Re: [ccp4bb] Query on density fitting to phosphate

[Joel Tyndall]

Have you tried sodium?

From: CCP4 bulletin board  On Behalf Of Arpita Goswami
Sent: Sunday, December 17, 2023 11:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Query on density fitting to phosphate

Dear All,

Hope you all are doing well.

The density in the image (in link below)  is fitted with PO4 ion, although the 
crystallization condition has both mono and dihydrogen phosphate which is not 
fitting without hydrogen. But the resolution is 2.5 A, so hydrogen may not be 
put in, or is there any way to do so? Otherwise placing water is the final 
option.

https://i.postimg.cc/4N7q2K0p/Screenshot-from-2023-12-17-16-07-07.png

Also the density is quite close to Aspartate, so PO4 may not be right. Can it 
be dihydrogen phosphate as two positively charged residues (Specially the 
lysine) are also nearby to neutralize positive charge? Other ions in the 
crystallization condition are Cl-, K+ and Na+. These are not put as both 
aspartate and lysine are at comparable distances from the density. The pH is 
6.2 in which dihydrogen phosphate is reported to interact with aspartate 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855859/).

Waiting eagerly for your reply.
--
Thanks and Merry Christmas in advance.
Best Regards,
Arpita



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Re: [ccp4bb] Question about BIOVIA DiscoveryStudio 2021

[Joel Tyndall]

Hi Fred,

I don't know about Discovery studio but I know in Pymol you can select the 
peptide ligand yourself, e.g. via a sequence view. It just depends on what type 
of analysis you are doing.

Joel

-Original Message-
From: CCP4 bulletin board  On Behalf Of Fred Vellieux
Sent: Monday, July 3, 2023 10:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question about BIOVIA DiscoveryStudio 2021

Folks, apologies for the non-CCP4 software question.

I have tried to contact the BIOVIA DiscoveryStudio support team, somehow my 
browser does not allow me to open their "contact form".

I am trying to visualize and perform an analysis on a protein:smaller molecule 
complex. The smaller molecule happens to be a long peptide.
Whatever I do with the PDB (change ATOM cards to HETATM, change residue names 
to PEP, UNK, LGD, introduce MODEL and ENDMDL cards) DiscoveryStudio indicates 
the input PDB file doesn't contain any ligand.

Would any one in this community have an idea of how to specify that a part of a 
coordinate file is the ligand, so that DiscoveryStudio 2021 recognises it as 
such and allows me to proceed?

Thanks,

Fred.

--
MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Protein models with Cofactors, metal clusters and heme

[Joel Tyndall]

Thanks for the recommendations.

From: Dias, Joao M. 
Sent: Thursday, 2 March 2023 10:17 AM
To: Joel Tyndall ; CCP4BB@JISCMAIL.AC.UK
Subject: RE: Protein models with Cofactors, metal clusters and heme

Hi Joel,
Have you tried Alphafill:
AlphaFold Filled 
(alphafill.eu)<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Falphafill.eu%2F=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=JI72AhH0pyFxXYdW7yGmou3ZSUa7ftuVhVHCLFJa4eg%3D=0>
https://alphafill.eu/


AlphaFill: enriching AlphaFold models with ligands and cofactors
Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten & Anastassis Perrakis
Nature Methods volume 20, pages205–213 (2023)
https://www.nature.com/articles/s41592-022-01685-y<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41592-022-01685-y=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=PxOYMNnpZMRl7IawZs6w8aK2wytbqkix3ghZ6cTrc8Q%3D=0>

Good luck,
Joao


Joao M. Dias, Ph.D.
Principal Scientist
Pfizer
Structural and Molecular Sciences
Building 220/ room 3263, MS-8220-3224
445 Eastern Point Rd.
Groton, CT 06340




From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Joel Tyndall
Sent: Wednesday, March 1, 2023 4:10 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [EXTERNAL] [ccp4bb] Protein models with Cofactors, metal clusters and 
heme

Hi,

I have a slightly off topic question around structure models, e.g. Homology 
modelling. It may appear that Alpha fold etc could make homology modelling 
somewhat redundant. However I have noticed that in at least two structures, 
either a cofactor or heme are not present on the Alphafold models (that I am 
aware of).

Is anyone aware of any webserver/package that will model these cofactors 
reliably (outside of modeller)?

Many thanks

J

Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Website | 
pharmacy.otago.ac.nz<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fpharmacy.otago.ac.nz__%3B!!H9nueQsQ!-8ToqYWLFzEomDSOyXoLqbjfu9cvBGCMHVQQL7xOvV9gs9bpoPV1GEZgbVvGdJiS5UoZz1DgybeZrnr_RfC3-xPE%24=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=iXwzY4qUseOcnLmdde%2BBciF%2Fkich8AFgX%2FXwH3DJCh8%3D=0>





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[ccp4bb] Protein models with Cofactors, metal clusters and heme

[Joel Tyndall]

Hi,

I have a slightly off topic question around structure models, e.g. Homology 
modelling. It may appear that Alpha fold etc could make homology modelling 
somewhat redundant. However I have noticed that in at least two structures, 
either a cofactor or heme are not present on the Alphafold models (that I am 
aware of).

Is anyone aware of any webserver/package that will model these cofactors 
reliably (outside of modeller)?

Many thanks

J

Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Website | pharmacy.otago.ac.nz





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Re: [ccp4bb] Crystallised PEG / Lys/ Gln...ASN

[Joel Tyndall]

Or ASN?

From: CCP4 bulletin board  On Behalf Of Joel Tyndall
Sent: Friday, 4 November 2022 4:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Crystallised PEG / Lys/ Gln

Hi all,

Quick question. I am well aware of seeing PEG crystallised with my protein in a 
circular shape around lysine residues. Can this also happen with GLN around the 
side chain nitrogen? Or even form an adduct? I see good evidence for at least 
the former option

Happy Friday

Joel

Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | 
pharmacy.otago.ac.nz<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpharmacy.otago.ac.nz%2F=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Cfee6d405baa34ab98c7f08dabe128660%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638031285528982149%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=iVmXW0l0Xr41CIgic8n2b%2F7JpFAo5A9qDCfgBK7eJKg%3D=0>





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[ccp4bb] Crystallised PEG / Lys/ Gln

[Joel Tyndall]

Hi all,

Quick question. I am well aware of seeing PEG crystallised with my protein in a 
circular shape around lysine residues. Can this also happen with GLN around the 
side chain nitrogen? Or even form an adduct? I see good evidence for at least 
the former option

Happy Friday

Joel

Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz





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Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Joel Tyndall]

PC, mac or linux?

-Original Message-
From: CCP4 bulletin board  On Behalf Of Dale C
Sent: Wednesday, 27 July 2022 12:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see 
the "Connected to Phenix" button in the toolbar on Coot.

- The 'fetch' command in Pymol no longer works either (I have attached a 
screenshot of the error message here)

- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

I feel they may be all related and my first thought is that it has something to 
do with my Python dependencies however I have no idea how to fix this or 
reinstall them.

Does anyone have an idea if they are all related? Or how i might fix this?

fyi I am using
- ccp4 program suit v8.0.002
- Coot 0.9.8.3
- Phenix-1.20.1-4487

Thanks in advance.

Dale.





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Re: [ccp4bb] Missing double bonds in the ligand

[Joel Tyndall]

Thanks Nigel, I meant the mmcif coordinate file format as an alternative to the 
pdb file.

I am now not convinced it contains the bond order etc

Alternatively, saving as a .mol2 file should  save atom types and bond order

From: Nigel Moriarty 
Sent: Friday, 8 July 2022 12:31 pm
To: Joel Tyndall 
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Missing double bonds in the ligand

Joel

You'll need to be more specific than ".cif" files. CIF can be used for models, 
data and restraints. Read more here.

http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2013_01.pdf#page=6<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fphenix-online.org%2Fphenixwebsite_static%2Fmainsite%2Ffiles%2Fnewsletter%2FCCN_2013_01.pdf%23page%3D6=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=b2fkWsdF77efNj%2FGHsKZJwizq%2FwZXC6elTwyl6HULhA%3D=0>

If you are referring to the restraints CIF, it is possible but I'm not sure 
which software uses it.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov<mailto:nwmoria...@lbl.gov>
Fax   : 510-486-5909  Web  : 
CCI.LBL.gov<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcci.lbl.gov%2F=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=iPFj31dUns0UNyytIR%2B3k15CYHTBqi%2FW%2FXSjCK0jtGY%3D=0>
ORCID : 
orcid.org/-0001-8857-9464<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F-0001-8857-9464=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=woV4FlAu6cCBn1YLMHScdFaesiLF8H5aFZuqeVi7v0M%3D=0>


On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall 
mailto:joel.tynd...@otago.ac.nz>> wrote:
Does the Schrodinger software read a .cif file? The bond order should be 
embedded in there.

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Nigel Moriarty
Sent: Friday, 8 July 2022 7:47 am
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Missing double bonds in the ligand

Further reading

https://en.wikipedia.org/wiki/The_Treachery_of_Images<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FThe_Treachery_of_Images=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=B46a7oKJkysY0BAH9MVj5hsmmNavmdkPmDDCsqnkmzI%3D=0>

https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fphenix-online.org%2Fphenixwebsite_static%2Fmainsite%2Ffiles%2Fnewsletter%2FCCN_2016_01.pdf%23page%3D10=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=xSoheHtkA8vI65EnwOuIUkqj277TLJMusGiTJU15d68%3D=0>

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov<mailto:nwmoria...@lbl.gov>
Fax   : 510-486-5909  Web  : 
CCI.LBL.gov<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcci.lbl.gov%2F=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=iPFj31dUns0UNyytIR%2B3k15CYHTBqi%2FW%2FXSjCK0jtGY%3D=0>
ORCID : 
orcid.org/-0001-8857-9464<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F-0001-8857-9464=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=woV4FlAu6cCBn1YLMHScdFaesiLF8H5aFZuqeVi7v0M%3D=0>


On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten 
mailto:robbie_joos...@hotmail.com>>

Re: [ccp4bb] Missing double bonds in the ligand

[Joel Tyndall]

Does the Schrodinger software read a .cif file? The bond order should be 
embedded in there.

From: CCP4 bulletin board  On Behalf Of Nigel Moriarty
Sent: Friday, 8 July 2022 7:47 am
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Missing double bonds in the ligand

Further reading

https://en.wikipedia.org/wiki/The_Treachery_of_Images

https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : 
CCI.LBL.gov
ORCID : 
orcid.org/-0001-8857-9464


On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:
Dear Anil,

Bond orders are not captured in PDB files explicitly. The way bonds are shown 
depends on the program and possibly additional information sources (i.e. 
molecular restraint or topology files).
So this is just a "problem" with Schrödinger.

Cheers,
Robbie

On 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" 
mailto:anilmarap...@gmail.com>> wrote:

Dear CCP4 Users,

We are working on a ligand-bound structure and would like to look at 
protein-ligand interactions using Schrodinger.

Molecule structure is:

When we load the ligand-fitted PDB file into Schrodinger, the molecule appears 
to be flat like it should be in the structure but it removed all the double 
bonds in the ligand where the above shown original molecular structure has 
double bonds in it.

When we load the same PDB file into pymol and look at the ligand it shows 
correctly



We would appreciate if any insight or suggestions for why this may be happening 
and how to ensure the ligand shows properly when the PDB is loaded into 
Schrodinger. Would this be an issue with Schrodinger software or with the PDB 
file?

I can be available by direct email for troubleshooting at 
amara...@purdue.edu.

--
Anil Kumar Marapaka, Ph.D.
Post-Doctoral Research Associate
Department of Medicinal Chemistry and Molecular Pharmacology (MCMP),
Purdue University, West lafayette,
Indiana-47907, USA.
Mobile 1: +1-765-409-6245 (USA)
Mobile 2: +91-995-998-5571 (India)
Email 1: amara...@purdue.edu
Email 2: anilmarap...@gmail.com




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Re: [ccp4bb] circular peptide structure refinement

[Joel Tyndall]

You will need to add the "link" line to the PDB file so the software recognises 
the covalent bond.

See the pdb file for 6U6K

Hope this helps

J

From: CCP4 bulletin board  On Behalf Of Jiang Xu
Sent: Thursday, 7 July 2022 10:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] circular peptide structure refinement

Hello everyone,
   I have a peptide that forms a peptide bond between the N terminal and C 
terminal.  I used X-ray crystallography to solve the structure and found the N 
and C terminals are pretty close to each other with extra electron densities 
clearly showing that they form a peptide bond. However in Coot I could not make 
the peptide bond, the two terminals seem to repel each other when I do real 
space refinement in coot and, couldn't form the peptide bond. Any suggestions 
on how to do it?
Thank you,
Best,
Jiang Xu
Lin Chen Research Group
Molecular and Computational Biology
Department of Biological Sciences
University of Southern California



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[ccp4bb] Easy/Silly question

[Joel Tyndall]

Hi folks,

I frustratingly cant find “maltose” as a ligand in the pdb or ccp4 database. 
Does any one have the code for the ligand? Surely its been used before.

Thanks in advance

J

Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz





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Re: [ccp4bb] [phenixbb] NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September

[Joel Tyndall]

Hi,
Any chance this will be recorded for those of us in a different dimension?

J

-Original Message-
From: phenixbb-boun...@phenix-online.org  
On Behalf Of Randy John Read
Sent: Friday, 27 August 2021 6:27 am
To: CCP4BB@jiscmail.ac.uk; PHENIX user mailing list 
Subject: [phenixbb] NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 
1 September

Hi,

I've just learned that this online workshop is generally open, not just to 
members of the Norwegian Artificial Intelligence Consortium (NORA), and it's 
free!  Information, including the current programme and a link to registration, 
can be found here: 

https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nora.ai%2Fevents%2FAlphaFoldv2.0-and-RoseTTAFold-workshop%2520.htmldata=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7Cd376abedf6994ecdf93e08d968bfc1af%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637655995083551647%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=Bn4T%2FOgLlA1Qher%2FUwOK5HTkJMLS264KWKR%2FtB7c71Q%3Dreserved=0

I'll be talking a bit about experiences with models from AlphaFold2 and 
RoseTTAFold, but the real draw should be talks by people who really understand 
these two deep learning algorithms: Minkyung Baek (first author on the 
RoseTTAFold paper, from David Baker's group) and a representative of the 
DeepMind team that developed the two versions of AlphaFold. Sameer Velankar 
will also be there to talk about the exciting new AlphaFold database at the EBI.

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk


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Re: [ccp4bb] how to fix helices-sheets getting converted to coil,

[Joel Tyndall]

HI,

I simply opened this in Pymol, saw the non designated structed, typed dss 
(https://www.pymolwiki.org/index.php/Dss) and then saw the secondary 
structure...

It "may" be that it is not designated in the pdb file (however I haven't 
looked).

J

From: CCP4 bulletin board  On Behalf Of Firdous Tarique
Sent: Wednesday, 18 August 2021 12:24 am
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] how to fix helices-sheets getting converted to coil,

Hi

The representation of secondary structures have changed in my model. Helices 
and sheets are no longer appearing in the form it should be but appearing in 
the coiled conformation.

It all started when I splitted the 40S ribosome into two parts: head and body 
(In order to make head and body from the 40S subunit, I had deleted a few 
nucleotides and amino acids in the connecting region.), then I did rigid body 
fitting in chimera, then saved them separately with respect to map, then opened 
these coordinates in coot and joined them together (merged)  and finally ran 
real space refinement in Phenix.

Now when I am opening the refined pdb in Chimera, while the secondary 
structures are in their proper shape and form in the body, all have changed 
into coil-coil conformation in the head of 40S.

Is this a problem of Chimera or ChimeraX or something changed in the output of 
the refinement job due to which this is happening?.

Is there any option in Chimera or ChimeraX to fix it ? I remember in Pymol one 
can assign secondary structures if there is misrepresentation from the original 
structure.

Your suggestions and advice are appreciated.

Attached is the model in case someone wants to have a look.

Best

Firdous






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Re: [ccp4bb] pymol 2.5 GUI font size too small

[Joel Tyndall]

Hi Ursula,

Can you provide some more information?

What OS are you using, Mac, Windows or Linux?
Are you referring to the text in the top window or labels in the graphical 
window?

J

From: CCP4 bulletin board  On Behalf Of Ursula 
Schulze-Gahmen
Sent: Wednesday, 21 July 2021 11:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pymol 2.5 GUI font size too small

I just updated my pymol version to 2.5, which now displays a tiny font in the 
internal GUI. The settings in pymol don't have an option for the GUI font. Does 
anybody have a suggestion on how to change the font size in the pymol GUI in 
version 2.5?

Thanks

Ursula

--
Ursula Schulze-Gahmen, PhD
Staff Research Scientist
The J David Gladstone Institutes
1650 Owens St.
San Francisco, CA 94158
(415) 734 4835




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Re: [ccp4bb] technical question

[Joel Tyndall]

You could probably do this via a mutate option in coot . Or at least use  the 
sulfoxide as a new residue (not mutate)

From: CCP4 bulletin board  On Behalf Of amit gaur
Sent: Saturday, 30 November 2019 7:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] technical question

Hi everbody,
I want to replace a particular methionine in a pdb with methionine sulfoxide( 
an oxidized form of methionine). Can body please tell me how to do this? I am 
familiar with pymol, chimera and coot software.
--
Amit Gaur
Post Doctoral Researcher
Thomas Jefferson University
1020, Locust Street, Suite 418
Philadelphia, PA 19107





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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Joel Tyndall]

Hi,

Polar interactions seems to make the most sense. This is what Pymol uses as I 
don't  think it differentiates

J

From: CCP4 bulletin board  On Behalf Of Sheila Boreiko
Sent: Tuesday, 18 September 2018 8:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] collective term for hydrogen bonds and salt bridges


Dear all,

 I had some literature search, but could not find clearly. Would there be 
an appropriate term to call the sum of hydrogen bonds (HB) and salt bridges 
(SB)? What about "hydrophilic interactions" or "polar interactions"? I am 
analyzing the different number of theses interactions in different monomers of 
my protein, as a totality I wanted to cite (compare) the number of HB + SB, yet 
I think to specify them separately could take out some focus of the discussion.

 Thank you,

Sheila



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Re: [ccp4bb] Electron density

[Joel Tyndall]

Did you happen to use glycerol as a cryoprotectant?

From: CCP4 bulletin board  On Behalf Of Daniel Garcia
Sent: Monday, 14 May 2018 12:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density

Dear all,

I am currently refining a structure and found a intriguing electron density at 
the protein surface (pictures attached, the Fo-Fc map is contoured at >3.5 
sigma). My first candidates were molecules from my protein prep or 
crystallisation buffer, but none of them seem to fit well. I can observe that 
the ligand is nearby the side chains of a tyrosine, a lysine, a threonine and a 
glutamate residue, and it is close to the carbonyl oxygens of the protein 
backbone of a nearby loop. The shape of this density is not pyramidal, but it 
is not planar either.

Do you have any suggestions to solve this density based on your own experience? 
My crystallisation buffer contains tartrate, ammonium sulphate, and CHES, and 
my protein is in Tris buffer containing DTT and sodium chloride.

Best regards,

--
Mario

Re: [ccp4bb] biological molecule?

[Joel Tyndall]

Hi Charlie,

I just visited the RCSB PDB website and looked up a random structure. You can 
still download the biological unit in pdb format from the download files 
pulldown

J

-Original Message-
From: CCP4 bulletin board  On Behalf Of Carter, Charlie
Sent: Tuesday, 10 April 2018 9:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] biological molecule?

I knew this would happen one day. I loathed the cif versions of the 
coordinates, but fortunately, I’ve never had to use a .cif file. 

Now, the pdb no longer offers anything but…

I cannot find in the .cif file where the instructions are to generate the 
biological molecule from the asymmetric unit. How does one do this please?

Thanks,

Charlie

Re: [ccp4bb] Atom clashes in active site?

[Joel Tyndall]

Could this be a covalent interaction?

Difficult to judge without seeing anything

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew 
Marshall
Sent: Tuesday, 20 December 2016 2:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Atom clashes in active site?

Hi all,

Thank you for your suggestions. I tried the pdb file edit (making the offending 
atoms of both the ligand and the protein 'B' altconf), but it didn't seem to 
make any difference to their positions after a single round of refinement..?
The atoms in the active site concern two acetyl groups - one from the 
substrate, acetyl-CoA, and the other from an acetylated cysteine in the protein 
- that I believe are poised ready for a condensation reaction. The closest 
contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3 (3.1A), but 
going off the density, I think these should be closer (more like 2.8 or 2.7A). 
It may be that I've trapped another reaction intermediate (which would be 
cool), but I don't think that fits the density quite as well. Any 
thoughts/ideas?

Thanks,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz 
> wrote:
Hi Andrew,
I'm curious- what are the atoms that are clashing? I worked on this sort of 
thing back in my Ph.D., and so I might have some useful tidbits if, for 
example, the S is clashing with a carbon of some sort.
Thanks,
Scott

On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall 
> 
wrote:
Hi all,

I have a structure of a condensing enzyme with substrate bound. The active site 
is very tight, requiring some of the substrate atoms to clash with a catalytic 
cysteine. This means that although the substrate fits the density nicely upon 
manual real-space refinement, phenix recognises the clash, resulting in the 
displacement of substrate atoms so that they are outside the density. I can 
mostly fix this by using distance restraints, but I'd rather allow it to refine 
in a less biased manner, but ignore the clash. Is this a acceptable way 
forward? If so, is there a parameter I can edit to tell phenix to ignore 
clashes between these specific atoms?

Thanks,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide



--
Scott Horowitz, Ph.D.
Postdoctoral Fellow

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
phone: 734-647-6683
fax: 734-615-4226

[ccp4bb] Last 2 updates - aimless and scala

[Joel Tyndall]

Hi folkd,

We have just collected some data and was busy processing and ran aimless having 
updated to the latest versions (upgrades 10 and 11 I think). Both aimless and 
then scala stops/fails almost immediately without writing any log files etc. I 
tried running the same unmerged mtz on an older version and it runs fine. Is 
this a bug?

J

_
Joel Tyndall, PhD

Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

Re: [ccp4bb] pdb2pqr generation

[Joel Tyndall]

Hi Tim,

You have sparked my interest in Coot ESP. Do you know of a link to explain how 
to display/export it? I can generate it but nothing happens (other than the 
protein disappearing

Cheers

Joel

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene
Sent: Wednesday, 10 December 2014 3:07 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] pdb2pqr generation

Dear abhishek,

one work-around is to split the PDB-file into four different PDB-files, one per 
chain, and concatenate the results back together.

Alternatively you can try Coot to calculate the ESP.

Bst,
Tim


On 12/09/2014 02:23 PM, abhishek jamwal wrote:
 Dear All,
 
 I wish to generate electrostatics surface cartoon for  a protein, 
 which is a tetramer.
 
 I am using pdb to pqr server (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) 
 to generate .pqr files as part of this process.
 
 I find that server is able to genetrate .pqr file contents, only when 
 input pdb file contains a single chain (monomer), it is failing to do 
 the same when I give it tetramer pdb co-ordinates, why is that ? and 
 how can I generate a .pqr file for teramer...what other options do I have ?
 
 many thanks in adavnce
 
 abhishek
 

--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

[ccp4bb] Small molecule cif files

[Joel Tyndall]

Hi all,

If a crystallographer determines a liganded structure  of say a new small 
molecule. Where does the cif file come from when the next version of 
ccp4/phenix gets released. Along the same lines. If a cif file is not quite 
correct (or were not parsed against the CSD) and is subsequently updated by an 
individual. Is there a process for updating existing ligand cif files?

My reason for the question is around several ligand complexes that we have had 
to generate new cif files in order to get the correct conformational parameters 
(centred around unsaturated rings)

Regards

Joel

_
Joel Tyndall, PhD

Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem

[Joel Tyndall]

Hi,

I saw Jeffs post with interest and have held off until now.  It is relatively 
easy to find structures with bad geometry for small molecules but it does not 
do any good simply pointing them out. What I believe is needed is a way to fix 
the problem. There are several possible ways. The pdb could parse new 
structures through a checking process to check the geometry of small molecules. 
This, I would presume, could be done via the CSD. I also believe that cif file 
generation can be improved. The developers of the available programs are doing 
a great job but as intelligent scientists we strive for perfection. I am 
unfortunately not in a position to develop software myself ( so maybe I should 
pipe down) but I would be happy to offer assistance (from my personal 
experience). In my experience I have had some issues with small molecule 
parametrisation ( or maybe I just deal with unusual molecules). By that I mean, 
on occasion I have had a .cif files that simply do not make sense or 
contradicts what you would  expect in the geometry of a small molecule. I am 
aware of one service that does check against the CSD when generating cif 
files.

I read in one of the editorials, or related posts that one of the structures 
was corrected. This is also an option assuming the data has been deposited.

My two cents

J

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene
Sent: Friday, 13 June 2014 5:54 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem

Hi Jeff,

there are quite a few implications in your brief email that each might open a 
long thread of discussion. As brief as possible I think one has to be a good 
scientist and a good crystallographier to fully understand the meaning of a 
crystal structure, and I think many people believe a crystal structure is just 
a set of coordinates.

If someone tells me some distance in yards and I assume that's about the same 
as a meter I will surely get some dodgy results up to creating the first car 
accident on Mars ;-)

Cheers,
Tim

On 06/12/2014 07:04 PM, Jeffrey Bell wrote:
 Hi, Tim,
 
 Thanks for your comment. Do you agree with the editorial's claim that some 
 25% of the deposited protein-ligand complexes might be dodgy in significant 
 details? 
 
 
 This editorial comment represents something that I often hear from drug 
 discovery professionals. Is it a matter of PR between crystallographers and 
 other scientists, or does a real problem exist?
 
 Cheers,
 
 Jeff Bell
 PrimeX developer
 Schrödinger, Inc.
 
 
 On Tuesday, June 10, 2014 10:27 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de 
 wrote:
  
 
 
 I hope that the contents of this section is obvious to most readers of 
 the ccp4 bulletin board.
 
 Cheer,
 Tim
 
 
 On 06/10/2014 03:40 PM, Jeffrey Bell wrote:
 An editorial comment about protein crystallography appeared under 
 that title. It's short and worth considering.
 http://pipeline.corante.com/
 
 
 

--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem

[Joel Tyndall]

Great news and I am in full support of the bug option. Where do we start?

(Caveat: we all make mistakes, I am sure I have!)

-Original Message-
From: Ethan A Merritt [mailto:merr...@u.washington.edu] 
Sent: Friday, 13 June 2014 8:45 a.m.
To: Joel Tyndall
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem

On Thursday, 12 June, 2014 20:24:43 Joel Tyndall wrote:
 Hi,
 
 I saw Jeffs post with interest and have held off until now.  It is relatively 
 easy to find structures with bad geometry for small molecules but it does not 
 do any good simply pointing them out. What I believe is needed is a way to 
 fix the problem. There are several possible ways. The pdb could parse new 
 structures through a checking process to check the geometry of small 
 molecules. This, I would presume, could be done via the CSD.

As of January 2014 this is indeed being done as part of the PDB deposition 
process.

Anyone who has deposited a structure containing a ligand this year has probably 
been surprised, pleasantly or otherwise, by the table of geometry 
violations/ouliers for each ligand.

If you missed the various announcements, you may wish to try it out on your own 
structures here:

http://wwpdb-validation.wwpdb.org/validservice/


 I also believe that cif file generation can be improved.

Indeed.  All of the library-generation tools I am aware of are flawed in
their own idiosyncratic ways.   I think I shall start a campaign to treat
errors in the cif libraries as bugs, and encourage people to report these 
bugs in the libraries we all use just as they do for bugs in the programs we 
all use.  

Ethan


 The developers of the available programs are doing a great job but as 
 intelligent scientists we strive for perfection. I am unfortunately not in a 
 position to develop software myself ( so maybe I should pipe down) but I 
 would be happy to offer assistance (from my personal experience). In my 
 experience I have had some issues with small molecule parametrisation ( or 
 maybe I just deal with unusual molecules). By that I mean, on occasion I have 
 had a .cif files that simply do not make sense or contradicts what you would  
 expect in the geometry of a small molecule. I am aware of one service that 
 does check against the CSD when generating cif files.
 
 I read in one of the editorials, or related posts that one of the structures 
 was corrected. This is also an option assuming the data has been deposited.
 
 My two cents
 
 J
 
 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
 Tim Gruene
 Sent: Friday, 13 June 2014 5:54 a.m.
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem
 
 Hi Jeff,
 
 there are quite a few implications in your brief email that each might open a 
 long thread of discussion. As brief as possible I think one has to be a good 
 scientist and a good crystallographier to fully understand the meaning of a 
 crystal structure, and I think many people believe a crystal structure is 
 just a set of coordinates.
 
 If someone tells me some distance in yards and I assume that's about 
 the same as a meter I will surely get some dodgy results up to 
 creating the first car accident on Mars ;-)
 
 Cheers,
 Tim
 
 On 06/12/2014 07:04 PM, Jeffrey Bell wrote:
  Hi, Tim,
  
  Thanks for your comment. Do you agree with the editorial's claim that some 
  25% of the deposited protein-ligand complexes might be dodgy in significant 
  details? 
  
  
  This editorial comment represents something that I often hear from drug 
  discovery professionals. Is it a matter of PR between crystallographers and 
  other scientists, or does a real problem exist?
  
  Cheers,
  
  Jeff Bell
  PrimeX developer
  Schrödinger, Inc.
  
  
  On Tuesday, June 10, 2014 10:27 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de 
  wrote:
   
  
  
  I hope that the contents of this section is obvious to most readers 
  of the ccp4 bulletin board.
  
  Cheer,
  Tim
  
  
  On 06/10/2014 03:40 PM, Jeffrey Bell wrote:
  An editorial comment about protein crystallography appeared under 
  that title. It's short and worth considering.
  http://pipeline.corante.com/
  
  
  
 
 --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Off topic: Homology modeling

[Joel Tyndall]

Hi Theresa,

I tackled a similar problem recently using modeller (Andrej Sali) which worked 
well. In the case of my transporter (or any model) your homology model will 
only be as good as the starting structure (resolution etc) and your sequence 
identity. I found that the homologues that I was looking at were simply too 
distant from the human transporter to actually be of any use.

Hope this helps

Joel

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa 
Hsu
Sent: Friday, 23 May 2014 7:49 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Off topic: Homology modeling

Dear all

I am working with a membrane protein without known structure. The closest 
protein in PDB has 10% sequence identity/25% similarity to my protein.

What is the best method and software to do homology modeling while I try to get 
the crystal? Is the ligand binding site prediction reliable? There is no 
available experimental data on this protein except to sugest it is some type of 
ion transport.

Thank you.

Theresa

Re: [ccp4bb] AW: appropriate torsion angles

[Joel Tyndall]

Dear Herman and Paul,

Thanks for your input. I have already looked at the  CSD and it conclusively 
tells me that both nitrogens are tetrahedral and both have a phenyl ring. I 
have added appropriate chiral restraints for the nitrogens. That part I am 
comfortable with. What I am looking to do is make the two (four) carbon atoms 
flexible enough (not adopt chair or boat alone) such that they could be a 
twisted boat conformation or the like. I need to adopt the opposite chirality 
at one of the nitrogens, probably the other, ensure that both adjacent phenyl 
rings remain relative stable (positionally) and optimise a H-bond to a water 
molecule

Herman, the molecule in question are known drug (itraconazole  posaconazole) 
so we don't have the option to not use it. It is hard to know what conformation 
(mess) is correct but I believe I had enough evidence to put my argument 
forward the way I believe it should go, I just need the parameters.

Regularizing in Coot doesn't help

Thanks both.

Joel


Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 
herman.schreu...@sanofi.com [herman.schreu...@sanofi.com]
Sent: Tuesday, April 15, 2014 8:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] AW: appropriate torsion angles

Dear Paul,

I find it difficult to predict when a pipirazine nitrogen will be sp2 and when 
sp3, so I usually search the csd with the exact substituent at hand and 
supposed that Joel will have done the same. In general, I find that auto 
generate programs are overly optimistic how far delocalization of binding 
electrons will extend, and also about the effect of steric hindrance by other 
substituents at staggered positions. So in general, compounds tend to be in 
reality less flat than cif generating programs think. It is also important to 
carefully look at the electron density maps and the fit of the compound. With 
large substituents like phenyl groups, choosing the wrong conformation should 
produce significant distortions.

Best,
Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Paul 
Emsley
Gesendet: Dienstag, 15. April 2014 10:28
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: appropriate torsion angles


Dear Joel and Herman,

On 15/04/14 04:39, 
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote:
Dear Joel,

I always tell our chemists not to include piperazine rings etc. in their 
compounds because of this conformational mess, but somehow they do not seem to 
listen. ;-)
Unfortunately, do did not tell us how and with software you auto generated your 
cif file, so I can only give some general remarks:
I would try grade from global phasing to generate your cif file. Grade uses 
Mogul, which consults the CSD to find the appropriate conformational parameters.
Is you nitrogen flat, or has it the wrong chirality? If the chirality is wrong, 
you should change all _chem_comp_chir.volume_sign’s from positive/negative to 
both. However, real-space refinement will usually not get through the energy 
barrier to change the chirality, so you will have to move the atoms manually. 
In the “Rotate Translate Zone” mode, you can move individual atoms by pressing 
cntrl and picking the atom with the left mouse button.

FWIW, for this sort of thing I usually fix atoms before refinement and 
ctrl-move fixed atoms during refinement.

If one of the R groups is merely a hydrogen, coot's refinement pathology 
detection should jump the hydrogen to the other side of incorrect chiral 
centres. You may need to try this in regularization mode sometimes.

In my experience, without a formal charge prodrg likes to make piperazine 
nitrogens sp2 if connected to at least one aromatic carbon (as in Joel's case - 
at least in my reading).  This may well be The Right Thing to do, so the whole 
boat/chair thing is a bit moot.



If the nitrogen is flat and you auto generate from a pdb file, you should make 
sure the nitrogen on the input file has a tetrahedral conformation. You may 
force the program to make a tetrahedral nitrogen by adding a proton (and 
positive charge) or remove the phenyl and copy the nitrogen parameters 
generated to the cif file for the complete molecule, but better would be to use 
grade.
Best,
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Joel 
Tyndall
Gesendet: Dienstag, 15. April 2014 07:03
An: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] appropriate torsion angles

Hi folks,

We are trying to model multiple instances of a small

[ccp4bb] appropriate torsion angles

[Joel Tyndall]

Hi folks,

We are trying to model multiple instances of a small molecule that contains a 
piperazine ring. I am looking for the appropriate torsion angles that are 
needed for a cif file in order for the piperazine ring to be able to adopt 
either a chair or a boat or any combination between the two (i.e. relaxed 
torsion restraints but remaining tetrahedral).

Any help would be much appreciated before I launch into writing a new cif file 
from scratch.

As a little background, the piperazine contains a phenyl substituent on the 
nitrogen which is tetrahedral according to the CSD for small molecules. This 
has meant that the auto generated cif files gave the wrong geometry for the 
nitrogen in the first place.

Many thanks

Joel

_
Joel Tyndall, PhD

Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

[Joel Tyndall]

Dear Xiaoming,

I would try using the graphical interface within phenix refine to add in the 
bond length/angle constraints for your link. This seemed to work fine with our 
system without actually needing a link record.

J

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiaoming 
Ren
Sent: Friday, 4 April 2014 9:17 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits 
file

Dear all:

I am encountering a problem. I built a monomer model which is a modified 
nucleotide with Sketcher in ccp4 suite and generated the .cif file of this 
monomer. However, I could not make it bind with other nucleotides in the 
nucleic acid chain. I have tried to write LINK lines into PDB file, and also 
edited .edits file for phenix.refine. In both conditions, phenix.refine works 
except that it wouldn't add covalent bonds between the residues as I expected.

I have used .edits file for covalent binding between residues before, and it 
worked well.

So there must be something wrong with my input files. But I couldn't fighure 
out where the problem is. 

Thanks a lot and best regards!
Xiaoming

Re: [ccp4bb] question on charge charge interactions

[Joel Tyndall]

Tom,

I would think the case can be made for sharing a proton (one ionised and one 
not) in either case but more so for acidic residues. See HIV protease Asp-Asp 
as a well-established example

Hope this helps

J

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat
Sent: Friday, 28 March 2014 12:12 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] question on charge charge interactions

Hello All, 

I am appealing to the community as I don't seem to be able to find through 
Google what I am looking for, and I just don't have the ability to look through 
every structure in the PDB to find this. 
I have what I think is an interesting case: a two domain protein structure with 
a mostly hydrophobic interface between the two domains- the kicker is that I 
have two charged residues buried in this domain and they are identical. 
That is, I'm looking for an Arg-Arg or Asp-Asp type interaction (not Arg-Asp) 
where these residues are less than 4 Angstroms apart. So I was wondering if 
anyone had seen this in any other structure(s)?  
The really interesting bit is that this interaction actually regulates the 
activity of the enzyme domain although the domain interface isn't that close to 
the catalytic site.  

Thanks in advance to all those who can find a reference to this kind of 
interaction. 
Cheers, tom

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

[Joel Tyndall]

Trying not to state the obvious but...HIV protease

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
Jacob
Sent: Friday, 28 February 2014 8:43 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Large Conformational Change Upon Binding Ligand...

Dear Crystallographers,

Does anyone know of good examples of large, reversible conformational changes 
occurring between ligand-free and -bound states? Could also be a non-relevant 
molecule binding, like sulfate or something inducing dubiously -relevant 
changes. I already know of the calmodulin and periplasmic binding protein 
families, but does anyone know of others out there?

All the best,

Jacob Keller

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] New ligand

[Joel Tyndall]

Carsten,

Phenix does do this a little differently and yes it ignores existing ligands 
(which I like). CCP4 comes with is own library of existing ligand cif files 
from the pdb which coot also uses. The best way is to try and find a unique 
code to call your new ligand. That way you can have some say in what it is 
coded rather than an arbitrary code.

J

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Schubert, 
Carsten [JRDUS]
Sent: Thursday, 27 February 2014 2:22 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] New ligand

Hi Louise,

for internal use the name of your ligand does not matter as long as you have a 
.cif file describing the restraints. I am not sure about the behavior of 
refmac, but in phenix the presence of a defined name in a .cif file takes 
precedence over any duplicate entry in your monomer library. As far as PDB 
submission is concerned: it is my experience that they will rename your ligand 
to some arbitrarily name anyhow upon annotating the entry, so I would not sweat 
that part too much. 

HTH

Carsten


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Louise 
Fairall
Sent: Wednesday, February 26, 2014 6:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] New ligand

Hello,
we have a structure with a novel ligand. I used to use LIG for new ligands but 
now that is taken in the PDB by 
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE. Any suggestions for a 
generic name that is not already used?
thanks and best wishes,
Louise

Re: [ccp4bb] Water or ion

[Joel Tyndall]

I agree with Robbie. It is difficult for an ion to interact with both oxygen 
(ionised) and amide N-H at the same time. You can also have bifurcated h-bonds

Hope this helps

J

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma Ratu
Sent: Sunday, 24 November 2013 1:15 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Water or ion

Dear All:


I use Coot to check water molecules in my model.
Most of them are in good coordinates for water.

Some of these waters have unusual coordinates.

For example, one is in the H-bond distance with 2 nitrogen and 2 oxygen of 
protein residues, plus one oxygen from ligand (W_230.jpg), and the other is in 
the H-bond distance with 3 nitrogen, 1 oxygen of protein residue, plus one 
water(W_300.jpg).

Would you advice if these molecules are water, or something else, ions?

I tried Coot - highly coordinated water, and check/delete water.
The program does not pick up anything unusual.

Thank you

Uma

[ccp4bb] refmac-linux-I'm out of touch question

[Joel Tyndall]

Hi folks,

I am wanting to ask for some linux help as I want to try a newer version of 
refmac (5.8) to test it against a refinement problem I have. My problem is that 
I rarely use linux these days and I'm at a loss as  to how to run the latest 
version as my knowledge of linux has disappeared.

I have downloaded the binaries for refmac 5.8 which gives me refmacgfortran and 
libcheckgfortran. And now I am stuck. Would someone be so kind as to instruct 
me on where to put these, if they need compiling etc?

Many thanks

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

Re: [ccp4bb] atomic coloring for the color blind

[Joel Tyndall]

Why not use yellow carbons (colour by atom menu) and hit the builder button in 
pymol which shows bond order (carbonyls).
You could also type colour gray, name o, this colours the carbonyls gray (or 
any other colour that works) name o* colours all oxygens

Hope this helps

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe A. 
Rice
Sent: Friday, 31 May 2013 1:35 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] atomic coloring for the color blind

I feel badly that one of my undergrads had trouble telling an O from a C in a 
pymol homework set because he's color blind. (The assignment involved telling 
me why the a GTP analog (GDPCP) wasn't hydrolyzed).
Is there a handy by-atom coloring scheme I can recommend that works for the 
red-green color blind?
  thanks,
  Professor Rice


++

Phoebe A. Rice
Dept. of Biochemistry  Molecular Biology
The University of Chicago

773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu
http://bmb.bsd.uchicago.edu/Faculty_and_Research/

http://www.rsc.org/shop/books/2008/9780854042722.asp

[ccp4bb] Overide refmac restraints

[Joel Tyndall]

H ithere,

I am trying to refine a covalently bound ligand to my protein and I am having 
trouble with the restraints. I have generated the cif file and link within 
Jligand and this is reasonable. However it appears that REFMAC is overriding 
these and fitting the ligand to the density.

I have added a keyword text file with externtal restraints such as :

exte angle first chain A resi 1 atom S12 second chain A resi 1 atom C10 third 
chain A resi 2 atom N value 120 sigma 3.0


The resulting structures has incorrect angles which do not match the external 
restraints or cif file. Am I missing something?

Any help muchly appreciated. (I am using the most upto date version of the CCP4 
package on a PC)

Joel
_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

Re: [ccp4bb] Modelling Software for beta turn design

[Joel Tyndall]

Dear Wenzong,

Could you provide a bit more details please? Do you simply require some 
visualisation tool e.g. pymol to superimpose your turn mimic on your 
protein/peptide structure or are you looking for more indepth modelling to say 
identify new scaffolds to build amino acid sidechains onto based on an insilico 
screen against your peptide? The latter requires more high end software

Cheers

Joel 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li
Sent: Monday, 22 April 2013 3:48 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Modelling Software for beta turn design

Dear All,

I want to use modelling software to design a tight beta turn replacing a loop 
between two beta strands. Can anyone suggest a program to do this sort of 
modelling?

Thank you
Wenzong

Re: [ccp4bb] Modelling Software for beta turn design

[Joel Tyndall]

Ahh Ok, now I see. I guess you need a search engine that idenitifies an 
antiparallel beta sheet with a turn. Whilst I don't know how to do it, maybe 
the pdb or epdb may do this or even modeller loop via accelrys interface

Joel 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li
Sent: Monday, 22 April 2013 4:17 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Modelling Software for beta turn design

I want to build the loop based on a computer screen against my peptide. 

Thanks

Wenzong

- Original Message -
From: Joel Tyndall joel.tynd...@otago.ac.nz
To: Wenzong Li wenzong...@cm.utexas.edu, CCP4BB@JISCMAIL.AC.UK
Sent: Monday, April 22, 2013 6:10:09 PM
Subject: RE: [ccp4bb] Modelling Software for beta turn design

Dear Wenzong,

Could you provide a bit more details please? Do you simply require some 
visualisation tool e.g. pymol to superimpose your turn mimic on your 
protein/peptide structure or are you looking for more indepth modelling to say 
identify new scaffolds to build amino acid sidechains onto based on an insilico 
screen against your peptide? The latter requires more high end software

Cheers

Joel 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li
Sent: Monday, 22 April 2013 3:48 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Modelling Software for beta turn design

Dear All,

I want to use modelling software to design a tight beta turn replacing a loop 
between two beta strands. Can anyone suggest a program to do this sort of 
modelling?

Thank you
Wenzong

Re: [ccp4bb] 2013年4月9日 16:39:16 自动保存莞

[Joel Tyndall]

Hi Quanju,

Pymol is good as it will show you polar contacts (h-bonds and electrostatic 
interactions/salt bridges). However pi-stacking and pi-cation interactions 
comes with experience to some extent i.e. being able to recognise them. Coot 
will help as it shows polar contacts as well as “close contacts”. You can 
tailor the parameters for “close contacts to assist you in identifying other 
interactions say up to 4 Angstrom.

My instinct still leads to experience. Have a look at a medicinal chemistry 
text book as a start e.g. Patrick, “An introduction to medicinal chemistry” 
although from memory there isn’t much on pi stacking. Also keep in mind there 
are numerous (3) modes of pi stacking; stacked, edge to face  as well as 
triangulated  interactions between three rings.

For pi-cation, it is somewhat simpler to look at specific amino acids (Arg/Lys) 
in your protein active site interacting with an aromatic ring (within 4 
Angstrom roughly).

Hope this helps

J

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
xiangquanju
Sent: Tuesday, 9 April 2013 8:51 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] 2013年4月9日 16:39:16 自动保存草稿

Hello everybody,
i am a freshman in structural biology. Right now i encountered two questions 
and need help from all of you:
1) from the paper, i saw there are three different interactions between the 
ligand and the residue:(i) hydrogen bonding, (ii) π�Cπ stacking and (iii) 
cation�Cπ interactions, how can i determine which kind of interaction did 
happen in my protein. i had chencked that there are no  hydrogen bonds between 
the ligand and the residue.
2) my protein is dimeric in the crystal, when i want to find the polar contacts 
of one residue (pymol) and found that this residue has differnet polar contacts 
in the two monomer. Is this acceptable?

Thanks in advance!
quanju

Re: [ccp4bb] homology modeling of dimeric proteins

[Joel Tyndall]

I have successfully used modeller (standalone software; Sali lab) to generate 
multimeric complexes up to 24-mers

Hope tis helps

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudipta 
Bhattacharyya
Sent: Friday, 22 March 2013 5:00 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] homology modeling of dimeric proteins

Dear All,

Could annyone please suggest me any program or server that can build homology 
based models of dimeric/oligomeric proteins? Previously I have used many 
software/servers which can build the monomer of my target proteins but not the 
dimers. Self docking of homology based monomer is not working in my case since 
at certain domain one monomer is to some extent wrapped around the adjacent 
monomer in the template structure. I have also tried the project mode of 
SWISS-MODEL server but the program is not running with an error message of 
sequence misalignment; although I think the alignment is fine!!! Please suggest 
something that would be fruitful.

Thanking you in advance for your kind cooperation.

Regards,
Sudipta Bhattacharyya,

Department of Biochemistry and Molecular Biology,
Colorado State University.

Re: [ccp4bb] unidentified density

[Joel Tyndall]

Do you have matching 2Fo-Fc density? It is not obvious from the pictures.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir 
Kumar
Sent: Thursday, 18 October 2012 12:07 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unidentified density

Dear all,
I have been working on the crystal structure of an enzyme in which I found the 
unidentified density (see images in attachments). Crystallization condition has 
Peg 1000, Peg 1500, Ethylene glycol, Tris and MPD. Does any one has any idea 
what it could be?
Thanks
--
best regards
Sudhir Kumar
Research Scholar
C/O Dr. S. Gourinath
Structural Biology Laboratory
SLS, JNU,
New Delhi-110067

Re: [ccp4bb] OFF TOPIC

[Joel Tyndall]

Hi Rex,

In Coot, under the file menu, “Get Fragment” and the type LBT (upper case).

This (LBT) is the three letter code for alpha-lactose. Unfortunately it is not 
that easy to find the codes. However on my windows machine the list is here:

C:\CCP4\6.3\lib\data\monomers\list

Hope this helps

Joel

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rex Palmer
Sent: Monday, 8 October 2012 9:12 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] OFF TOPIC

Can anyone please tell me how to extract the pdb for a ligand, eg alpha 
lactose, from the COOT library, prior to fitting into difference density.
Thanks in advance.

Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com

Re: [ccp4bb] Problem with making PDB from Coot

[Joel Tyndall]

You should type Dss into pymol and this will assign more appropriate secondary 
structure

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of meisam 
nosrati
Sent: Tuesday, 24 July 2012 9:47 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problem with making PDB from Coot

Dear CCP4ers

It seems like the text has not showed up, but I have a problem with making pdbs 
from coot. As I refine my structure ( with MR solution ) the beta sheets become 
loops while H-bondings are still there.

I am not sure, if the problem is originating from making PDBs from coot.

I will appriciate your help

Meisam
On Mon, Jul 23, 2012 at 5:31 PM, Meisam Nosrati 
meisam.nosr...@gmail.commailto:meisam.nosr...@gmail.com wrote:

Re: [ccp4bb] Chiral volume outliers SO4

[Joel Tyndall]

Hi all,

Thanks very much to all who responded so quickly. The fix is a one liner in the 
SO4.cif file (last line)

SO4  chir_01  S  O1 O2 O3both 

which I believe is now in the 6.3.0 release.

Interestingly the chirality parameters were not in the SO4.cif file in 6.1.3 
but then appeared in 6.2.0.

Once again I'm very happy to get to the bottom of this and get it fixed. I do 
wonder if it had become over parametrised.

Cheers

Joel



-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie 
Joosten
Sent: Thursday, 12 July 2012 12:16 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4

Hi Ian,

 
  @Ian: You'd be surprised how well Refmac can flatten sulfates if you 
  have a chiral volume outlier (see Figure 1d in Acta Cryst. D68: 
  484-496
 (2012)).
 But this is only because the 'negative' volume sign was erroneously 
 used
in
 the chiral restraint instead of 'both' (or better still IMO no chiral
restraint at
 all), right?  If so I don't find it surprising at all that Refmac 
 tried to
flip the
 sulphate and ended up flattening it.
  Seems to be a good illustration of the GIGO (garbage in - garbage
 out) principle.  Just because the garbage input in this case is in the
official
 CCP4 distribution and not (as is of course more commonly the
 case) perpetrated by the user doesn't make it any less garbage.
The problem is that in the creation of chiral volume targets chemically 
equivalent (groups of) atoms are not recognized as such. So any new or 
recreated restraint files will have either 'positiv' or 'negativ' and the 
problem starts all over again. That is why it is better to stay consistent and 
choose one chirality (the same one as in the 'ideal' coordinates in the PDB 
ligand descriptions). This will also make it easier compare ligands after 
aligning them (this applies to ligands more complex than sulfate).
Obviously, users should not be forced to deal with these things. Programs like 
Refmac and COOT should fix chiral volume inversions for the user, because it is 
only relevant inside the computer. That is the idea of chiron, just fix these 
'problems' automatically by swapping equivalent atoms whenever Refmac gives a 
chiral volume inversion warning.  It should make life a bit easier.


 The point I was making is that in this and similar cases you don't 
 need a
chiral
 restraint at all: surely 4 bond lengths and 6 bond angles define the
chiral
 volume pretty well already?  Or are there cases where without a chiral 
 restraint the refinement still tries to flip the chirality (I would 
 fine
that hard to
 believe).
I agree with you for sulfate, and also for phosphate ;). I don't know what 
happens in other compounds at poor resolution, when bond and angle targets (and 
their SDs) are not equivalent. I guess that some angle might 'give way'
before others. That is something that should be tested. I have a growing list 
of chiral centers that have this problem if you are interested.

Cheers,
Robbie

Re: [ccp4bb] Chiral volume outliers SO4

[Joel Tyndall]

Hi Dale,

Thanks for the input. I guess as a relatively transient user I am not 
appreciating the depth of the problem. However, by at least raising this issue, 
I'm hoping that the fight can be sorted out. Where does my sulfate problem 
stem from? Is it from importing the fragment in COOT? Is it the actual cif file 
which is read by COOT? As noted, software updates tend to be quicker than we 
can refine our structures (That albeit is relatively slow on our behalf). I am 
all for standardisation, but in the long run (at least for me) the sulfate(s) 
becomes a minor part of the structures.

I'll look at swapping the oxygens in the SO4's.

Cheers

Joel

-Original Message-
From: Dale Tronrud [mailto:det...@uoxray.uoregon.edu] 
Sent: Friday, 13 July 2012 10:22 a.m.
To: Joel Tyndall
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4


   While this change has made your symptom go away it is stretching it a bit to 
call this a fix.  You have not corrected the root problem that the names you 
have given your atoms do not match the convention which is being applied for 
SO4 groups.  Changing the cif means that you don't have to worry about it, but 
people who study such details will be forced to deal with the incorrect labels 
of your model in the future.

   Wouldn't it just be easier to swap the names of two oxygen atoms in each 
SO4, leaving the cif alone?  Your difficulties will go away and people using 
your model in the future will also have a simpler life.

   This labeling problem is not new.  The fight to standardize the labeling of 
the methyl groups in Valine and Leucine was raging in the 1980's.  
Standardizing the labels on the PO4 groups in DNA/RNA was much more recent.  It 
helps everyone when you know you can overlay two models and have a logical 
solution without a rotation matrix with a determinate of -1.

   Besides, you will continue to be bitten by this problem as you use other 
programs, until you actually swap some labels.

Dale Tronrud

On 07/12/12 15:00, Joel Tyndall wrote:
 Hi all,
 
 Thanks very much to all who responded so quickly. The fix is a one 
 liner in the SO4.cif file (last line)
 
 SO4  chir_01  S  O1 O2 O3both 
 
 which I believe is now in the 6.3.0 release.
 
 Interestingly the chirality parameters were not in the SO4.cif file in 6.1.3 
 but then appeared in 6.2.0.
 
 Once again I'm very happy to get to the bottom of this and get it fixed. I do 
 wonder if it had become over parametrised.
 
 Cheers
 
 Joel
 
 
 
 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
 Robbie Joosten
 Sent: Thursday, 12 July 2012 12:16 a.m.
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Chiral volume outliers SO4
 
 Hi Ian,
 
  
 @Ian: You'd be surprised how well Refmac can flatten sulfates if you 
 have a chiral volume outlier (see Figure 1d in Acta Cryst. D68:
 484-496
 (2012)).
 But this is only because the 'negative' volume sign was erroneously 
 used
 in
 the chiral restraint instead of 'both' (or better still IMO no chiral
 restraint at
 all), right?  If so I don't find it surprising at all that Refmac 
 tried to
 flip the
 sulphate and ended up flattening it.
  Seems to be a good illustration of the GIGO (garbage in - garbage
 out) principle.  Just because the garbage input in this case is in 
 the
 official
 CCP4 distribution and not (as is of course more commonly the
 case) perpetrated by the user doesn't make it any less garbage.
 The problem is that in the creation of chiral volume targets chemically 
 equivalent (groups of) atoms are not recognized as such. So any new or 
 recreated restraint files will have either 'positiv' or 'negativ' and the 
 problem starts all over again. That is why it is better to stay consistent 
 and choose one chirality (the same one as in the 'ideal' coordinates in the 
 PDB ligand descriptions). This will also make it easier compare ligands after 
 aligning them (this applies to ligands more complex than sulfate).
 Obviously, users should not be forced to deal with these things. Programs 
 like Refmac and COOT should fix chiral volume inversions for the user, 
 because it is only relevant inside the computer. That is the idea of chiron, 
 just fix these 'problems' automatically by swapping equivalent atoms whenever 
 Refmac gives a chiral volume inversion warning.  It should make life a bit 
 easier.
   
 
 The point I was making is that in this and similar cases you don't 
 need a
 chiral
 restraint at all: surely 4 bond lengths and 6 bond angles define the
 chiral
 volume pretty well already?  Or are there cases where without a 
 chiral restraint the refinement still tries to flip the chirality (I 
 would fine
 that hard to
 believe).
 I agree with you for sulfate, and also for phosphate ;). I don't know what 
 happens in other compounds at poor resolution, when bond and angle targets 
 (and their SDs) are not equivalent. I guess that some

[ccp4bb] Chiral volume outliers SO4

[Joel Tyndall]

Hi people,

We are refining a structure with sulfates and we are getting the Chiral volume 
outliers issue. I understand the problem as being computational where the 
oxygens are in reality equivalent but computationally named differently. I have 
seen the recent Acta Cryst D paper (April 2012 - PDB_REDO) which talks about 
this issue and mentions the development of Chiron which could fix this issue.

Is there a way to fix this problem using existing tools (or editing).

We have ~20 sulfates in our protein (10-mer system)

Thanks heaps

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

[ccp4bb] PS: Chiral volume outliers SO4

[Joel Tyndall]

Sorry I should have added, that the issue occurs following refinement in 
refmac. (error in log file and SO4's are distorted)

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

Re: [ccp4bb] Capping peptide

[Joel Tyndall]

Hi Chris,

Depending on your caps the monomers should be available to import directly into 
Coot and refine in refmac. You can find a full list of available monomers if 
you drill down in the ccp4 libraries directory. I'm guessing you may have and 
acetylated amino terminus which would be ACE.

Drop me another email if you can't find the list

Joel

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Chris 
BROWN (P53LAB)
Sent: Friday, 22 June 2012 4:37 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Capping peptide

Hi all

I m just finishing the refinement of several peptide:protein complex structures 
and have become unstuck at modifying the N and C terminal ends (of the 
synthetic peptides) with the generic acetyl and amide capping groups 
respectively.  Could some one please explain to me the most straight forward 
way of accomplishing this.

regards

Chris

[ccp4bb] Coot get monomer issue

[Joel Tyndall]

Hi folks,

Sorry for the cross post / off topic question. I have just noticed a 
recurring/repeatable problem when using the get monomer option in Coot. E.g. 
when getting ILE (and a few others) but not ala, Coot freezes on a windows 7 
machine (using 64-bit thingies). I am using 0.6.2 and there is cross talk with 
ccp4  6.2.0.

The coot-real.exe window comments

Refmac monomer code Ile
BL INFO: We founds C:\\CCP4 packages...\libcheck.exe

This does not happen with windows XP with ccp4 6.1.13.

Any thoughts?

Thanks
Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

[Joel Tyndall]

Marc,

As someone with limited experience in publishing structures but with other 
experience reviewing the same I feel strongly about this. I am hoping to submit 
any future papers with the pdb structure already released or submit the 
coordinates as supplementary material. As a reviewer I find it difficult to 
visualise a structure based on a static 2D figure.

I would like to see coordinates/structure factors supplied for review or 
released on the pdb. I believe that if released on the pdb then this should 
give you enough security that it is still your structure.

Just my thoughts

Joel

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marc 
Kvansakul
Sent: Thursday, 19 April 2012 10:34 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Dear CCP4BBlers,

I was wondering how common it is that reviewers request to have a copy of the 
PDB coordinate file for the review purpose. I have just been asked to supply 
this by an editor after several weeks of review, after one of the reviewers 
requested a copy.

Not having ever been asked to do this before I feel just a tad uncomfortable 
about handing this over...

Your opinions would be greatly appreciated.

Best wishes

Marc

Dr. Marc Kvansakul
Laboratory Head, NHMRC CDA Fellow
Dept. of Biochemistry| La Trobe University | Bundoora
Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia
T: 03 9479 2263 | F: 03 9479 2467 | E: 
m.kvansa...@latrobe.edu.aumailto:m.kvansa...@latrobe.edu.au |

Re: [ccp4bb] refining phosphorylated residues

[Joel Tyndall]

As a follow up question the bulletin board, why is SEP a peptide (L-peptide) 
and TPO not (non-polymer)?

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh 
kumar
Sent: Thursday, 22 March 2012 12:00 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] refining phosphorylated residues

Dear All,

I have a structure of a protein and peptide complex, in which peptide has 
modified residues ( phosphoserine and phosphothreonine).
During refinement these both gets disconnected  with adjacent residues and its 
hard to connect them.
Could you please suggest me some options.

Thanks
Rajesh

Re: [ccp4bb] Water

[Joel Tyndall]

Hi Uma,

Water has the capability of making 4 h-bonds, 2 from the two non-bonding pairs 
of electrons (h-bond acceptors - expect an N-H from an amide for example) as 
well as the two hydrogens (h-bond donors). I would refine all those waters and 
assume they are waters. If the distance to the other atoms is between 2.5-3.2 
then you can assume the water to be correct. In many cases waters will h-bond 
(only)  to other water molecules.

The B-factor is displayed in Coot along the bottom (left) when you middle click 
on an atom. You can also see the B-factor when you read the pdb file as text

Hope this helps.

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma Ratu
Sent: Thursday, 8 March 2012 10:22 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Water

Dear Roger:

Thank you very much for your comments. I use them as guideline and remove many 
'false waters.

Still, I am not clear of some of these 'waters' are real or not. I have the pic 
attached.

In Pic-W11-1, the 'water' is connected to the adjust residues with 4 contacts, 
which are 'N' or 'O' atoms. I would consider this 'water' is false. My question 
is: if these 4 contacts include C from residues, will it be a polar contact 
or not?

In Pic-W12-1, the 'water' is connected to the adjust residues with 3 contacts. 
The 4th is to another 'water'.
Will this 'water' is true or not? Similar case is seen in Pic-W190-1

In Pic-W109-1, some 'waters' are connected to adjust residues, some not. Are 
these 'water' true or not?

Further more,
 and the b-factors are not way out of line,

I am not clear on how to define out of line.
How to find b-factor of individual residue in Coot? I search the web, but find 
no answer.

Thank you for advice

Uma
On Wed, Mar 7, 2012 at 11:44 AM, Roger Rowlett 
rrowl...@colgate.edumailto:rrowl...@colgate.edu wrote:
Uma,

Remember that your structure, ultimately, is a model. A model is your best 
judgment of the true representation of the protein structure in your crystal. 
Your model should make chemical sense. Coot is pretty good at placing waters, 
but it cannot substitute entirely for the experimentalist. Coot will miss some 
waters, and mis-assign others into weak, unmodeled or alternate side- or 
main-chain density, or into density that might be attributable to cations and 
anions or other crystallization materials. Your waters should be subjected to 
inspection and verification. It is really helpful to turn on environment 
distances in Coot when you do this. Even in a large protein model, it is 
possible to inspect all waters for reasonableness pretty quickly. If you have 
no significant positive or negative difference density, and the b-factors are 
not way out of line, and hydrogen bonding partners are reasonable, then 
modeling a water is probably a good call.

Waters should have hydrogen bonding partners with side chains or main-chain 
polar atoms, within reasonable distances, or be withing hydrogen bonding 
distance of other waters that are (chains of waters). If a water has strong 
electron density and more than 4 polar contacts, you might consider anion or 
cation occupancy. Most anions and cations will have higher electron density, 
and appropriately different types of polar contacts. (e.g. you might find 
sulfates near a cluster of basic residues). Low occupancy anions can often look 
a lot like water. PEGs can create ugly snakes of variable density that may be 
challenging to model. Modeling non-protein structural bits is endlessly 
entertaining for the protein crystallographer. ;)

Cheers,

___
Roger S. Rowlett
Gordon  Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245tel:%28315%29-228-7245
ofc: (315)-228-7395tel:%28315%29-228-7395
fax: (315)-228-7935tel:%28315%29-228-7935
email: rrowl...@colgate.edumailto:rrowl...@colgate.edu


On 3/7/2012 11:20 AM, Uma Ratu wrote:
Dear All:

I try to add water to my model.

Here is how I did:
Coot: Find Wates
 Map: FWT PHWT;  1.8 rmsd; Distances to protein atoms: 2.4 
min/3.2 max

Coot found 270 water molecules.

I then examed these waters. Most of them had ball shape. Some had two or more 
balls together. Some had irregular shape (not glabol shape).

I run Water Check. The program did not find any mis-matched water.

Here is my question: how could I tell the waters are real? Or something else?

Thank you for advice

Ros

[ccp4bb] Zero occupancy and bad geometry

[Joel Tyndall]

Hi folks,

I have a case where I have changed the occupancy of a lysine residue to 0.00 
and after refinement the geometry is wrong, i.e. one of the bonds is extended 
(no connectivity in Coot and length is 1.76A). I have seen this before with 
other residues and a previous data set. The break in this case occurs between 
CG (1.00 occ) and CD (0.00 occ).

Any thoughts on why this is occurring?

Cheers

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

Re: [ccp4bb] surface residue mutation

[Joel Tyndall]

Steve Kent has published a few more (at least 1 other) since HIV...

3ODV http://www.rcsb.org/pdb/explore/explore.do?structureId=3ODV  

Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein 
crystallography.

Pentelute, B.L.,  Mandal, K.,  Gates, Z.P.,  Sawaya, M.R.,  Yeates, T.O.,  
Kent, S.B.,  

Journal: (2010) Chem.Commun.(Camb.) 46: 8174-8176

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob 
Keller
Sent: Thursday, 16 February 2012 7:36 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] surface residue mutation

Right on the money!

JPK

On Wed, Feb 15, 2012 at 12:28 PM, David Schuller dj...@cornell.edu wrote:
  On 02/15/12 12:41, Jacob Keller wrote:

 Are there any all-D proteins out there, of known structure or 
 otherwise? If so, do enantiomer-specific catalyses become inverted?

 JPK

 I looked a little harder, and at least one D-enantiomeric protein was 
 an
 enzyme:

 Total chemical synthesis of a D-enzyme: the enatiomers of HIV-1 
 protease show demonstration of reciprocal chiral substrate specificty 
 R.C. deL. Milton, S.C.F. Milton, S.B.H. Kent (1992) Science 256(5062) 
 1445-1448.

 I guess that answers your question.


 --
 ==
 =
 All Things Serve the Beam
 ==
 =
                               David J. Schuller
                               modern man in a post-modern world
                               MacCHESS, Cornell University
                               schul...@cornell.edu



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Generating parameters/cif files for macrocyclic ligands

[Joel Tyndall]

Hi Garib,

Thanks for that (and thanks Herman). How do I declare a non-natural amino acid 
a peptide? My ligand contains two peptidic cycles (non-N to C) where the side 
chains are cyclised. I think I'll be able to use several linbk records for the 
connections but the non-natural amino acid are complicating the issue

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Garib N 
Murshudov
Sent: Wednesday, 8 February 2012 11:56 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Generating parameters/cif files for macrocyclic ligands

Hi Joel

Herman is right:
If you are refining cyclic peptides then the easiest way is to use link record 
linking C-terminus with N terminus. the name of the link should be TRANS. Here 
is an example:

LINK ALA S  21 ASN S   1TRANS

It will force ALA 21 to be linked (with torsion, angles, planes, bonds etc) to 
ASN 1 of chain S.
This way you do not have to create description for large molecule. If you still 
want to create one molecule and you have mol2 file with coordinates then you 
can use libcheck to generate full dictionary using following commands

libcheck

file_mol mol_file_name
nodist y


It should generate fdescription. However I would prefer using link record. this 
way you keep amino acid names etc intact. If you amino acids are not among 
existing then you will need to create their description first and declare them 
peptide.

regards
Garib

On 8 Feb 2012, at 10:33, 
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote:


Hi Joel,

The way I solved this problem was by generating a linear peptide and then 
connecting the ends using a LINK card in the header of the pdb.

Good luck!
Herman


From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK]mailto:[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf 
Of Joel Tyndall
Sent: Tuesday, February 07, 2012 10:44 PM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Generating parameters/cif files for macrocyclic ligands
Hi folks,

I have an intriguing problem. I'm trying to generate a cif file for a 
macrocyclic peptide (of the likes in 
pdb1d4khttp://www.rcsb.org/pdb/explore/explore.do?structureId=1d4k). They are 
cyclic tripeptides units. I can generate a pdb or mol2 file easily. I have used 
PRODRG to generate a .cif file and Coot read thjis in nicely. However, as it is 
cyclic one cannot adjust the dihedral angles. I have previously done this using 
CNS where you can break the tricyclic peptide into residues and generate 
parameters to specify bonds/links between the residues (which allows this kind 
of movement). I can't come up with a way to do this  without using CNS. I have 
looked ta J-ligand which allows for one link between two separate residues 
which precludes a macrocycle. I have looked at sketcher within CCP4 which reads 
the pdb files but I don't believe this can be done here. Within Coot I can 
refine the whole ligand but not certain components.

Any suggestions greatly appreciated . ( I may stick to coot refinement with 
fixed atoms at this stage)

Regards

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.ukmailto:jen...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.ukhttp://www.mrc-lmb.cam.ac.uk/

[ccp4bb] Generating parameters/cif files for macrocyclic ligands

[Joel Tyndall]

Hi folks,

I have an intriguing problem. I'm trying to generate a cif file for a 
macrocyclic peptide (of the likes in 
pdb1d4khttp://www.rcsb.org/pdb/explore/explore.do?structureId=1d4k). They are 
cyclic tripeptides units. I can generate a pdb or mol2 file easily. I have used 
PRODRG to generate a .cif file and Coot read thjis in nicely. However, as it is 
cyclic one cannot adjust the dihedral angles. I have previously done this using 
CNS where you can break the tricyclic peptide into residues and generate 
parameters to specify bonds/links between the residues (which allows this kind 
of movement). I can't come up with a way to do this  without using CNS. I have 
looked ta J-ligand which allows for one link between two separate residues 
which precludes a macrocycle. I have looked at sketcher within CCP4 which reads 
the pdb files but I don't believe this can be done here. Within Coot I can 
refine the whole ligand but not certain components.

Any suggestions greatly appreciated . ( I may stick to coot refinement with 
fixed atoms at this stage)

Regards

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

Re: [ccp4bb] How to make covalent bond in COOT

[Joel Tyndall]

Oops,

Meant to hit reply all...


Hi there,

You can generate a link via jligand which gives you a covalent linkage with 
your enzyme / ligand.as well as a cif file

Try the tutorial ftp://ftp.ccp4.ac.uk/JLigand/tutorial_link.html

J

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Saugata 
Hazra
Sent: Wednesday, 7 December 2011 11:11 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to make covalent bond in COOT

Hello Everyone,

I'm sorry if its a silly question. I used to use O and recently started 
working with COOT. I am wondering how to make covalent bond in coot, between 
a modified substrate and regular protien residue. I can not figure out how to 
make the bond.

Thanks  Regards,
Saugata

Re: [ccp4bb] sugar and coot

[Joel Tyndall]

You can also try Jligand to generate your cif file
J

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan van 
Agthoven
Sent: Tuesday, 22 November 2011 1:17 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] sugar and coot

Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Jan

Re: [ccp4bb] crystallization of synthetic peptides

[Joel Tyndall]

Some HIV protease structures have been done using synthetic HIV protease (99 
amino acid monomers). Look at J. Martin et al from UQ in Queensland. I believe 
this was done with Steve Kent. The protein contains some non-natural amino 
acids too.

Hope this helps

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of H. 
Raaijmakers
Sent: Friday, 11 November 2011 4:17 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] crystallization of synthetic peptides

Dear crystallographers,

Because of the low cost and speed of synthesizing 40- to 60-mer peptides, I 
wonder whether anyone has (good or bad) experiences crystalizing such peptides. 
In literature, I've found up to 34-mer synthetic coiled coils, but no other 
protein class. I can imagine that a protein sample with a few percent random 
deletion mutants mixed into it won't crystallize easily, but has anyone 
actually tried?

cheers,

Hans

Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13

[Joel Tyndall]

Hi folks,

Anyone know if this site is temporarily down or is it more permanent?

http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu
 

Cheers

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. 
Berry
Sent: Tuesday, 9 August 2011 2:28 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13

유상헌 wrote:
 Dear all,
 
 First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit 
 Fedora 13.
 
 If there is anyone who successfully installed ccp4 on 64bit fedora13,
 
 please, instruct me how to install this program in detail.
 

I recently installed CCP4-6.1.3 from source on fedora 14, 64-bit.
After googling solved a few problems it went easily.

Maybe the problems are all fixed in 6.2 so try that first.
Un-tar the package- read INSTALL (or INSTALL.html or .ps) in the top directory 
Try to follow the instructions for installing from source and see where you get 
stuck.
Check the list of problems reported and see if there are solutions
   at http://www.ccp4.ac.uk/problems.php

For me, this site had most of the answers:

http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu

For fedora, use yum install instead of apt-get install
and yum provides (or whatprovides) instead of apt-file search
(And unless you are a mac person, you might be more comfortable becoming root 
rather than prepending every privilege-requiring command with sudo)



If you have trouble with TCL/TK read below-quoted message.
Mosflm site has more suggestions.
better yet: 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12

Mark Del Campo wrote:

 Okay, I got the problem resolved in the following way (thanks go to 
 Clint
 Leysath):
 
 1. removed the tcltk++ directory that came with my ccp4 download 2. 
 installed Activestate's tcltk 8.4.19.2 from 
 https://www.activestate.com/activetcl/downloads/
 3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from 
 http://sourceforge.net/projects/blt/files/
 4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z 
 directory 5. patched the blt installation (patch -p1 -i 
 blt2.4z-patch-2) 6. then reordered statements in blt2.4z/src/bltTree.c 
 [this is detailed at http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html 
 under the heading Compilation failure in bltTree on 64-bit machines] 
 7. configured the blt install (./configure 
 --with-tcl=/path/to/ActiveTcl-8.4)
 8. installed blt (make)
 9. for some reason bltwish did not end up in 
 /path/to/ActiveTcl-8.4/bin even though the configure script said that 
 is where it would be put, so I moved it to /path/to/ActiveTcl-8.4/bin 
 10. edited 1 line in ccp4.setup-bash  (setenv CCP4I_TCLTK
 /path/to/ActiveTcl-8.4/bin/)
 11. opened a new terminal window  ccp4i works
 

Re: [ccp4bb] error after install

[Joel Tyndall]

Hi Tim,

$ stat /opt/CCP4/Python-2.6.7/bin/python
  File: `/opt/CCP4/Python-2.6.7/bin/python'
  Size: 4279369 Blocks: 8360   IO Block: 4096   regular file
Device: 801h/2049d  Inode: 1189874 Links: 2
Access: (0755/-rwxr-xr-x)  Uid: (13003/ UNKNOWN)   Gid: (10602/ UNKNOWN)
Access: 2011-09-26 09:11:48.946003302 +1300
Modify: 2011-08-16 02:26:38.0 +1200
Change: 2011-09-22 16:24:09.857165116 +1200

It maybe that python was not installed correctly, will update after the core 
group gets back to me.

Cheers

Joel 

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] 
Sent: Friday, 23 September 2011 8:26 p.m.
To: Joel Tyndall
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] error after install

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Joel,

reinstalling operating systems is fairly common also to other ones than linux 
;-)

The behaviour of the command 'ccp4' is actually correct for it is aliased to 
tg@shelx8:/xtal/Suites/CCP4/ccp4-6.2.0$ type -all ccp4
ccp4 is aliased to `pushd $CCP4/dev/null'

I suppose you mean 'ccp4i' instead in order to start the CCP4 interface.

About the python:
What is the output of the command
stat /opt/CCP4/Python-2.6.7/bin/python

Maybe you do not have executable permission.

Tim

On 09/23/2011 12:29 AM, Joel Tyndall wrote:
 Hi folks,
 
 My love/hate relationship continues with linux. I have had to 
 reinstall everything and when I install CCP4 6.2.0 It seems to work 
 fine but upon opening a shell I get the error below and by typing
 ccp4 I simply get changed to the ccp4 directory.
 
 *** Fatal Error: Incomplete 
 libtbx environment\! ***
 Please re-run the libtbx/configure.py command.
 
 On a little searching I found some evidence of this error before but 
 little solutions to the problem. When I run:
 
 python configure.py
 
 I get the error
 
 bash: /opt/CCP4/Python-2.6.7/bin/python: No such file or directory
 
 This file does exist.
 
 I am running Ubuntu 10.10 as a guest on a windows 7 machine. I am 
 running in a bash shell. This error occurs when nothing else is 
 installed. The libtx/configure.py is in three places
 
 /opt/CCP4/ccp4-6.2.0/lib/cctbx-utf/cctbx_sources/cctbx_project/libtx
 /opt/CCP4/ccp4-6.2.0/lib/cctbx/cctbx_sources/cctbx_project/libtx
 /opt/CCP4/ccp4-6.2.0/src/phaser/phaser-2.3.0/libtx
 
 I recently installed CCP4 6.1.12 with no issues. Any help to solve 
 this problem would be much appreciated
 
 Joel _ Joel Tyndall, PhD
 
 Senior Lecturer in Medicinal Chemistry National School of Pharmacy 
 University of Otago PO Box 56 Dunedin 9054 New Zealand Skype:
 jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te 
 Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 
 Otepoti 9054 Aotearoa
 
 Ph / Waea   +64 3 4797293 Fax / Waeawhakaahua +64 3
 4797034
 
 

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.11 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFOfEKOUxlJ7aRr7hoRAjDSAJsHVlJPFlBHxNmWty1NfvTz46pWzACg3QUk
D4wNrN3iLTd/JFE4x1s0+rE=
=BhZt
-END PGP SIGNATURE-

[ccp4bb] error after install

[Joel Tyndall]

Hi folks,

My love/hate relationship continues with linux. I have had to reinstall 
everything and when I install CCP4 6.2.0 It seems to work fine but upon opening 
a shell I get the error below and by typing ccp4 I simply get changed to the 
ccp4 directory.

***
Fatal Error: Incomplete libtbx environment\!
***
Please re-run the libtbx/configure.py command.

On a little searching I found some evidence of this error before but little 
solutions to the problem. When I run:

python configure.py

I get the error

bash: /opt/CCP4/Python-2.6.7/bin/python: No such file or directory

This file does exist.

I am running Ubuntu 10.10 as a guest on a windows 7 machine. I am running in a 
bash shell. This error occurs when nothing else is installed. The 
libtx/configure.py is in three places

/opt/CCP4/ccp4-6.2.0/lib/cctbx-utf/cctbx_sources/cctbx_project/libtx
/opt/CCP4/ccp4-6.2.0/lib/cctbx/cctbx_sources/cctbx_project/libtx
/opt/CCP4/ccp4-6.2.0/src/phaser/phaser-2.3.0/libtx

I recently installed CCP4 6.1.12 with no issues. Any help to solve this problem 
would be much appreciated

Joel
_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

Re: [ccp4bb] Saving distances drawn in Coot 0.6.1

[Joel Tyndall]

Hi Romain,

I am not aware of how to do this in Coot but you can easily do this in PyMOL 
using the save session option (with maps etc).

Cheers

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Romain 
Talon
Sent: Monday, 5 September 2011 6:59 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Saving distances drawn in Coot 0.6.1

Hello everybody from the CCP4bb,

I would like to know if there is any way to save dotted lines distances drawn 
in Coot in order to recover the information then opening a new session, even if 
the program was closed before ?

I have already tried the save session option but it didn't work.

I apoIogize if the question was already asked before and I thank you a lot.

Best regards.

Romain.

--
-

--
Romain TALON
Extremophile and Large Molecular Assemblies Team (E.L.M.A) Institut de Biologie 
Structurale 41, rue Jules Horowitz 38027 GRENOBLE Cedex 1
Tel: +33 (0)438.78.95.93
--