
Dear CCP4BB, I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this size of the molecule. 11mer is rich in G, so we expect the G-tetraplex formation. Data were collected to almost 1 A, so it should be enough for trials with direct methods/ab initio solution. What I should do first to find correct SG and/or cell parameters? Best regards, Rafal -- |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Macromolecular Crystallography Team | |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803215 | |Cell: +48 502897781 | |--|
[ccp4bb] Another problem after last CCP4 update...
Dear CCP4 users, I observed problems with "Real space refine zone" in Coot after CCP4 package last update, which revealed a complete disaster in phosphate groups of nucleotides... Windows 8.1 system Best regards, Rafal -- |------| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Macromolecular Crystallography Team | |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803215 | |Cell: +48 502897781 | |--|
[ccp4bb] Dyes for DNA crystals
Dear All, Sorry for non-CCP4 question. I'm looking for some dyes, like Hampton IZIT, suitable for DNA crystals and, of course safe for crystals. Is IZIT useful for that application? As I read, it is recommended for macromolecular crystals. What about Jena Bioscences dyes? Thank you for some advices, Rafal Dolot |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803215 | |Cell: +48 502897781 | |--|
[ccp4bb] Problem with aimless/ctruncate
Dear CCP4 users, After last update of CCP4 package for Windows (I work on Win8.1) I found some error during use of aimless with ctruncate. The output from log looks like this: *** * Information from CCP4Interface script *** The program run with command: ctruncate -hklin C:/ccp4temp/hint1_ew432_03_2_3_mtz.tmp -hklout C:/ccp4temp/hint1_ew432_03_2_5_mtz_XDSdataset.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout XDSdataset has failed with error message child killed: segmentation violation *** When I use old truncate, it works fine. Best regards Rafal |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803215 | |Cell: +48 502897781 | |--|
[ccp4bb] Diffraction image viewer with display of resolution circles
Dear CCP4 users, I'm looking for the diffraction image viewer, which will be able to display of resolution circles and export it to new image. I tried use idiffdisp, but after choose of the Show/clear resolution circles, there is no action. Images were collected using Rayonics MX-225 detector - maybe detector format is a problem? Best regards, Rafal |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803215 | |Cell: +48 502897781 | |--|
[ccp4bb] Question about stereo on LCD monitor
Dear CCP4BB users, Sorry, for non-CCP4 question. I'm looking for any freeware program for molecule model building, especially for perfect matching RNA duplex. Could you help me? I found some programs with options of de novo protein chain building, but without options of DNA/RNA chain building. With best wishes Rafal |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803215 | |Cell: +48 502897781 | |--|
[ccp4bb] Software for RNA model building
Sorry, for mistake in the title of my last post. Please ingnore it. Dear CCP4BB users, Sorry, for non-CCP4 question. I'm looking for any freeware program for molecule model building, especially for perfect matching RNA duplex. Could you help me? I found some programs with options of de novo protein chain building, but without options of DNA/RNA chain building. With best wishes Rafal |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803215 | |Cell: +48 502897781 | |--|
Re: [ccp4bb] Question about stereo on LCD monitor
Hi Warren, Thank you for your answer. I've checked last news from web and I found information that ViewSonic and Samsung start with production of 120Hz 22 LCD monitors (ViewSonic VX2265wm, Samsung SyncMaster 2233rz and 2243(or hz, depends on the source)). Samsung should be avaiable in april, probably with 3D shutter glasses. According to your info about Zalman monitor - do you know how is realized connection of glasses? Via Stereo 3D from graphic card? I would buy Quadro FX 3700 card with stereo glasses, but now I think I should waiting for new information about these LCD's... With best wishes Rafal |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6819744 | |--| Rafal, Actually, things only really started to change last month... Please see http://pymol.org and scroll down most of the way to the February 13th entry regarding the $600 Zalman ZM-M220W stereo-capable LCD. In my opinion, that is the best option on the market until the powers that be start supporting 120 Hz LCDs with OpenGL drivers -- which could be days or months, but hopefully not years. Once that happens, 120 Hz LCDs will likely become the preferred option. I don't know whether O, Coot, or CCP4 support this monitor yet, but they really should if they do not! (It only takes a couple dozen lines of code beyond standard QBS stereo -- developers please see the code I've posted at http://pymol.org/zalman/howto.html ) Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Rafal Dolot Sent: Friday, March 20, 2009 4:17 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question about stereo on LCD monitor Dear CCP4BB users, After one long year I'm back to crystallography again :) Actually I try to organize a crystallographic lab in new work place. Of course one of important thing what I need is a good computer machine for crystallographic calculations and molecular graphics. And now I need yours advices/opinion... - is it actually possible use a LCD monitor in stereo mode, for example in COOT or O, with shutterglasses? - what kind of graphic card, not so expensive, but with good quality of generated graphic is actually on the top? During my PhD I worked on machine with Quadro FX1300 graphic card with shutterglasses, but with CRT Iiyama monitor. Maybe after 2-3 years something changes in this subject... With best wishes Rafal Rafal Dolot, Ph.D Polish Academy of Sciences Centre of Molecular and Macromolecular Studies Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Lodz, Poland
[ccp4bb] Question about stereo on LCD monitor
Dear CCP4BB users, After one long year I'm back to crystallography again :) Actually I try to organize a crystallographic lab in new work place. Of course one of important thing what I need is a good computer machine for crystallographic calculations and molecular graphics. And now I need yours advices/opinion... - is it actually possible use a LCD monitor in stereo mode, for example in COOT or O, with shutterglasses? - what kind of graphic card, not so expensive, but with good quality of generated graphic is actually on the top? During my PhD I worked on machine with Quadro FX1300 graphic card with shutterglasses, but with CRT Iiyama monitor. Maybe after 2-3 years something changes in this subject... With best wishes Rafal Rafal Dolot, Ph.D Polish Academy of Sciences Centre of Molecular and Macromolecular Studies Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Lodz, Poland
