Re: [ccp4bb] Sketcher problem
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 each atom pair) -- the ring will rotate freely if no torsion or angle restraints are defined between the ring and the metal, i.e. no need to define the imaginary axis. (Bond, angle and planar restraints for the ring itself will still have to be defined to keep it in a decent shape, needless to say.) I would personally edit the 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 everyone, This is my first post here. I am trying to build a compound on sketcher. The molecule is ruthenium-centered, with 4 coordination ligands around the ruthenium (picture is attached). Three of the ligands are definite atoms, but the fourth one is a benzene derivative. My problem is I want this benzene ring to be able to spin (at least on coot) around to the 'hypothetical' axis between ruthenium atom and the centre of the benzene ring. While the axis for the other three ligands can be easily defined on the library file, I dont know how to set a description for the benzene ring as there is no real atom in the centre of the benzene that can be used to define the axis. Please advise me on this matter. Thanks a lot Best regards, Reyhan -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [ccp4bb] Sketcher problem
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 each atom pair) -- the ring will rotate freely if no torsion or angle restraints are defined between the ring and the metal, i.e. no need to define the imaginary axis. (Bond, angle and planar restraints for the ring itself will still have to be defined to keep it in a decent shape, needless to say.) I would personally edit the restraints file by hand, but you might wish to try JLigand -- the tool of choice for metal containing ligands. I agree with that. Just to say that Coot (seeing as you mentioned it), as yet, does not deal with cross-compound torsion manipulation. Sorry about that. Having said that, as Judit suggests, it is not obvious that you need it. Paul.
Re: [ccp4bb] Sketcher problem
I just tried your suggestion, and it seems to work satisfactorily. Great. Many thanks. best, reyhan From: Paul Emsley paul.ems...@bioch.ox.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, 21 October 2011, 18:10 Subject: Re: [ccp4bb] Sketcher problem 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 each atom pair) -- the ring will rotate freely if no torsion or angle restraints are defined between the ring and the metal, i.e. no need to define the imaginary axis. (Bond, angle and planar restraints for the ring itself will still have to be defined to keep it in a decent shape, needless to say.) I would personally edit the restraints file by hand, but you might wish to try JLigand -- the tool of choice for metal containing ligands. I agree with that. Just to say that Coot (seeing as you mentioned it), as yet, does not deal with cross-compound torsion manipulation. Sorry about that. Having said that, as Judit suggests, it is not obvious that you need it. Paul.
[ccp4bb] Sketcher
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 National Institutes of Health - NIDDK The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov
Re: [ccp4bb] sketcher
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 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 On Wed, Jun 9, 2010 at 12:28 PM, Garib Murshudov ga...@ysbl.york.ac.uk wrote: 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 the best way of generating ligand. In any case you have to check you ligand after it has been generated. One tiny electron or proton can change chemistry completely. regards Garib On 9 Jun 2010, at 12:23, Matthias Zebisch wrote: 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 (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: 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 to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de
[ccp4bb] sketcher
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 to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui
Re: [ccp4bb] sketcher
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 atom and defined each bond type. Then I ran save file, create library description. The pdb file was loaded to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui
Re: [ccp4bb] sketcher
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 (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: 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 to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de
Re: [ccp4bb] sketcher
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 the best way of generating ligand. In any case you have to check you ligand after it has been generated. One tiny electron or proton can change chemistry completely. regards Garib On 9 Jun 2010, at 12:23, Matthias Zebisch wrote: 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 (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: 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 to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de
Re: [ccp4bb] sketcher
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 On Wed, Jun 9, 2010 at 12:28 PM, Garib Murshudov ga...@ysbl.york.ac.ukwrote: 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 the best way of generating ligand. In any case you have to check you ligand after it has been generated. One tiny electron or proton can change chemistry completely. regards Garib On 9 Jun 2010, at 12:23, Matthias Zebisch wrote: 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 (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: 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 to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de
Re: [ccp4bb] Sketcher and Bonds
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. Then you load the pdb generated by sketcher (with trans bonds) into coot, model cis bonds manually and regularize. Coot will regularize cis bonds according to the edited cif file. Good luck, Oliv On Thu, Feb 25, 2010 at 9:52 PM, SUBSCRIBE CCP4BB Anonymous moloch...@gmail.com wrote: 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 2/6 which I assume assigns priority. So how do I actually implement what I want to do? I've read the manual, fiddled with settings, and found an old post on a similar subject but I still cant get my bonds to hold after creating a library. Old Post: Sketcher and stereochemistry - Mon, 19 Mar 2007 Thanks for any ideas! -Jon -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eid...@blur.compbio.ucsf.edu
[ccp4bb] Sketcher and Bonds
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 2/6 which I assume assigns priority. So how do I actually implement what I want to do? I've read the manual, fiddled with settings, and found an old post on a similar subject but I still cant get my bonds to hold after creating a library. Old Post: Sketcher and stereochemistry - Mon, 19 Mar 2007 Thanks for any ideas! -Jon
[ccp4bb] Sketcher and Refmac monomer library construction
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 lib files in my local directory. Assuming I can get this to work (see below), then refmac should recognize the monomer files in the local directory from the residue name and use the proper restraints? Or do I need to explicitly read in the lib file(s) (e.g., libcheck_RTC.cif) in the LibIn field in CCP4i? I can read in the RTC PDB file below into sketcher and change the CO bonds to triple (they come up double on read-in), but then running libcheck dutifully makes the carbons sp2 and adds riding hydrogens. Agh. Running libcheck at the command line does the same thing with or without the HFLAG set. I would be grateful for any assistance/suggestions. I thought this would be an easy task... :) I must be missing something obvious. BTW, the RTC monomer in the HIC-UP server is incorrect: it is meridional instead of (the correct) facial geometry. THe PDB file below is correct. ATOM 1976 RE RTC B 905 39.199 36.612 61.900 1.00 20.26 RE ATOM 1977 O1 RTC B 905 41.664 36.504 60.063 1.00 20.75 O ATOM 1978 O2 RTC B 905 40.911 37.753 64.220 1.00 20.54 O ATOM 1979 O3 RTC B 905 39.925 33.794 62.879 1.00 20.49 O ATOM 1980 C1 RTC B 905 40.757 36.541 60.750 1.00 20.06 C ATOM 1981 C2 RTC B 905 40.269 37.327 63.349 1.00 20.00 C ATOM 1982 C3 RTC B 905 39.667 34.827 62.518 1.00 20.04 C Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
[ccp4bb] sketcher and nitrogen in rings
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 geometry or fiddle around with the cif file. Is there a proper way to make it right in the first place? Thanks Jan
Re: [ccp4bb] Sketcher and stereochemistry
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 If your chirality ideal is -2 and the calculated value is +2 then think whether you have built the ligand wrongly or whetherthe sign is wrongly defined. Eleanor PS - you will also find the bad clashes .. Garib Murshudov wrote: 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 dictionary. This way you can handle severla stereoisomers (configurations) with the same dictionary. Regards Garib On 20 Mar 2007, at 00:49, Vu Thai wrote: 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 columns have any significance? Vu On Mon, 19 Mar 2007 15:35:43 -0700, Dale Tronrud [EMAIL PROTECTED] wrote: 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 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 your stereochemistry. Does any one know how sketcher reads these three columns to determine the stereochemsitry? Thanks in advance for your help. Cheers, Vu
Re: [ccp4bb] Sketcher and stereochemistry
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 dictionary. This way you can handle severla stereoisomers (configurations) with the same dictionary. Regards Garib On 20 Mar 2007, at 00:49, Vu Thai wrote: 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 columns have any significance? Vu On Mon, 19 Mar 2007 15:35:43 -0700, Dale Tronrud [EMAIL PROTECTED] wrote: 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 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 your stereochemistry. Does any one know how sketcher reads these three columns to determine the stereochemsitry? Thanks in advance for your help. Cheers, Vu
