On Sat, Jul 21, 2012 at 9:43 AM, Pavel Afonine wrote:

I see (d_min/3) in your formula above as a grid step factor. Most of map calculations in phenix.refine and tools around it use (d_min/4). Putting this into your formula

map_size = 8 * a * b * c * (d_min/4)^3

will obviously result in a smaller map, which isn't true. Am I missing something?

No, I am - the final multiply operation should be a divide: map_size = 8 * a * b * c / (d_min/resolution_factor)^3 But the resolution_factor is inconsistent - for the FFT structure factors calculation (which is unavoidable), we are definitely using 1/3 (I assume for speed reasons). For most of the other optional tasks like rotamer correction and filling missing F-obs, it's 1/4. -Nat

Dear Nat and Pavel, thank you so much for your explanations. Assuming that the 8 in Nat's formula provides conversion to bytes, it is not such a big RAM requirement. I guess most virus structures should be approachable with an 8GB machine. About the CPU, I think I'm going to invest in a quad-core. I feel quite comfortable in command line and I don't have fear paralelizing existing code. Thanks again, Jon 2012/7/21 Pavel Afonine

But the resolution_factor is inconsistent - for the FFT structure

...

factors calculation (which is unavoidable), we are definitely using 1/3 (I assume for speed reasons). For most of the other optional tasks like rotamer correction and filling missing F-obs, it's 1/4.

Yes, we use 1/3 for structure factors and gradients calculations, and 1/4 in map calculation if the map is going to be used for things like water picking, real-space refinement, etc. This is intentional.

Pavel

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Carsten phenix.refine will automatically link a non-standard aminoacid into the chain if the main chain atoms are named in the same fashion as the standard, i.e. C, CA, N, O. Unfortunately, the PDB decided to name the N7D in a "non-compliant" fashion. You have choices. 1. Use the cif link facility to link them. phenix.ligand_linking model.pdb may provide this for you but I'd appreciate the copy of the three residues involved to double check the validity of the links. 2. Rename the atoms in your model to the standard names for the main chain (and ideally change the residue to something else) and run phenix.elbow model.pdb --residue=NWM to get a new cif file for the new residue. eLBOW attempts to match the main chain restraints in the other restraints files if it detects that the residue is an aminoacid. Cheers Nigel On Fri, Jul 27, 2012 at 10:43 AM, Schubert, Carsten [JRDUS] wrote:

What are the current best practices for modified aminoacids? I have a peptide with and N-terminal Acetyl-proline which I am trying to model. The initial approach was to locate the aminoacid in the chemical components dictionary (N7P) and replace the residue in coot. Unfortunately the link to the next residue is not recognized, so the residue is just floating about. Next I just added an acetyl next to the proline and added some restraints in the .def file. That sort of works, but looks a bit cludgy. Is there a way to do this more cleanly?

Cheers,

Carsten

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Bump. I have an S-methylcysteine sulfoxide so I downloaded it from WebCSD from the CCDC website. So far so good. Available in three formats but I wanted it to work as a modified residue so I followed the advice here. Opened it in PyMol, saved it as a pdb file and edited the atoms in a text editor to fit with a normal residue. But phenix.elbow doesn't treat sulfur correctly. The geometry is right but it adds an extra hydrogen to the sulfur and the oxygen - they should have a double bond instead. If I run phenix.elbow directly on the files downloaded from WebCSD I get the double bond but I also get a flat system; as if my sulfur was a carbon. Yes, I tried --opt. Attached the best results. My phenix version is 1299. tl;dr phenix.elbow fails at parameterising DMSO. Help? Cheers, Morten On 29 July 2012 04:41, Paul Emsley wrote:

On 27/07/12 13:43, Schubert, Carsten [JRDUS] wrote:

What are the current best practices for modified aminoacids? I have a peptide with and N-terminal Acetyl-proline which I am trying to model. The initial approach was to locate the aminoacid in the chemical components dictionary (N7P) and replace the residue in coot.

do the restraints specify that N7P is a non-polymer (in which case coot will treat it as such) or as an L-peptide?

Unfortunately the link to the next residue is not recognized, so the residue is just floating about.

Doesn't sound very much like how a L-peptide should behave to me...

Paul.

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Hi Jon, you can find the answer without wasting time on guesswork... Take a few extreme cases from PDB (big model, many reflections, tricky space group), and run them from the command line: phenix.refine model.pdb data.mtz ordered_solvent=true --show-process-info The log file should contain memory usage throughout the run. Look for the max memory intake in the last record (towards the end of log file). This will give you an idea about how much memory you may need. Pavel On 7/22/12 4:31 AM, Jon Agirre wrote:

Dear Nat and Pavel,

thank you so much for your explanations. Assuming that the 8 in Nat's formula provides conversion to bytes, it is not such a big RAM requirement. I guess most virus structures should be approachable with an 8GB machine.

About the CPU, I think I'm going to invest in a quad-core. I feel quite comfortable in command line and I don't have fear paralelizing existing code.

Thanks again,

Jon

2012/7/21 Pavel Afonine mailto:[email protected]>

But the resolution_factor is inconsistent - for the FFT structure factors calculation (which is unavoidable), we are definitely using 1/3 (I assume for speed reasons). For most of the other optional tasks like rotamer correction and filling missing F-obs, it's 1/4.

Yes, we use 1/3 for structure factors and gradients calculations, and 1/4 in map calculation if the map is going to be used for things like water picking, real-space refinement, etc. This is intentional.

Pavel

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